Poster_Abstracts-NSC44

 Registration
C.V.Raman
Auditorium
10thJuly2016
C.V.Raman
Auditorium
ProgramScheduleNSC44
Venue
InauguralSession
PL1
PL2
10:00AM 2:00PM
2:00PM
2:30PM
PlenarySessionChair:M.Vijayan
PlenaryI StructuralandMagneticPhaseTransitionsinOxidePerovskites
2:30PM 3:15PM
DhananjaiPandey,IIT(BHU),Varanasi
PlenaryII X-raypowderdiffraction:Newopportunityinstructural
crystallographyandpathologicalcalcificationanalysis
3:15PM 4:00PM
AlokKMukherjee,JadavpurUniversity,Kolkatta
TeaBreak
ParallelSessionI:StructuralChemistryChair:ParthapratimMunshi
IL1
LHC101
IL2
IL3
IL4
Diversityofpolymorphismindonor-acceptorchromophore
ParthapratimMunshi,ShivNadarUniversity,TehsilDadri,UP
Designerarchitectures:Applicationincatalysis,anionrecognitionandenergytransfer
RajeevGupta,UniversityofDelhi
Completetransmetallationinmetal-organicframeworkthroughmetalion
metathesisinsinglecrystalforselectivesensingofphosphateanioninaqueous
medium
SukhenduMondal,IISERThiruvananthapuram
Covalentorganicframeworks-crystallineorganicpolymersasnewclassof
poroussupportsfornanoparticles
R.Vaidhyanathan,IISERPune
4:30PM
5:00PM
5:00PM
5:30PM
5:30PM
6:00PM
6:00PM
6:30PM
ParallelSessionII:ProteinNucleicAcidInteractionsChair:DeepakT.Nair
LHC103
IL5
IL6
IL7
IL8
StructuralbasisofmutagenicandtranslesionDNAsynthesisbyDNApolymerase
IVfromEscherichiacoli
DeepakT.Nair,RegionalCentreforBiotechnology,Faridabad
Understandingtheaccessorygeneregulator(agr)basedphenotypeswitchin
Staphylococcusaureus
B.Gopal,IndianInstituteofScience,Bengaluru
CrystalstructureanddynamicsofSpt16NdomainofFACTcomplex
RavindraMakde,RRCAT,Indore
EnlistingRAMinthefightagainsttuberculosis
RavishankarRamachandran,CSIR-CentralDrugResearchInstitute,Lucknow
4:30PM
5:00PM
5:00PM
5:30PM
5:30PM
6:00PM
6:00PM
6:30PM
C.V.Raman
Auditorium
TeaBreak
SL1
Prof.M.VijayanLectureChair:M.R.N.Murthy
Electroncryomicroscopy:Structuralstudiesexsituandinsitu
6:45PM 7:45PM
WolfgangBaumeister,MaxPlanckInstituteofBiochemistry,Martinsried,Germany
Dinner(Venue:DiningHallComplex)7:45pm-10:00pm
11thJuly2016
C.V.Raman
Auditorium
Venue
PL3
PL4
PlenarySessionChair:C.G.Suresh
PlenaryIII Solidsolution,Vegard'slaw,chemicalpressureandallthat
9:00AM 9:45AM
D.D.Sarma,IndianInstituteofScience,Bengaluru
PlenaryIV Chiralproofreadingduringtranslationofthegeneticcodeandits
functionalimplications
9:45AM 10:30AM
R.Sankaranayanan,CSIR-CentreforCellularandMolecularBiology,
Hyderabad
TeaBreak
ParallelSessionIII:CrystalEngineeringChair:AshwiniNangia
IL9
LHC101
IL10
IL11
IL12
Binuclearandtrinuclearcoordinationcage
DillipKumarChand,IITMadras,Chennai
Importanceofnon-covalentintra-andinter-molecularinteractionstowards
stabilizationandemergentpropertiesofelectronicallyresponsiveorganic
materials
PritamMukhopadhyay,JawaharlalNehruUniversity,NewDelhi
Acofacialorganicclickcageasanefficientreceptorforpolycyclicaromatic
hydrocarbons
R.Natarajan,CSIR-IndianInstituteofChemicalBiology,Kolkata
Ternarypharmaceuticalcocrystals
AshwiniNangia,CSIR-NationalChemicalLaboratory,Pune
11:00AM 11:30AM
11:30AM 12:00PM
12:00PM 12:30PM
12:30PM 1:00PM
ParallelSessionIV:InfectiousDiseaseChair:PunitKaur
Mycobacteriumtuberculosishistidinebiosynthesispathwayenzymes:
understandingtheirstructuralandbiochemicalaspectstodesignnewanti-TB
inhibitors
BichitraKumarBiswal,NationalInstituteofImmunology,NewDelhi
11:00AM 11:30AM
IL14
EvidenceforfunctionalroleofC-H…Shydrogenbondinenzymecatalysisand
substratespecificity:typeImethionineaminopeptidase
AnthonyAddlagatta,CSIR-IndianInstituteofChemicalTechnology,Hyderabad
11:30AM 12:00PM
IL15
UnderstandingthephagocyticcupformationinEntamoebahistolytica:structural
12:00PM 12:30PM
andfunctionalstudiesofindividualcomponents
S.Gourinath,JawaharlalNehruUniversity,NewDelhi
Largescaleconformationalchangesandsurfacechargeredistributionuponsugar
bindingdictatesthefidelityofphosphorylationbyfructokinase
12:30PM 1:00PM
UdayadityaSen,SahaInstituteofNuclearPhysics,Kolkata
LHC103
IL13
IL16
LunchBreak&PosterSession(Venue:DiningHallComplex)1:00pmto2:45pm
ParallelSessionV:AlliedTechniquesChair:SaibalBasu
IL17
NeutronandX-rayreflectometry:characterizationatmesoscopiclengthscale
LHC101
SaibalBasu,BhabhaAtomicResearchCentre,Mumbai
IL18
IL19
IL20
MergingLowResolutionWithLowConfidenceToGetRelevance:
UsingSAXSDataToFindANewNephro-ProtectiveMolecule
Ashish,CSIR-InstituteofMicrobialTechnology,Chandigarh
CrystalStructure,MagnetismandMagnetodielectricEffectinA-SiteOrdered
ChromateSpinelOxidesLiMCr4O8(M=Ga,In,Fe)
A.Sundaresan,JNCASR,Bengaluru
MechanismofNearInfraredPersistentLuminescence:InsightsthroughEXAFS
K.R.Priolkar,GoaUniversity,Goa
3:00PM
3:30PM
3:30PM
4:00PM
4:00PM
4:30PM
4:30PM
5:00PM
ParallelSessionVI:EnzymeMechanismChair:S.Ramaswamy
IL21
LHC103
IL22
IL23
IL24
Thefinerthingsinenzymecatalysis-adeeperdiveintomechanismsfroma
structuralperspective
S.Ramaswamy,InStem,Bengaluru
UnderstandingthestructuralbasisofuniquefunctionalpropertiesofAspergillus
nigerglutamatedehydrogenase
PrasenjitBhaumik,IITBombay,Mumbai
3:00PM
3:30PM
3:30PM
4:00PM
Thestructuralbasisoftheenhancedpollutant-degradingcapabilitiesof
engineeredbiphenyldioxygenases
PravindraKumar,IITRoorkee,Roorkee
4:00PM
4:30PM
Thecrystalstructureoftheligandbindingregionofserine-glutamaterepeat
proteinA(SgrA)ofEnterococcusfaeciumrevealsanewproteinfold:Structurebasedinsightsintoitsadhesionfunction
KarthePonnuraj,UniversityofMadras,GuindyCampus,Chennai
4:30PM
5:00PM
C.V.RamanAuditorium
TeaBreak
PL5
PlenarySessionChair:K.Sekar
Structure-baseddesignofantithyroiddrugusing
PlenaryV lactoperoxidase/thyroidperoxidaseasdrugtargets
5:30PM 6:15PM
T.P.Singh,AIIMS,NewDelhi
GeneralBodymeetingofICA6:15pmto7:45pm
BanquetDinner(Venue:DiningHallComplex)7:45pm-10:00pm
12thJuly2016
C.V.Raman
Auditorium
Venue
PL6
PlenarySessionChair:K.Suguna
PlenaryVI StructuralstudiesofflexibleMOFsandzeolitesasadsorbentsand
catalysts
9:00AM 9:45AM
PaulWright,UniversityofSt.Andrews,UK
Photosession&TeaBreak
ParallelSessionVII:MetalOrganicFrameworksChair:TomWoo
IL25
LHC101
IL26
IL27
IL28
ConstructionofHypotheticalMOFsofAnyNetTopologyforHighThroughput
ScreeningandDataMining
TomWoo,UniversityofOttawa
Metalorganophosphates:Anewclassofporoussolids
R.Murugavel,IITBombay,Mumbai
Structure-PropertyCorrelationStudiesofFunctionalMetal-OrganicFrameworks
(MOFs)
SujitK.Ghosh,IISER,Pune
MOFcontainingcompoundsasfunctionalmaterials:crystaltocrystal
transformationsandelectrocatalyticwateroxidation
SamarDas,UniversityofHyderabad
11:00AM 11:30AM
11:30AM 12:00PM
12:00PM 12:30PM
12:30PM 1:00PM
ParallelSessionVIII:NewStructures-IChair:AmitDas
IL29
LHC103
IL30
IL31
IL32
CrystalstructuredeterminationandepitopemappingofMycobacterium
tuberculosiscomplexspecific28kDaantigen
11:00AM 11:30AM
AmitDas,IITKharagpur
ATP-inducedstructuralremodelingintheantiactivatorFleNenablesformationof
11:30AM 12:00PM
thefunctionaldimericform
DeeptiJain,RegionalCentreforBiotechnology,Faridabad
Crystalstructureofglucose-1-phosphatethymidylyltransferasefromNeisseria
gonnorrhoeaeandinvestigatingsubstratepromiscuityinsugar
nucleotidylytransferases
BalajiPrakash,CSIR-CFTRI,Mysuru
BiochemicalandstructuralstudiesonEhRabX3,anovelGTPasefromEntamoeba
histolyticawithtandemG-domains
SunandoDatta,IISERBhopal
12:00PM 12:30PM
12:30PM 1:00PM
LunchBreak&PosterSession(Venue:DiningHallComplex)1:00pmto2:45pm
LHC101
IL33
ParallelSessionIX:NanomaterialsChair:AshokGanguli
Microscopicunderstandingofgrowthofanisotropicnanostructuresinreverse
micelles
3:00PM 3:30PM
AshokGanguli,InstituteofNanoscience&Technology,Mohali
IL34
Doesparticlesizecontrolcrystalstructure?
IL35
PushanAyyub,TataInstituteofFundamentalResearch,Mumbai
Porousandlayeredmaterialsforgassorptionandseparationapplications
M.Eswaramoorthy,JNCASR,Bengaluru
IL36
3:30PM
4:00PM
4:00PM
4:30PM
X-raypowderdiffractioninvestigationsofsomeII-VIsemiconductorandmagnetic
4:30PM
nanoparticles
SulabhaKulkarni,IISERPune
5:00PM
ParallelSessionX:NewStructures-IIChair:B.Padmanabhan
IL37
LHC103
IL38
IL39
IL40
Structure-baseddrugdiscoveryofsmallmoleculesforthehumanSuperoxide
Dismutase(hSOD1)associatedwithALS
B.Padmanabhan,NIMHANS,Bengaluru
CrystalstructureanalysisofaperiplasmicmetalbindingproteinfromCandidatus
Liberibacterasiaticus
AshwaniSharma,IITRoorkee,Roorkee
3:00PM
3:30PM
3:30PM
4:00PM
Structure,mechanismofATPbindingandinteractionswithσ54oftheheptameric
bEBP,FlrCthatregulatesflagellarsynthesisinVibriocholerae
4:00PM
JhimliDasgupta,St.Xavier'sCollege,Kolkata
4:30PM
CrystallographiccharacterizationofthefirstLPMOproteinfromplants
PremaGVasudev,CSIR-CIMAP,Lucknow
4:30PM
5:00PM
TeaBreak
ParallelSessionXI:StudenttalksChair:RaymondJ.Butcher
ST1
LHC101
ST2
ST3
ST4
ST5
ST6
Anultrahydrophobicfluorousmetal-organicframeworkasapromisingplatform
totacklemarineoilspills
SoumyaMukherjee,IISERPune
Supramoleculararchitecturesofcopper(II)coordinationsolidsofbioactive
phenanthrolineinvolvingdicarboxylatoligands
DebajitDutta,CottonCollege,Guwahati
Understandingtheconformationalflexibilityandelectrostaticpropertiesof
curcuminintheactivesiteofrhAChEviamoleculardocking,moleculardynamics
andchargedensityanalysis
K.Saravanan,PeriyarUniversity,Salem
ColorimetricselectiveCu2+detectionbylanthanidebasedhybridcomplexes
associatedwithasinglecrystalgrowthmediatedtransformation
SoumyabrataRoy,JNCASR,Bengaluru
StructuralandmagneticstudiesonDyMnO3crystalsgrownbyOFZtechnique
P.P.AravinthKumar,SSNCollegeofEngineering,Chennai
Ab-initiocrystalstructuredeterminationofthreebenzoicacidderivativesfromXraypowderdiffractiondata
SamiranPramanik,JadhavpurUniversity,Kolkata
5:30PM
5:45PM
5:45PM
6:00PM
6:00PM
6:15PM
6:15PM
6:30PM
6:30PM
6:45PM
6:45PM
7:00PM
ParallelSessionXII:StudentTalksChair:RajaniKant
ST7
ST8
LHC103
ST9
ST10
ST11
ST12
StructuralandbiochemicalstudiesonVibriocholeraeHsp31revealsanovel
dimericformandglutathione-independentglyoxalaseactivity
SanghatiRoyChowdhury,SahaInstituteofNuclearPhysics,Kolkata
Effectofoligomerisationontheactivesitegeometry.AcasestudyinvolvingM.
tuberculosisPanK
AnjuPaul,IndianInstituteofScience,Bengaluru
CrystalstructureofsubstrateandAMPPNP-boundpropionatekinasefrom
Salmonellatyphimurium:substratespecificityandphosphatetransfermechanism
SubashiniMathivanan,IndianInstituteofScience,Bengaluru
Mechanisticinsightsintotherecognitionof5-methylcytosineoxidation
derivativescontainingduplexDNAbytheSUVH5SRAdomain
NaveenKumarNakarakanti,IITHyderabad
XRD2:Indo-Italianscientificpartnershipforadedicatedmacromolecular
crystallographybeamlineatElettraSincrotroneTrieste
NishantKumarVarshney,ElettraSincrotroneTrieste,Italy
StructuralbasisofselectivearomaticpollutantsensingbyMopR,anNtrCfamily
transcriptionalregulator
ShamayeetaRay,IITBombay,Mumbai
5:30PM
5:45PM
5:45PM
6:00PM
6:00PM
6:15PM
6:15PM
6:30PM
6:30PM
6:45PM
6:45PM
7:00PM
SpecialDinner(Venue:DiningHallComplex)7:30PM-10:00PM
13thJuly2016
C.V.Raman
Auditorium
Venue
PL7
PlenarySessionChair:SantanuBhattacharya
PlenaryVII Importanceofcrystallographyinmaterialschemistry:select
examples
9:00AM 9:45AM
S.Natarajan,IndianInstituteofScience,Bengaluru
TeaBreak
ParallelSessionXIII:SynchrotronsChair:Surinder.M.Sharma
LHC101
IL41
IL42
IL43
IL44
AnoverviewofIndiansynchrotronbeamlineeffort
SurinderM.Sharma,BhabhaAtomicResearchCentre,Mumbai
ProteincrystallographybeamlineofIndus-2
AshwaniKumar,RRCAT,Indore
StructuralinvestigationofmaterialsunderextremeconditionsatECXRD
beamline,Indus-2
H.K.Poswal,BhabhaAtomicResearchCentre,Mumbai
UnderstandingepitaxialthinfilmsusinghighresolutionX-raydiffraction
TapasGanguli,RRCAT,Indore
10:30AM 11:00AM
11:00AM 11:30PM
11:30PM 12:00PM
12:00PM 12:30PM
ParallelSessionXIV:SponsoredTalksChairs:H.S.Subramanya&KVyas
LHC103
SP1
SP2
SP3
SP4
Applicationsofelectron-countingdirectdetectioncamerasinhigh-resolutioncryoelectronmicroscopy
10:30AM 11:00AM
ChrisBooth,GatanInc
XtaLABSynergy:Fast,precise,intellegent
11:00AM 11:30PM
AlexandraM.Griffin,RigakuOxfordDiffraction,UK
Pushingbackfrontiers:Advancedin-housecrystallographyusingnextgeneration
D8VENTURE
11:30PM 12:00PM
VernonSmith,BrukerAXSGmBH,Germany
NGCchromatographysystem-Helpingyoupreparediffractionqualityprotein
crystals
KarthikBanuchander,Bio-Rad
C.V.RamanAuditorium
ConcludingSession12:30PMto1:00PM
Lunch(Venue:DiningHallComplex)1:00PM
12:00PM 12:30PM
Poster Abstracts
Biological Sciences
Poster Name
Number
B001
Amandeep Singh
B002
Ameya D. Bendre
B003
B004
Anandsukeerthi Sandholu
Anil K. Jamithireddy
B005
Anil Kumar Shakya
B006
Anjali Malik
B007
Anshul Assaiya
B008
Archana
B009
Ashwani Kumar
B010
Bhawna Burdak
B011
Chitra Latka
B012
Chitra Latka
B013
Deepak Kumar
B014
Deepanjan Ghosh B015
B017
Dhakaram Pangeni Sharma
Dhamodharan Prabhu
Harvijay Singh
B018
Ishan Rathore
B019
Ishtiyaq Ahmad
B020
Ithayaraja M.
B021
Jay Prakash Kumar
B022
Jessy Mariam
B023
Jeyakanthan J.
B024
Jyoti Baranwal
B025
Kamalendu Pal
B026
Katta Suma
B027
Kriti Chopra
B028
Madhusudhanarao Katiki
B029
Mahesh Kumar Chand
B016
Institute
Title
Molecular Biophysics Unit, Indian Biochemical and crystallographic studies on the second single strand DNA Institute of Science, Bangalore
binding protein from Mycobacterium smegmatis
Biochemical Sciences Division, CSIR-­‐ Kunitz Trypsin Inhibitor 2 from Chickpea: Unravelling the β-­‐ trefoil
National Chemical Laboratory, Pune Biochemical Sciences Division, CSIR-­‐ Structural studies on iridoid synthase: revealing substrate specificity of PGR National Chemical Laboratory, Pune family
Molecular Biophysics Unit, Indian Effects of mutations on the structure-­‐function relationship of proteins
Institute of Science, Bangalore
CSIR-­‐Central Drug Research Trypanothione synthetase as novel drug target in Leishmania
Institute, Lucknow
Department of Biotechnology, Structural and functional analysis of enzyme from polyamine biosynthetic Indian Institute of Technology, pathway of Entamoeba histolytica
Roorkee
National Centre for Cell Science, Structural and Functional studies on Drosophila Ionotropic receptors
Pune
Molecular and Structural Biology Crystal Structure of a Novel Insecticidal Protein from the Fern Tectaria Division, CSIR-­‐Central Institute of macrodonta
Medicinal and Aromatic Plants, Lucknow
National Centre for Cell Science, Structural and functional studies on hypoxia protein Rv0081 in Mycobacterium Pune tuberculosis during latency
National Centre for Cell Sciences, Structural studies on Nup93-­‐Nup188 complex of vertebrate Nuclear pore Pune
complex
Genome Informatics and Structural Preliminary crystallisation trials of Inhibitory Domain of Sub16, a Sedolisin Biology Unit, CSIR-­‐Institute of Serine protease of a dermatophyte, Trichophyton rubrum
Genomics and Integrative Biology, New Delhi
Genome Informatics and Structural A genomics approach for identification of proteases as major potential virulence Biology Unit, CSIR-­‐Institute of factors in the pathogenic fungus, T. rubrum
Genomics and Integrative Biology, New Delhi
National Institute of Immunology, Mycobacterium tuberculosis HisB: Structural and Biochemical study to design New Delhi
new anti-­‐TB Inhibitors
Biochemical Sciences Division, CSIR-­‐ Engineering of the Tat Pathway Chaperons
National Chemical Laboratory, Pune
School of Life Sciences, Jawaharlal Exploring the role of DnaG primase at replication fork from Vibrio cholorae
Nehru University
Department of Bioinformatics, Function prediction of hypothetical protein L-­‐aspartate oxidase from Thermus Alagappa University, Karaikudi
thermophilus HB8: An in silico and in vitro approaches
Department of Biotechnology, Active site gating of Chikungunya nsP2Pro by interdomain flexible loops
Indian Institute of Technology, Roorkee
Department of Biosciences and Structural, functional and inhibition studies on Histo-­‐Aspartic Protease (HAP) Bioengineering, Indian Institute of and Plasmepsin II
Technology Bombay Biology Division, Indian Institute of Identification and Characterization of Type III Restriction-­‐modification Enzyme Science Education and Research, from Mycoplasma bovis Pune
Molecular Biophysics Unit, Indian X-­‐ray crystal structure of a thiolase from Escherichia coli at 1.8 Å resolution
Institute of Science, Bangalore
Institute for Stem Cell Biology and Identification of conformational chaperones for the Na+/Galactose transporter
Regenerative Medicine, NCBS-­‐TIFR, Bangalore
Department of Chemistry, Indian Dynamics at the stalling fork barriers
Institute of Technology, Bombay, Mumbai
Department of Bioinformatics, Crystal Structure of Glutaminyl-­‐tRNA Synthetase (TtQRS) from Thermus Alagappa University, Karaikudi
thermophilus HB8 and its complexes with ATP and AMP
Biology Division, Indian Institute of Structural and Biochemical studies of a small Ras like GTPase MglA from Science Education and Research, Myxococcus xanthus to understand the spatial positioning of motility complexes
Pune
Saha Institute of Nuclear Physics, Structural and functional studies on Vc-­‐YaeO a Rho inhibitor
Kolkata
CSIR -­‐ Centre for Cellular and A unique function of DTD to correct mischarging of glycine by alanyl-­‐tRNA Molecular Biology, Hyderabad
synthetase
National Centre for Cell Science, Analysis of interaction network of channel nucleoporins with adapter ring of Pune
vertebrate nuclear pore complex
Department of Biotechnology, Structural studies on OXA-­‐58 of Acinetobacter Baumannii revealing the active Indian Institute of Technology site structural elements essential for carbapenem hydrolysis by this enzyme
Roorkee, Roorkee
Biology Division, Indian Institute of Structural and functional characterization of Type ISP Restriction-­‐Modification Science Education and Research, Enzymes
Pune
B030
Malti Yadav
B031
Manu. M. S
B032
Mohd Akif
B033
Monika Chandravanshi
B034
Mukesh Saran
B035
Nandini
B036
Neetu
B037
Nidhi Saikhedkar
B038
Nitin Bayal
B039
NSK Mulukala
B040
Omantheswara N.
B041
Pankaj Kumar Madheshiya
Pankaj Singh Parihar
Poonam Kumari
B042
B043
B044
B045
B046
B047
B048
B049
B050
B051
B052
B053
B054
B055
B056
B057
B058
B059
B060
B061
B062
B063
Crystallography and Molecular Biology division, Saha Institute of Nuclear Physics, Kolkata
Biochemical Sciences Division, CSIR-­‐
National Chemical Laboratory, Pune
Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati
Department of Physics, Manipal University Jaipur
Department of Chemistry, Indian Institute of Technology, Mumbai Department of Biotechnology, Indian Institute of Technology Roorkee
Biochemical Sciences Division, CSIR-­‐
National Chemical Laboratory, Pune
National Centre for Cell Science, Pune
Department of Biochemistry, University of Hyderabad, India
University of Mysore, Mysuru Structural and functional studies of Eal, a c-­‐di-­‐GMP phosphodiesterase, from Vibrio cholerae 0395
Plant GET3-­‐ Deciphering the modus operandi
Towards stability optimization of a recombinant leptospirosis vaccine scaffold from comparative biophysical analysis of homologous antigenic domains
Heterogeneous behavior of metalloproteins towards metal ion binding and selectivity: insights from molecular dynamics studies
Cloning, expression, purification and preliminary crystallographic studies of a ribokinase super-­‐family Pyridoxal kinase from Lactobacillus plantarum WCFS1
Cross talk between the two functional domains in Formylglycinamide -­‐ ribonucleotide amidotransferase
Characterization of Cra from Enterohemorrhagic E. coli to elucidate its structure-­‐
activity relationship
Reactive centre loop tripeptides of Pin-­‐II serine protease inhibitors as insect control agents against Helicoverpa armigera
Thioredoxin reductase-­‐thioredoxin (TR-­‐Trx) from Mycobacterium leprae: Structural and Functional studies
Structural Characterization of Podocin and Assessment of Nephrotic Syndrome Associated Podocin Mutants
Structure of multiple sugar binding transport ATP-­‐binding protein from Pyrococcus horikoshii
Structural analysis of interaction network of channel nucleoporins with adapter ring of vertebrate nuclear pore complex
[Title]
National Centre for Cell Science, Pune
Molecular & Structural Biology Division CDRI, Lucknow School of Life Sciences, Jawaharlal Characterization of phosphoserine phosphatase from E. histolytica
Nehru University
Pratibha Bharti
National Centre for Cell Science, Structural and Functional Characterization of cystine-­‐knot AMPAR modulating Pune
protein (CKAMP44)
Pravin Dewangan
National Centre for Cell Science, Structural Studies on central channel of the nuclear pore complex from various Pune
species
Prema G. Vasudev Molecular and Structural Biology Crystallographic Characterization of the First LPMO Protein from Plants
Division, Central Institute of Medicinal and Plants, Prerana Gogoi
Department of ABromatic iosciences and In silico analysis suggests that PH0702 and PH0208 encode for methylthioribose-­‐
Bioengineering, Indian Institute of 1-­‐phosphate isomerase and ribose-­‐1,5-­‐bisphosphate isomerase, respectively, Technology Guwahati, Guwahati
rather than aIF2Bβ and aIF2Bδ
Pushparani D Biochemical Sciences Division, CSIR-­‐ Structural Insights From a Novel Dimeric Marine Cholyolglycine hydrolase from Philem
National Chemical Laboratory, Pune Shewanella loihica PV-­‐4
Rajkanwar Centre for Cellular and Molecular Structure-­‐Function Analysis of Xanthomonas oryzae pv. oryzae Virulence Factor Nathawat
Biology, Hyderabad CbsA
Rastogi N
Department of Biophysics, All India Structure of tryptically produced iron-­‐free C-­‐lobe of lactoferrin and its functional Institute of Medical Sciences, New significance in the gut
Delhi
Ravi Guru Raj Rao Department of Bioinformatics, Cloning, Expression and Purification of Glycinamide Ribonucleotide (GARS) Alagappa University, Karaikudi
synthetase from Pyrococcus horikoshii OT3 Sagar Khavnekar
UM-­‐DAE Centre for Excellence in The structure of B. subtilis RecU Holliday Junction resolvase in complex with a Basic Science, University of Mumbai, palindromic DNA fragment and its solution studies using SAXS and MD; Mumbai elucidating a novel inverted manhole ascent mechanism
Sanchari Banerjee Institute for Stem Cell Biology and Structure of a heterogeneous, glycosylated, lipid-­‐bound, in vivo grown protein Regenerative Medicine, Bangalore crystal at atomic resolution from viviparous cockroach, Diploptera punctata
Sangeeta Niranjan National Centre for Cell Sciences, Exploring Structural and Biochemical basis of Nup155 in NPC assembly
Pune
Sapna Sugandhi
National Centre for Cell Sciences, Structural studies on redox proteins of Mycobacterium tuberculosis
Pune
Satyaprakash Yadav Department of Biophysics, All India Structure of PCNA (Proliferating cell nuclear antigen) from Leishmania Donovan
Institute of Medical Sciences, New Delhi
Shankar Prasad Department of Biosciences and Structural insight into the glycerophosphocholine binding protein, a subunit of Kanaujia
Bioengineering, Indian Institute of ABC transporter
Technology Guwahati, Guwahati
Shivam Shukla
Indian Institute of Science Education Structural and functional studies on YbeY
and Research, Kolkata
Shramana Saha Institute of Nuclear Physics, Structural and functional aspects of Low Molecular Weight Protein Tyrosine Chatterjee
Kolkata
Phosphatase from Vibrio cholera 0395
Shubhangi Agarwal Post Graduate Department of Structure insights of exogenous siderophores and heme uptake proteins VcFhuD Biotechnology, St. Xavier’s College, and VcHutB of Vibrio cholerae
Kolkata
Someswar R. Dept. of Genetics & Biotechnology, Design, Insilco analysis and synthesis of novel imidazole derivatives as an anti-­‐
Sagurthi
Osmania University, Hyderabad
angiogenesis and anticancer agents
Suman Pandey
Department of Biosciences and Structural studies on ppGBP provide evolutionary insights and basis for Bioengineering, IIT Bombay, structure-­‐based sub-­‐classification of periplasmic sugar binding proteins
Mumbai
Surabhi Johari
Dibrugarh University, Dibrugarh
[Title]
B064
Surbhi Dhingra
B065
U. Yadava
B066
Vandana Gaded
B067
Vandana Mishra
B068
Vijaykumar Pillalamarri
B069
Zenia Motiwala
National Centre for Cell Sciences, Pune
Department of Physics, DDU Gorakhpur University, Gorakhpur
Department of Chemistry, Indian Institute of Technology, Mumbai Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay Center for Chemical Biology, Indian Institute of Chemical Technology, Hyderabad
Biochemical Sciences Division, CSIR-­‐
National Chemical Laboratory, Pune
Expression, Purification and Crystallization of Prokaryotic Glutamate receptor
Characterizations of Solute Binding Proteins by Differential Scanning Fluorimetry and Crystallography
Structure and function determination of an uncharacterized enzyme from Mycobacterium smegmatis of the cytidine deaminase superfamily
Understanding the activation mechanism of Plasmepsins from Plasmodium falciparum and their structural studies to develop antimalarial inhibitors
Discovery of new genetic variants from Vibrio cholera, V. parahaemolyticus and V. corallilyticus
Exploring hematopoietic stem cell regulation at the atomic level with ASRIJ
Chemical And Material Sciences
Poster Name
Number
C001
Abdul Ajees A.
C002
Amit Chakraborty
C003
Anant Kumar Srivastava
C004
Ancy I.
C005
Arghya Basu
C006
C007
C008
C009
C010
C011
C012
C013
C014
C015
C016
Karunagaran N.
C018
Keshab M. Bairagi
C019
Kiran K S
C021
Department of Atomic and Molecular Physics, Manipal University, Manipal Physical/Materials Chemistry Division, CSIR-­‐National Chemical Laboratory, Pune Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune
Department of Physics, Periyar University, Salem-­‐636 011, India
Physical and Material Chemistry Division, National Chemical Laboratory, Pune Arjun Halder Polymers and Advanced Materials Laboratory, CSIR National Chemical Laboratory, Pune
Ashok Nuthanakanti Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune
Ashok Yadav
Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune
Babulal Das
Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati
Basanta Saikia
Department of Chemical Sciences, Tezpur University, Assam
Chandani Singh School of Chemistry, University of Hyderabad, Hyderabad
Dinesh Mullangi
Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune
Ekta Sangtani
CSIR-­‐National Chemical Laboratory, Pune Fayaz Baig
Department of Chemistry, Birla Institute of Technology and Science, Pilani, Pilani Campus, Rajasthan
Hema M. K.
Department of Studies in Physics,University of Mysore, Manasagangotri, Mysuru
Kalaiarasi C.
Department of Physics, Periyar University, Salem-­‐636 011, India
C017
C020
Institute
Centre for Crystal Growth, SSN College of Engineering, Chennai
Department of Chemistry, Visvesvaraya National Institute of Technology (VNIT), Nagpur
Department of Physics, Bangalore University, Bangalore
Title
Rapid crystallization of amino acids using biocompatible nucleant with Nd:YAG laser
Synthesis of Heterometallic 3d-­‐4f Complexes using new Multisite Coordination Ligand
Potential Ferroelectric Response In {CuIIL2}n Assemblies Derived From Pyridyl-­‐
functionalized Flexible Amino-­‐P(V) Ligands
Exploring the topological properties of electron density, electrostatic potential and intermolecular interactions of Zidovudine via experimental charge density analysis
Near-­‐Infrared Luminescent Sn(IV) Complexes of N-­‐Confused Tetraphenylporphyrin
Decoding the Morphological Diversity in Two Dimensional Crystalline Porous Polymers by Core Planarity Modulation
Structure of bacterial ribosome decoding site RNA containing conformation-­‐
sensitive fluorescent ribonucleoside
Anion Induced Potentially High Ferroelectric Polarization in a Luminescent [Zn6L8]12+ Octahedral Cage
Novel multicomponent crystals of L-­‐tryptophan with three isomers of pyridinedicarboxylic acids
Control Sulfathiazole Polymorph Nucleation on Functionalized Surface
Encapsulation of a Keggin Cluster Anion in ZIF-­‐8 Cage: A Supramolecular Host-­‐
Guest System having potential to act as a Water Oxidation Catalyst
Low overpotential electrocatalytic water splitting with noble metal-­‐free nanoparticles supported in a sp3 N-­‐rich flexible COF Colour Cocrystal Polymorphism: Cocrystals of Furosemide with Pyridines
Structural transformations of coordination polymers on the counter anion exchange and metal-­‐metathesis
Synthesis and crystal structure of (Z) 2-­‐(4-­‐chlorophenyl)-­‐N’-­‐hydroxy acetamidine
Topological characterization of electron density, electrostatic potential and intermolecular interactions of 2-­‐nitroimidazole: An experimental and theoretical study
Investigations on synthesis, growth and physical properties of AgGa0.5In0.5S2 single crystals for Mid-­‐IR application Structural analysis of dihydropyrimidine based organic compounds Crystal and Molecular docking studies of 3-­‐hydroxy-­‐2-­‐((2-­‐hydroxy-­‐4, 4-­‐dimethyl-­‐
6-­‐oxocyclohex-­‐1-­‐enyl) (4-­‐methoxyphenyl) methyl)-­‐5,5-­‐dimethylcyclohex-­‐2-­‐
enone with focal adhesion kinase inhibitors
Krishnamurthy M.S. Department of Studies in Chemistry, Synthesis and Crystallographic analysis of fluoro substituted arylidene Bangalore University, Bangalore
derivatives of thiazolopyrimidines
Kunal Kumar Jha
Department of Chemistry, School of Unraveling Charge-­‐transfer Mechanism in Organic NLO Materials via Natural Science, Shiv Nadar Experimental and Theoretical Charge Density Analysis
University
C022
C023
C024
C025
C026
C027
C028
C029
C030
Lalitha P.
Department of Physics, SrimadAndavan Arts and Science College , Trichy Luminita Harnagea Department of Physics, Indian Institute of Science Education and Research (IISER) Pune
Mahadevaiah
Center for Materials Science, University of Mysore, Mysore
Manas Pal
Physical and Materials Chemistry Division, CSIR-­‐National Chemical Laboratory, Pune
Manju V V
Department of Physics, Vidyavardhaka college of Engineering, Mysuru
Manjula S
Department of Physics, Periyar University, Salem
Nandaprakash M. B. Department of Studies in Physics, University of Mysore, Manasagangotri, Mysuru
Pallavi. G.B
P.G Department of Physics, Bharathi College, K M. Doddi, Mandya Dist
Partha Pratim Jana Department of Chemistry, Indian Institute of Technology Kharagpur
C031
Prachi Telang
C032
Prasad N.L
C033
Rabindranath Bag
C034
Rajiv Khatioda
C035
C036
C037
C038
C039
C040
C041
C042
C043
C044
C045
C046
C047
C048
C049
C050
C051
C052
Single Crystal Growth, Structural and Physical Characterizations of novel superconductors and topological insulators
Synthesis and Computation of crystallite shape in Silk Films using X-­‐ray diffraction data
Facile formation of core-­‐shell silicon@mesoporous TiO2 heterostructure and their photoelectrochemical property
Crystallite shape computation in four different varieties of cotton fibers using X-­‐
ray powder diffraction data
Structure, charge density distribution and the electrostatic properties of Andrographolide molecule -­‐ An experimental and theoretical study
Crystallite Shape For Wild Silks Using X-­‐ray Powder Diffration Data
Crystal Structure of (2-­‐Amino-­‐thiazol-­‐4-­‐yl)-­‐acetic acid hydrazide Reinvestigation of δ-­‐, η-­‐ phase region in the gold-­‐cadmium binary system: synthesis, crystal structure analysis and thermal stability
IISER Pune
Anomalous volume collapse in pyrochlore Iridate Eu2Ir2O7 upon isovalent doping of Bi at the Eu site
Department of Studies in Chemistry, Crystal structure of Diethyl 2, 6-­‐dimethyl-­‐4-­‐(naphthalen-­‐1-­‐yl)-­‐1,4 Bangalore University, Bangalore
dihydropyridine-­‐3,5-­‐dicarboxylate
IISER Pune
Department of Chemical Sciences, Tezpur University, Napaam
Ramprasad N.
Department of Physics, Govt. First Grade College, Mulbagal, Kolar Dist
Rupali Thorave
Department of Chemistry Savitribai Phule Pune University, Pune
Saiadali Fathima K. School of Physics, Madurai Kamaraj University, Madurai
Sakharam B. Tayade Department of Chemistry, Savitribai Phule Pune University, Pune.
Samir. R. Shaikh
Center for Materials Characterization, CSIR-­‐National Chemical Laboratory, Pune Sanjib Chetry
Department of Chemistry, Cotton College, Guwahati
Shobhana Department of Chemistry, Indian Krishnaswamy Institute of Technology, Madras Shouvik Mitra
Physical/Materials Chemistry Division, CSIR-­‐National Chemical Laboratory, Pune
Shridhar H. Thorat Center for Materials Characterization, CSIR-­‐National Chemical Laboratory, Pune Shyamapada Nandi IISER Pune
Soumendranath Panja
Suman Chandra
Powder X-­‐ray diffraction pattern analysis of Hydronium adipate
IISER Pune
Physical/Materials Chemistry Division, CSIR-­‐National Chemical Laboratory, Pune Suman Kumar Department of Chemistry, School of Mandal
Natural Science, Shiv Nadar University
Suresh Madhu
Organic Chemistry Division, CSIR-­‐
National Chemical Laboratory, Pune
Susanta K. Nayak
Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur Tanusri Dey Department of Physics, Jadavpur University, Kolkata Vivekanand Sharma Department of Chemistry, Indian Institute of Technology Kanpur
Yadav T. P. Department of Physics, Institute of Science, Banaras Hindu University, Varanasi
Single crystal growth in travelling-­‐solvent floating-­‐zone method of Spin Chains SrCuO2, Sr2CuO3 and Spin Ladders Sr14Cu24O41
2D COF as Heterogeneous Catalyst for Control Oxidation of Benzyl Alcohols
Crystal Structure of 7, 8-­‐Benzocoumarin-­‐4-­‐acetic acid
Investigation of binding behavior of p-­‐sulfonatocalix[4]arene with quinoline in the solid state
Synthesis, Growth and Characterzation of 2-­‐((1H-­‐benzo[d]imidazol-­‐2-­‐yl) amino)-­‐
1-­‐phenylethan-­‐1-­‐one (C15 H13 N3 O) single crystal
Supramolecular Self-­‐Assembled Motifs
Quinoline-­‐Based Reversible Turn-­‐on Fluorescent Probe: Detection of Acids in Solution and Vapor-­‐state
Supramolecular π-­‐π and C-­‐H-­‐-­‐π interactions in Mn(II) and Zn(II) coordination solids involving pyrazolyl and bipyridyl ligands
Molecular self-­‐assembly in [2]catenanes obtained via the mechanical interlocking of D-­‐shaped macrocycles Self-­‐Exfoliated Guanidinium-­‐Based Ionic Covalent Organic Nanosheets (iCONs)
Molecular Salt Hydrate of an Anticancer Drug Gefitinib and a Loop Diuretic Drug Furosemide: An Alternative for Multidrug Treatment
A single-­‐ligand ultra-­‐microporous MOF for pre-­‐combustion CO2 capture and hydrogen purification
Relieving geometrical frustration through structural distortion in 114 Swdenborgite
Phosphoric Acid Loaded Covalent Organic Frameworks as Proton Conducting Materials
Quantitative Analysis of Hydrogen Bonding in Proteins: A Charge Density Database Transfer Approach
Supramolecular Engineering of Guest-­‐Adaptable Porous Organic Frame Work for Ammonia and Reaction Intermediates Trapping
In situ cryocrystallography of low melting halogen-­‐bonded complexes
Three Oxime Ethers: Structural Characterization with Single-­‐ and Powder-­‐ Crystal X-­‐ray Diffraction and Molecular Electrostatic Potential Calculations
Solvent Induced Unusual 2D to 3D Transformation in a Zn(II)-­‐Framework via SC-­‐
SC Fashion
Surface studies of Ag-­‐In-­‐Gd 1/1 quasicrystalline approximant
B1
Biochemical and crystallographic studies on the second single strand
DNA binding protein from Mycobacterium smegmatis
Singh A, Vijayan M.
Molecular Biophysics unit, Indian Institute of Science, Bangalore-560012, India
Email: amandeep@mbu.iisc.ernet.in, mv@mbu.iisc.ernet.in
Abstract
A second, less well-known, single stranded DNA binding protein (SSBb) occurs in some
bacterial species including mycobacteria. This protein from Mycobacterium smegmatis has
been cloned, expressed and purified. Preliminary solution studies indicate the protein to be a
tetramer with comparatively low affinity for ssDNA, as compared to the canonical paralogous
SSBa .The DNA binding affinity of the protein is modulated by the presence of Mg
2+
and
NaCl in the buffer. The protein crystallizes in hexagonal space group P6522 with half a
tetrameric molecule in the asymmetric unit of a cell with dimensions a = b =73.61 Å, c =
216.21 Å. The tetramer is a dimer of dimers having 222-symmetry, with one molecular dyad
coinciding with a crystallographic 2-fold axis. Each subunit exhibiting an OB fold, has a
globular core formed by a seven-stranded β-barrel, which is capped by an α-helix. Like other
previously characterized mycobacterial SSBa's, MsSSBb also has an additional strand β7 that
forms a hook-like structure at the extremities of the dimer to provide additional stability to
the molecule. However, MsSSBb exhibits many differences when compared to SSBb's of
known structures from B.subtilis and S.coelicolor.
Kunitz Trypsin Inhibitor 2 from Chickpea: Unravelling the β- trefoil
1
2
Ameya D. Bendre , Sureshkumar Ramasamy , Dhanasekaran Shanmugam
Structural Biology Group, Biochemical Sciences Division, CSIR- National
Chemical Laboratory, Pune (India) 411008
Email: ad.bendre@ncl.res.in, s.ramasamy@ncl.res.in
Kunitz type trypsin inhibitor (KTI) family is one of the most versatile families of protease
inhibitors. Their exact physiological role in plants is still unclear. According to some reports,
KTIs are involved in growth and development of plants, while others suggested their role in
recovery from physical damage, and defence from pests and pathogens. Some reports also
suggest their efficacy against HIV proteases, cancer etc. Today, under Kunitz legume family
in Pfam (PF00197), about 766 sequences under 124 plant species with 55 (9 native and 46
mutant) structures in PDB have been reported.
Chickpea is world’s 3rd legume crop with India as a top producer in the world. Leguminous
plants are known to have more than one isoforms/ variants of Kunitz inhibitors, yet very little
is known about chickpea KTIs. From draft chickpea genome, we identified about 8 sequences
that could fit into Kunitz family of which 2 have been already reported. Based on sequence
analysis, we have cloned 4 genes into E. coli. and carried out their expression, purification.
We could get crystals of one inhibitor Ca18406 which diffracted at 1.5 Å. Structure solution
and crystallisation trials of Ca18406, Ca18407, Ca01740 and Ca27052 are in progress.
Meanwhile we docked modelled Ca18406 with structures of trypsin from three different
sources viz. Fusarium oxysporum, Helicoverpa armigera and bovine pancreas. Docked
complexes were simulated using the NAMD2.8 simulation package with the CHARMM22
all-atom force field with CMAP correction. All complexes seemed stable which could be
supported with preliminary biochemical assay using artificial substrate BApNA.
B3
Structural studies on Iridoid synthase: Revealing substrate specificity of PGR
family
1
2
*2
*1
Anandsukeerthi.Sandholu , Ramakrishnan Krithika ,Thulasiram.H.V , Kiran A.Kulkarni
1
Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune-411008
2
Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune-411008
email id: as.sandholu@ncl.res.in, ka.kulkarni@ncl.res.in
Iridoids are the major class of monoterpene indole alkaloids (MIA’S). These are important plant
secondary metabolites. C.Roseus is the major source of iridoid derived MIA’S and it known to
contain over 2000 alkaloids in various tissue. Among these there are several important
compounds such as Vinblastin, vincristine are being used as anticancer drugs widely.
Iridoid synthase (IDS) is a short-chain dehydrogenase/reductase (SDR) belonging to
Progesterone 5β-reductase (DlP5βR) family. It produces the ring skeletons for the production of
vinblastine and vincristine. Iridoid synthase uses the linear monoterpene 10-oxogeranial as
substrate and couples an initial NAD(P)H-dependent reduction step with a subsequent
cyclization step via. Michael addition and hetero Diels–Alder cycloaddition. Structural alignment
studies have shown that IDS and P5βR exhibit the same topological arrangement of helices in the
catalytic site with the specific standard nucleotide binding double rossman fold, in contrary IDS
and DlP5βR manifests different substrate specificities. To address this specific problem, the
crystal structure of IDS-NAHPH complex has been determined. These structural studies guided
us to understand the catalytic mechanism, mode of substrate binding and substrate selectivity in
comparison to DlP5βR.
Trypanothione synthetase as novel drug target in Leishmania
Anil Kumar Shakya
CSIR-Central Drug Research institute, Lucknow
Trypanothione synthetase is an essential enzyme involved in the biosynthesis of trypanothione in
Leishmania. It is also involved in antioxidant mechanism and defense against cellular oxidants.
The trypanothione synthetase is a bifunctional enzyme responsible for the formation of
trypanothione by catalyzing biosynthesis and hydrolysis of the glutathione-spermidine. This
enzyme is not present in humans. Trypanothione synthatase is suggested as valuable drug target
in leishmania. To know the structure of protein we need to crystallized and the work under
progress it could be noble drug target.
Effects of mutations on the structure-function relationship of
proteins
B5
Anil K. Jamithireddy and B. Gopal
anil.pcu@gmail.com, bgopal@mbu.iisc.ernet.in
Molecular Biophysics Unit, Indian Institute of Science, Bangalore - 560012
Abstract:
The primary structure determines the conformation, function and stability of proteins. Mutations
alter conformation and/or activity of proteins either due to direct effects on activity or indirectly
because of altered protein structure and stability. Here we study the effects of mutations on the
structure-function relationship of CcdB toxin from E.coli. A repertoire of CcdB point mutants
has been studies both in vivo and in vitro, but structural studies on these mutants have been
largely undetermined. A subset of these mutants, apart from the active site/interface were found
to differ to a greater extent from the wild type protein, in terms of activity, melting temperature,
stability and cellular expression levels. We have structurally characterized a few of these mutants
by X-ray crystallography. Our crystal structures indicate that the mutations are causing a
conformational instability (inferred from B-factor analysis). The mutation of a buried residue
leads to the destabilization of hydrophobic core in one of the mutants and is responsible for its
lower stability. Thus, mutations in non-active site regions could affect the structure and thus the
activity of proteins as evident from our experimental data.
Structural and functional analysis of enzyme from polyamine biosynthetic
pathway of Entamoeba histolytica
Anjali Malik, Harvijay Singh and Shailly Tomar
Department of Biotechnology, Indian Institute of Technology, Roorkee – 247667, India
malik.anjali26@gmail.com, shailfbt@iitr.ac.in
Entamoeba histolytica is a parasitic protozoan, affecting the digestive tract of predominantly
humans and other primates causing serious health problems and accounting for 50 million annual
infections worldwide. As parasitic protozoans utilize polyamine biosynthetic pathway for their
growth, proliferation, survival in host and to evade the host immune mechanism, so enzymes of
polyamine biosynthetic pathway are novel targets for the structure based drug designing. Also
enzymes of parasite exhibit features which are significantly different from the host thus, inhibitor
molecules targeting these enzymes can lead to development and designing of new anti-parasitic
drugs. In this study, we have focused on arginase enzyme which hydrolyses L-arginine to Lornithine to be used as substrate for polyamine biosynthetic pathway. Here, we report cloning of
arginase from E. histolytica (EhArg), expression of the recombinant protein in soluble form and
purification of His-tag EhArg using affinity chromatography. The purified EhArg was found to
be active confirmed by enzymatic assay and was used for crystallization and for doing
thermodynamic studies using Isothermal Titration Calorimetry. Additionally the effect of high
salt concentration on the oligomeric state of the protein has been investigated using gel-filtration
chromatography. Gel-filtration chromatography was also used to analyze the concentration
dependent oligomerisation of the protein. Multiple sequence alignment showed that the metal
binding and active site residues are highly conserved, which helped us in developing an inactive
mutant of EhArg. Homology modeling was performed to generate a 3D structure of EhArg using
1CEV as template. Further, crystallization trials, biophysical and biochemical characterization of
the protein is still in progress.
Structural and Functional studies on Drosophila Ionotropic
receptors
B7
Anshul Assaiya, Janesh Kumar
National Centre for Cell Science, Pune, Maharashtra, India
G protein coupled receptors mediate the olfactory sensation, but in Drosophila melanogaster a subset
of chemosensory receptors called Ionotropic receptors(IRs) have been identified which are ligand
gated ion channels. The IRs exhibit a modular organization similar with the ionotropic glutamate
receptors (iGluRs) but they do not function at synapses. This indicates that IRs are the functional
descendants of the iGluRs. They directly interact with the environmental clues and exhibit odor
evoked responsiveness. IRs can be broadly classified as IR coreceptor and IR odor specific receptors.
The expression and ciliary localization of the odor specific IRs is dependent on the IR coreceptors.
The amino terminal domains (ATD) of iGluRs are involved in their assembly and therefore ATDs of
IRs can be interrogated to unveil their mechanism of heteromeric assembly. The molecular basis of
the expression, assembly, and colocalization of functional ligand gated ion channel by IRs is still not
defined and structural studies will reveal the mechanism of their assembly and the functional parallels
with the iGluRs. To investigate the role of IR ATDs in the assembly of functional receptors, we have
cloned and optimized expression of IR8a, IR 25a, IR75a and IR84a ATDs from transinetly transfected
mammalian cells. Biochemical, biophysical chracterization and crystallization trials for their structure
determination is ongoing. Functional analysis of IRs will act as a promising model system to
understand the evolution of diverse odor recognition and signalling properties. Moreover, the modular
organization of IRs provides an opportunity to selectively modulate their odor specificity, ligand
recognition and localization, this will also provide important insights into how olfactory receptors
achieve a diverse ligand specificity.
Crystal Structure of a Novel Insecticidal Protein from the Fern Tectaria
macrodonta
1
2
2
Archana , Sunil Kumar Yadav , Pradhyumna Kumar Singh , Prema G Vasudev
1
1
Molecular and Structural Biology Division, CSIR-Central Institute of Medicinal and Aromatic
Plants, Lucknow, India.
2
Genetics and Plant Molecular Biology, CSIR-National Botanical Research Institute, Lucknow,
India.
Email: archanaa843@gmail.com, Supervisor: premavasudev@cimap.res.in
An insecticidal protein (Tma12) isolated from an edible fern Tectaria macrodonta, which is
active against the sap sucking pest Bemisia tabaci (whitefly), was crystallized and characterized.
Sequence analysis revealed that the protein belonged to chitin-binding family CBM33. The
protein crystallized in tetragonal space group P43212 and the initial model was obtained by
Molecular Replacement. A lytic polysaccharide monooxygenase (LPMO) protein 4OY7 which
showed 45% sequence identity with Tma12 was used to create the search model for Molecular
Replacement. The final, 2.2 Å resolution structure is refined with Rcryst and Rfree values of 19%
and 23%, respectively. The crystal structure of Tma12 revealed an immunoglobulin-like β sandwich fold, which is typical of the carbohydrate binding proteins belonging to the AA10
family in the Carbohydrate Active enZyme (CAZy) database, with a Cu(I) ion bound to His1
residue. This is the first structural characterization of AA10 proteins from plants. The overall
structure of Tma12 is similar to the bacterial AA10 proteins. Details of the crystallization,
structure determination and refinement of Tma12 and its characteristic structural features will be
presented.
B9
Structural and functional studies on hypoxia protein Rv0081 in Mycobacterium
tuberculosis during latency
Ashwani Kumar, C. M. Santosh Kumar, Swastik Phulera, Parshuram Sonawane,
*
Shekhar C. Mande
National Centre for Cell Science, NCCS Complex, University of Pune
Campus, Ganeshkhind, Pune 411007, Maharashtra, India
Email: ashwanikumar@nccs.res.in, shekhar@nccs.res.in.
ABSTRACT
Tuberculosis (TB) is detrimental infectious disease caused by Mycobacterium
tuberculosis (Mtb). Although, about one third of human population is infected by Mtb, only
10% of the population show active TB infection, while in the rest the bacterium remains
dormant or latent. In immuno-suppressed conditions, pathogen is believed to be reactivated
from latency. Therefore controlling onset of latency or reactivation is fundamental challenge.
Latency is characterized by up and down regulation of DosR regulated genes. Formate
hydrogenlyase complex (FHL) is encoded by the rv0081-rv0088 operon, which is regulated
by DosR (Rv3133c) as well as Rv0081 (a Smt family transcription factor) during dormancy.
An in-silico study employing protein functional linkages and gene expression profiles of
latency models, have indicated that Rv0081 acts as a latency signal switch between DosR and
NDH-I (complex-I) via Rv0082 (a putative oxidoreductase). Furthermore, investigating
hypoxia/re-aeration related Mtb transcriptome demonstrated Rv0081 as a regulatory hub.
Thus, we aim to elucidate molecular details of Rv0081 and FHL complex to understand in its
role in Mtb latency. We have expressed purified and crystallized Rv0081 protein; solved
Rv0081 structure at 3.3 Å resolution. Furthermore, to identify putative metal binding domain
and DNA binding regions, we superimposed Rv0081 structure with SmtB (a structural
homolog bound to metal ion) and NoIR (a structural homolog bound to DNA). Results
indicated that structure of Rv0081 shows absence of metal binding site but shows the
presence of DNA binding domain. Studies to validate absence of metal binding site are in
progress. To validate the identified DNA binding region, an Rv0081 mutant with mutated
putative DNA binding residues was generated. EMSA with wild type as well as mutant
Rv0081 showed that DNA binding is diminished in mutant Rv0081. Since Rv0081
crystallizes as homo-dimer oligomerization analysis in solution are underway.
Structural studies on Nup93-Nup188 complex of vertebrate Nuclear pore
complex
Bhawna Burdak and Radha Chauhan
National centre for cell sciences
Email address: bhawna.burdak@gmail.com, radha.chauhan@nccs.res.in
Eukaryotic cells are having refined machinery to control the supply of macromolecules to and
fro of nucleus called nuclear pore complex (NPC). NPC are found embedded in nuclear
envelope. It is the largest protein complex composed of ~30 different nucleoporins which are
present in multiple copies, thereby making different sized NPC, in yeast ~66MDa and
~112MDa in vertebrates. NPC can be broadly classified into scaffold proteins (Nup93 sub
complex imparts structural support to NPC) and functional proteins (central channel Nup62
complex involved in macromolecular transport). It is known that the N-terminal coiled coil
region of Nup93 interacts with Nup62 complex and helps in recruitment of NPC assembly
forming central channel. The C-terminal domain of Nup93 binds either to Nup188 or
Nup205. Our major focus is on scaffold proteins (Nup93 and Nup188) from vertebrates to
understand their role in NPC assembly. On the basis of secondary structure prediction we
have made different constructs of Nup93 and Nup188 which will be used for both structural
as well as interaction studies. For structure determination we will attempt to purify individual
protein or its domain or protein complex by using mammalian /baculovirus expression
system. For complex purification we have generated stable cell line of Nup188 to purify
Nup188-Nup93 complex via pulling down Nup93 along with Nup188. Purified proteins will
be further subjected to crystallization trials & cryo-EM. Structural elucidation through these
strategies may give us insight into the role of adaptor nucleoporins in NPC assembly
B 11
A genomics approach for identification of proteases as major potential virulence
factors in the pathogenic fungus, T. rubrum
1,2
Chitra Latka
, Sanchita Sanchaya Dey
3
4
1,2
1
1
, Siddharth Mahajan , Ramachandira Prabu ,
4
4
5
Pramod Kumar Jangir , Chhavi Gupta , Shukla Das , VG Ramachandran , SN Bhattacharya ,
6
2,3
Rajesh Pandey , Rakesh Sharma
1
, S Ramachandran
1,2
and Bhupesh Taneja
1,2
*
Genome Informatics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative
2
Biology, New Delhi, India; Academy of Scientific and Innovative Research, New Delhi, India; ;
3
4
Microbial Biotechnology and Genomics Unit, CSIR-IGIB, New Delhi, India. Department of
5
Microbiology, UCMS & GTB Hospital, Dilshad Garden, Delhi, India; Department of
6
Dermatology, UCMS & GTB Hospital, Dilshad Garden, Delhi, India; CSIR Ayurgenomics Unit
- TRISUTRA, CSIR-IGIB, New Delhi, India
e-mail:
Presenting author : chitra.latka@igib.in
Supervisor : btaneja@igib.res.in
Trichophyton rubrum are a monophyletic group of fungi best known for affecting the skin of
animals and humans. These fungi cause a variety of skin diseases, including athlete’s foot (tinea
pedis), jock itch (tinea cruris), and ringworm (tinea capitis or tinea corporis, depending on area of
the body infected). In order to gain insight into the major virulence factors of T. rubrum, whole
genome sequencing of a clinical isolate, designated as Trichophyton rubrum IGIB-SBL-CI1 was
carried out. 8265 putative protein coding genes were identified using Augustus web server followed
by annotation with Blast2GO. Proteases were identified as the major secretory family encoded in
the genome and further validated to have differential expression patterns in acidic, neutral or
alkaline pH Comparative analysis of the secretome of T. rubrum IGIB-SBL-CI1 with other
dermatophytes and non dermatophytes revealed enrichment of serine protease family in
Trichophyton rubrum thereby further supporting their functional importance as potential virulence
factors. Comparative genomics of T. rubrum IGIB-SBL-CI1 with ten other whole genome
sequences of T. rubrum (including Refseq) available at NCBI was carried out to understand strain to
strain variations. Further characterisation will help in better understanding the action of these
proteases of T. rubrum. Details of this work will be presented.
Preliminary crystallisation trials of Inhibitory Domain of Sub16, a Sedolisin
Serine protease of a dermatophyte, Trichophyton rubrum
1,2
Chitra Latka
1
1
, Jagga Bikshapathi and Bhupesh Taneja
1,2
*
Genome Informatics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative
2
Biology, New Delhi, India; Academy of Scientific and Innovative Research, New Delhi, India;
Email: chitra.latka@igib.in, btaneja@igib.res.in
Trichophyton rubrum are a monophyletic group of fungi best known for affecting the skin of
animals and humans. These fungi cause a variety of skin diseases, including athlete’s foot (tinea
pedis), jock itch (tinea cruris), and ringworm (tinea capitis or tinea corporis, depending on area of
the body infected). During disease, these exclusively infect and multiply within keratinized host
structures-the epidermal stratum corneum, nails or hair. During in vitro cultivation with protein as
sole nitrogen and carbon source, dermatophytes were proven to secrete multiple proteases, some of
which have been identified and are thus putative virulence factors. Clustering of secreted proteins of
Trichophyton rubrum revealed several protease and keratinase that might play major role in
establishment of infection by degrading proteins present in skin of host. Comparative secretome
analysis along with other dermatophytes and non dermatophytes revealed enrichment of serine
protease family in Trichophyton rubrum thereby further supporting their functional importance in
Trichophyton rubrum. Serine proteases are formed as inactive proteases. Pro domain / inhibitor I9
domain act as molecular chaperone leading to proper folding of active protein along with keeping
the mature form inactive. In order to gain insights into the mechanism of inhibition and subsequent
activation of the functional protease by the inhibitory Pro domain of Sub16, a member of S53
sedolisin family, we cloned the domain in a N-term His tag vector. Recombinant Sub16 pro was
expressed in E.coli Rosetta DE3 cells and purified over a Ni-NTA resin. Sitting drop crystallisation
trials were set up using commercial screens and at different temperatures and initial crystals were
obtained. Further optimisation was carried out by microseeding to obtain good diffraction quality
crystals. Details of this work will be presented.
B 13
Mycobacterium tuberculosis HisB: Structural and Biochemical study to design
new anti-TB Inhibitors.
1
1
Deepak Kumar Mohammad Syed Ahangar1 and Bichitra K. Biswal
1
National Institute of Immunology, New Delhi, 110067, India
E-mail: deepakdskumar@nii.ac.in
th
HisB, also known as imidazoleglycerol-phosphate dehydratase, catalyzes the 6 step of the
histidine-biosynthesis pathway. Owing to its significance in the growth, survival and
pathogenesis of Mycobacterium tuberculosis (Mtb), we have been studying its structurefunction relationships, in the context of designing inhibitors through a structure guided
approach. In this aspect, the study has reported the 3-dimensional crystal structures of
native, substrate (imidazoleglycerol-phosphate (IGP)) and inhibitor (3-amino-1, 2, 4triazole (ATZ)) bound forms to resolution of 2.0 Å, 2.1 Å and 2.3 Å, respectively. Both the
structural and the kinetics data demonstrate that ATZ is a competitive inhibitor of HisB
with a moderate inhibitory potential.
To improve the efficacy of inhibition, ATZ derivatives were virtually screened and their
binding energies at the HisB active site were determined through a computational approach.
Of few hits that were acquired and ATZ derivative (ATZ-C1) showing optimal binding was
selected for further studies. Biochemically, ATZ-C1 demonstrated a stronger competitive
inhibition with an IC50 value of 75 nM. Three dimensional structure of HisB bound ATZC1 to a resolution of 1.7 Å revealed a stronger binding interaction with the active site as
compared to ATZ, which also corroborates well with the kinetics data. Anti-mycobacterial
activity of ATZ-C1 was assessed in Mycobacterium smegmatis cultures, wherein it
effectively inhibited the growth in a rather dose dependent manner.
Engineering of the Tat Pathway Chaperons
1, ♯
Deepanjan Ghosh and Sureshkumar Ramasamy
1
Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune♯
411008 Email: s.ramasamy@ncl.res.in
The Twin Arginine translocase (Tat) pathway is unique as compared to other export pathways
such as the Sec pathway because it is able to export mature, folded proteins. The main
components of the Tat pathway are TatA/E, TatB, TatC and Tat Chaperons. The quality-control
mechanism for substrates transported by the Tat machinery is taken care of by chaperones. These
chaperones mask the twin-arginine signal and ensure proper folding and substrate maturation.
This machinery if properly modulated that can be used as a universal expression system for
expression of properly folded functional protein. One such chaperon is DmsD which helps in the
transport of Dimethylsulfoxide reductase complex (DmsABC). DmsD binds to the Tat signal
sequence of DmsA in the complex but the exact interaction i.e. the binding site and the molecular
interaction between DmsD on DmsA remains undetermined. A fusion construct (DD fusion)
containing the TAT signal sequence in DmsA (residues 1-53) and DmsD was expressed to study
the interaction between the two. As interaction between DmsD and the Tat signal sequence in
DmsA has already been confirmed, it was assumed that the expressed DD fusion protein
molecules would interact with each other. DD fusion crystallized in in H32 Space group and
diffracted upto 3.0 Å with unit cell parameters as a=b= 127.19, c= 96.69. The refinement is in
progress. From this study the ideal Tat signal can be designed to make an efficient expression
system with folding quality control.
Exploring the role of DnaG primase at replication fork from
Vibrio cholorae
Dhakaram Pangeni Sharma, SA Abdul Rehman, Preeti Panday, S. Gourinath*
DNA replication is a fundamental process that occurs in all living organisms and is
the basis for biological inheritance. Although the replication initiation involves
several proteins, DnaB replicative helicase and DnaG primase play central role. To
better understand the poor conservation of the helicase binding domain of primases
(DnaGs) among the eubacteria, we determined the crystal structure of the Vibrio
cholerae DnaG C-terminal domain (VcDnaG- CTD) at 2.5 Å. The structure has a
globular subdomain connected to a helical hairpin. Structural comparison has revealed
that globular subdomains, despite the variation in number of helices, have broadly
similar arrangements across the species, whereas helical hairpins show different
orientations. The dimerization pattern of C-terminal domain is also different in
different organism. In H. pylori the dimerization surface is symmetric while in both V.
cholerae and E. coli non symmetric dimerization is seen. Surface plasmon resonance
(SPR) based interaction study of DnaG-CTD with single stranded DNA binding
protein (SSB) of Vibrio cholerae and E. coli showed Kd to be 114 nM and 294 nM
respectively. The closer examination of the putative binding region of the globe
region as mapped for E. coli, gives enough indication that like helicase primase
differential binding, primase-SSB binding may vary from species to species
depending upon the amino acid composition of the DnaG-CTD which ultimately
determines the pattern. Little or no conservation in the helicase interaction domain
may serve as the target for developing therapeutic agents against pathogenic
organisms.
B 15
Function prediction of hypothetical protein L-aspartate oxidase from Thermus
thermophilus HB8: An in silico and in vitro approaches
Dhamodharan Prabhu, Mutharasappan Nachiappan, Ravi Guru Raj Rao and Jeyaraman
Jeyakanthan*
Structural Biology and Biocomputing Lab, Department of Bioinformatics, Science Campus,
Alagappa University, Karaikudi – 630 004. Tamil Nadu,
India. * Corresponding Author: jjkanthan@gmail.com
Thermus thermophilus HB8 is a rod shaped, gram negative, aerobic thermophilic
bacterium isolated in a thermal vent, Japan (1971). T. thermophilus HB8 genome reveals the
existence of approximately 40% hypothetical proteins, from which TTHA0983 was selected
based on the data mining study. TTHA0983 gene construct in pET11a vector was transformed in
Escherichia coli and transformants were over-expressed with the help of 0.5 mM IPTG for large
scale protein production. Targeted protein was purified using chromatographic techniques.
Simultaneously, by the use of bioinformatics tools, TTHA0983 was predicted as L-Aspartate
Oxidase and molecular weight of hypothetical protein was 52.66 kDa. Three dimensional
structure of TTHA0983 protein was modeled in Schrodinger-Prime using the template (PDB ID:
1CHU) from E.coli with 55% of similarity. Structural similarity search using DALI server was
performed to analysis the similar structure available in the protein repository and found highest
scoring of 39% EcLASPO structure identical to the TtLASPO. Molecular dynamics simulation
(MDS) was performed for 30 ns to optimize the modeled structure and also to understand the
structural stability. Active site of the TtLASPO was predicted using the schrodinger-SiteMap.
The site with high sitescore and drugable score is selected for the further studies towards lead
identification and mechanism elucidation.
Keywords: TTHA0983, Hypothetical Protein, LASPO, Function Prediction, MDS.
Acknowledgement:
Authors
are
grateful
to
the
funding
agencies
DBT
(BT/PR15407/BRB/10/923/2011), UGC (No. F. 14-13/2013 [Inno/ASIST]) and DST (F.No.
SR/SO/BB-0079/2012), New Delhi for the facilities and financial support.
Active site gating of Chikungunya nsP2Pro by interdomain flexible loops
B 17
Harvijay Singh, Manju Narwal, Shailly Tomar
Department of Biotechnology, Indian Institute of Technology, Roorkee
shailfbt@iitr.ac.in, har13dbt@iitr.ac.in
Chikungunya virus (CHIKV) is a pathogenic Arthropod borne virus, which belongs to the
Alphavirus genus of Togaviridae family. Chikungunya genome is around 11.8 kb long positive
sense ssRNA which is consist of two major part viz. N-terminal nonstructural regions and Cterminal structural region. Nonstructural region is further divide into various nonstructural
proteins including nsP2 protease. NsP2 protease of chikungunya (CHIKV nsP2Pro) is one of the
essential components of viral replication and it plays a crucial role in the cleavage of polyprotein
precursors for the viral replication process. Therefore it is one of the major potential target for
drug discovery.
CHIKV nsP2Pro domain is ~321 amino acid long which comprises of two major domain i.e. Nterminal protease domain, responsible for the processing of the nonstructural polypeptide chain
and a C-terminal Methyltransferase-like domain function of which is yet to be ascertain. Active
site of nsP2proprotease possesses a catalytic dyad of Cys-478 and His-548 located in the
protease domain. We have purified, crystallized and determined the crystal structure of CHIKV
nsP2Pro. Structure analysis shows the presence of mobile loops near the active site of the
protein. These loops seem to be regulating the entry of substrate molecules. Near the active site,
Leu-670 of the MTase-like domain is observed to be interacting with Asn-547 of the protease
domain and hence contributing to the closing and opening of the active site. These residues
lining this region were found to have high B factor pointing towards the high flexibility of this
region.
Structural, functional and inhibition studies on Histo-Aspartic Protease (HAP) and
Plasmepsin II
1
1
2
3
4
Ishan Rathore , Vandana Mishra , Huogen Xiao , Rickey Yada , Alla Gustchina , Alexander
4
1
Wlodawer and Prasenjit Bhaumik
1
Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay 400076,
India.
2
Department of Molecular and Cellular Biology, University of Guelph, Ontario, N1G2W1,
Canada.
3
Faculty of Land and Food Systems, University of British Columbia, 248-2357 Main Mall
Vancouver, BC V6T 1Z4, Canada.
4
Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer
Institute, Frederick, Maryland 21702, United States
E-mail: ishanrathore@iitb.ac.in, pbhaumik@iitb.ac.in
The malarial parasite Plasmodium falciparum is responsible for the death of millions of people
yearly. Its deadly symptoms of malaria is attributed to the role of plasmepsins, a family of
aspartic proteases in P. falciparum, which degrade hemoglobin. KNI inhibitors have been
developed to selectively inhibit plasmepsins, previously been shown to inhibit HIV-1 protease.
Plasmepsin II (PMII) is one of the most studied among Plasmepsins, but still its interaction with
potent KNI inhibitors is not known. In our study we have solved multiple structures of PMII
bound with KNI inhibitors (10006, 10773, 10343). These high resolution structures accurately
show the binding mode of the inhibitor, contradicting previously hypothesized binding mode.
Thus, paving a way for designing and modifying more potent KNI inhibitors.
Plasmepsin zymogens converts to the mature form at low pH, even in the presence of potent
inhibitor Pepstatin A, suggesting that an active site independent pathway exists for activation.
One of the plasmepsins, Histo-Aspartic Protease (HAP), is a novel protease with aspartic protease
like fold with a substitution of His in place of Asp in one of the active site residues. We have
determined two structures of HAP zymogen at 2.0Å and 2.5Å resolution where the promature
region is present in different orientations indicating the intrinsic flexibility of this region along
with high B-factor, supported by MD simulations studies. Thus, under acidic conditions the noncovalent interactions in the prosegment is weakened with concomitant movement of loop
generating stress in the promature junction and ultimately cleavage of the bond to form the
mature enzyme.
Identification and Characterization of Type III Restriction-modification
Enzyme from Mycoplasma bovis
1*
1
B 19
1*
Ishtiyaq Ahmad Khan , Manasi Kulkarni , Dr. Saikrishnan Kayarat
1
Department of Biology, Indian Institute of Science Education and
*
*
Research kishtiyaq@students.iiserpune.ac.in, saikrishnan@iiserpune.ac.in
Restriction-modification (RM) are a defense mechanism evolved to protect bacteria from
invading foreign DNA, such as bacteriophage genome. These enzymes are composed of two
components. The modification (Mod) component, which by its methytransferase activity
methylate’s the host DNA at specific sites giving it the mark of self. Restriction (Res)
component, which by its nuclease activity, cleaves the foreign DNA lacking host specific
methylation mark. Some RM require Nucleoside triphosphate (NTP) to carry out nucleolytic
cleave and are called NTP-dependent RM enzymes. Based on the subunit assembly, mode of
cleavage and characteristics of NTP hydrolysis, they are further classified into three type i.e.,
Type I, Type III and Type IV. Type III RM enzymes are heterooligomers composed of two
subunits Mod and Res. Mod catalyzes the site specific methylation of host DNA, while Res on
forming complex with Mod catalyzes the nucleolytic cleavage of foreign DNA lacking host
DNA methylation pattern. For efficient cleavage of foreign DNA to occur type iii RM enzymes
require two inversely oriented recognition sites, which can be thousands of base pair apart.
Nucleolytic cleavage always happens 25-27 bp downstream of any one target site. One of the
models explaining nucleolytic cleavage requires the bidirectional diffusion of the enzyme along
the DNA. According to this model upon binding of the Type III RM to its recognition site ATP
hydrolysis occur, the ATP hydrolysis cause large conformation change in the enzyme by virtue
of which the enzyme now enters diffusive state. When a diffusive enzyme collides with the other
site bound enzyme, DNA cleavage is triggered. In order to understand the mechanism of action
of these enzyme, we have initiated structural studies of a newly identified Type III RM enzyme
from Mycoplasma bovis. I will present the preliminary biochemical characterization of the
enzymatic activities, including DNA-binding properties, nucleolytic and ATPase activities of the
enzyme.
X-ray crystal structure of a thiolase from Escherichia coli at 1.8 Å resolution
1
1
2
3
1
M. Ithayaraja , N. Janardan , Rik K. Wierenga H.S. Savithri , and M.R.N. Murthy
1
2
Molecular Biophysics Unit, Indian Institute of Science
Faculty of Biochemistry and Molecular Medicine, University of Oulu, Finland
3
Biochemistry Department, Indian Institute of Science, Bangalore
E:mail: ithayaraja@gmail.com and mrn@mbu.iisc.ernet.in
Thiolases catalyze the Claisen condensation of two acetyl CoA molecules to acetoacetylCoA as well as its reverse degradative reaction. Four genes coding for thiolases or thiolase-like
proteins are found in the Escherichia coli genome. In this communication, we report the
successful cloning, purification, crystallization and structure determination of a homotetrameric
E. coli thiolase at 1.8 Å resolution. The structure of E. coli thiolase co-crystallized with acetylCoA determined at 1.9 Å resolution is also reported. As observed in other tetrameric thiolases,
the present E. coli thiolase is a dimer of two tight dimers and probably functions as a
biodegradative enzyme. Comparison of the structure and biochemical properties of the E. coli
enzyme with those of other well studied thiolases reveals certain novel features of this enzyme
such as modification of a lysine in the dimeric interface, possible oxidation of catalytic Cys88 in
the structure of the enzyme obtained in the presence of CoA and active site hydration. The
tetrameric enzyme also displays an interesting departure from exact 222 symmetry, which is
probably related to the deformation characteristics of the tetramerization domain that stabilizes
the oligomeric structure of the protein. The current study allows identification of substrate
binding amino acid residues and water networks at the active site and provides the structural
framework required for understanding the biochemical properties as well as physiological
function of this E. coli thiolase.
B 21
+
Identification of conformational chaperones for the Na /Galactose
transporter
Jay Prakash Kumar
1, 3
1
4
1
, Vinod Nayak , Balaji M. Rao , S. Ramaswamy and Jeff Abramson
1, 2
1
4
Institute for Stem Cell Biology and Regenerative Medicine, NCBS-TIFR, Bangalore560065, Karnataka, India
2
Department of Physiology, David Geffen School of Medicine, University of California, Los
Angeles, CA, USA.
3
School of Chemical & Biotechnology, SASTRA University, Thanjavur -613401, Tamilnadu,
India.
Department of Chemical and Biomolecular Engineering, North Carolina State University, North
Carolina, USA.
E-mail: kumarjp@instem.res.in,ramas@instem.res.in,jabramson@mednet.ucla.edu
+
+
Na /galactose transporters (SGLTs) are integral membrane proteins, which co-transport Na
with sugars from the periplasmic space into the cytoplasm. According to the alternating access
model for secondary active transporters, these proteins alternate between outward and inwardfacing conformations during the transport cycle. The currently available structures from a
bacterial homolog of SGLT from Vibrio parahaemolyticus, (vSGLT) are in the substrate-bound
inward-occluded and the substrate-free inward-open conformations. Despite much effort,
structures of the outward conformations remain elusive.
Isolation of distinct conformations of transporter is a major obstacle for X-ray crystallography
due to their conformational heterogeneity. Crystallization chaperones based on various protein
scaffolds have emerged as a promising tool to increase the crystallization probability of a
selected target protein. Sso7d is a highly stable binding protein derived from the
hyperthermophilic archaeon Sulfolobus solfataricus. It has a versatile scaffold for generating
binding protein for a wide spectrum of targets. Sso7d-derived proteins are far easier to produce
in bacteria and due to their small size, they are capable of targeting areas that are not accessible
to standards antibodies.
We screened an Sso7d-based yeast display library using flow cytometry to find conformational
chaperones for the SGLT transporter. We have isolated and purified clones that bind the SGLT
protein. The micro-molar interaction between Sso7d-binder and SGLT was determined by
microscale thermophoresis and isothermal titration calorimetry. We are currently attempting cocrystallization of SGLT with conformatnal chaperones. We anticipate that SGLT will be
crystallized in the outward open conformation which will provide mechanistic insights of the
transport cycle.
DYNAMICS AT THE STALLING FORK BARRIERS
Jessy Mariam, Anwesha Biswas, G Krishnamoorthy, Ruchi Anand
Department of Chemistry, Indian Institute of Technology, Bombay, Mumbai-400076
Email: jessy_mary31@iitb.ac.in, ruchi@chem.iitb.ac.in
For efficient synthesis of the ribosome, eukaryotic organisms contain several copies (~150200) of ribosomal DNA (rDNA). To maintain stringent control and to avoid head on collision
of the replication and transcription machinery, in yeast Fob1 protein is present. Fob1 has been
shown to bind specific replication fork barrier (RFB) sequences present in the non-transcribed
region between the 35S and the 5S rDNA. Fob1 is also implicated in cellular aging by stalling
forks, which can promote recombination leading to excision of these repeats. Due to the lack
of structural data the mechanism of polar arrest as well as the mode by which it promotes
recombination is not well understood. Here, we employ fluorescence lifetime and anisotropy
studies as a technique to complement structural methods and to understand the underlying
molecular mechanism that governs Fob1 function. A series of prosthetic RFB containing
oppositely directed forks as well as dead end holiday junction sequences, were designed
incorporating site specifically labelled 2-aminopurine or 6-methylisoxanthopterin at various
positions. The analysis revealed that Fob1 clamps to the double stranded region, few
sequences ahead of the progressing fork and preferentially blocks the non-permissive directed
forks. Moreover, it binds to multiple RFB sequences with varying affinity and strongly
dampens the dynamics of RFB1 in comparison to RFB3 sequence. Comparative studies with
HJ and ds RFB sequences showed that Fob1 can discriminate between the two structures by
altering its oligomeric state. While it interacts with double stranded sequence as a tetramer, it
forms a dimeric complex with HJ.
Crystal Structure of Glutaminyl-tRNA Synthetase (TtQRS) from
Thermus thermophilus HB8 and its complexes with ATP and AMP
a
b
a
b
B 23
b
Nachiappan. M , Vitul Jain , Sureka. K , Yogavel. M , Amit Sharma and
a
Jeyakanthan. J *
Structural Biology and Biocomputing Lab, Department of Bioinformatics,
Alagappa University, Karaikudi - 630 004, Tamil Nadu, India.
b
Structural and Computational Biology, International Centre for Genetic Engineering
and Biotechnology, Aruna Asaf Ali Margh, New Delhi – 110 067, India.
* Email: jjkanthan@gmail.com
a
Aminoacyl-­‐tRNA synthetase is an enzyme that catalyses the esterification of a specific amino acid to one of its compatible cognate tRNAs to form an aminoacyl tRNA, prior to translation in the cytosol. Each synthetases has a specific molecular mechanism to distinguish the right pair of substrates from the various amino acids and isologous tRNA molecules. The gene for Glutaminyl-­‐tRNA synthetase (TtQRS), a Class I enzyme from the extreme thermophile Thermus thermophilus HB8 was cloned. As the enzymes from hyperthermophile is stable at very high temperature, it can be used as a model organism to study the general characteristics of enzymes. Sequence analysis revealed an open reading frame that codes for a protein of 548 amino acid residues (64 kDa). Codon usage in the Glutaminyl-­‐tRNA synthetase (TtQRS) is similar to the characteristic usage in the genes for proteins from bacteria of the genus thermus, and the G+C content is as 66%. The amino acid sequence of TtQRS shows 25-­‐50% similarity with other bacterial Glutaminyl-­‐tRNA synthetase sequences. By expression of the TtQRS gene in Escherichia coli, the thermostable enzyme was overproduced and purified to homogeneity by heat treatment and affinity chromatography. The protein is remarkably thermostable and retains 50% of its initial tRNA aminoacylation activity after 30 minutes of incubation at 70°C. Aminoacylation and thermal shift assay studies have proved that L-­‐Gln and ATP mediates the formation of Gln-AMP product which shows higher
affinity and strong binding with TtQRS. The crystals of the enzyme were obtained from O.2 M Ammonium sulfate, 0.1 M Sodium cacodylate trihydrate pH 6.5 and 30 % PEG 8000 solutions by vapour diffusion techniques. X-­‐ray diffraction data were collected at a resolution of 2.6 Å and the complexes with ATP and AMP diffracted at a resolution of 2.4 Å. The structural details will be discussed.
Structural and Biochemical studies of a small Ras like GTPase MglA from
Myxococcus xanthus to understand the spatial positioning of motility complexes
1
1
2
Jyoti Baranwal , Priyanka Rajendra Gade , Smarth Lakhanpal and Gayathri Pananghat
1,2
Biology Division, Indian Institute of Science Education and Research, Pune, 411008,
India E-mail: jyoti.baranwal@students.iiserpune.ac.in
Movement in bacteria is achieved by means of appendages such as flagella and pili, or without
appendages. Gliding motility is a type of motility observed in bacteria where no visible appendages have
been observed. Myxococcus xanthus is a gram-negative, rod-shaped bacterium which uses both types of
motility i.e. type IV pili-based and adventurous gliding motilities for their movement. Interestingly, both
types of motility are regulated by a small Ras-like GTPase, MglA and a GTPase activating protein
(GAP), MglB. This motility is analogous to eukaryotic cell migration where focal adhesion complexes,
cytoskeletal proteins and small Ras-like GTPases are involved. Focal adhesion-like complexes, MreB (an
actin-like protein) and GTPases play an important role in M. xanthus adventurous gliding motility. MglA
and MglB are involved in deciding polarity and direction of movement. They oscillate from one pole to
another during reversal of direction accompanying movement of the bacterium. Structural and
biochemical studies are required to understand the molecular mechanism of how these proteins carry out
the oscillation and effect motility. To accomplish this, MglA and MglB from M. xanthus have been
expressed and purified in Escherichia coli. Biochemical studies have shown that both proteins interact
and MglB activates GTP hydrolysis. Preliminary crystallographic studies have been carried out for MglA,
MglB and complex of MglAB in the presence of nucleotide. Further structural analysis and supporting
experiments are in progress.
Structural and functional studies on Vc-YaeO a Rho inhibitor
B 25
Kamalendu Pal, Ramanuj Banerjee & Udayaditya Sen*
Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata-700064
Email: kamalendu.pal@saha.ac.in ; Udayaditya.sen@saha.ac.in
Efficient and accurate transcription termination is required for the correct regulation of bacterial
gene expression. Transcription termination is the process by which a nascent RNA is released
from its complex with RNA polymerase and DNA template. In bacteria, two main mechanisms
of transcription termination have been described. These mechanisms, commonly referred to as
Rho-independent and Rho-dependent termination (1). Rho-independent termination occurs at a
GC rich self-complementarily region that forms a stem-loop structure believed to cause the RNA
polymerase to pause, allowing the release of the RNA (2). Rho-dependent termination, on the
other hand, requires the presence of a hexameric helicase, Rho (3). Rho is an essential
transcription factor that binds nucleic acids at specific termination sites (rut) and translocates
along the RNA until it reaches the transcription complex (4, 5). There, it facilitates termination
by unwinding RNA/DNA heteroduplexes upon hydrolysis of ATP (6).
Currently, only two Rho-specific inhibitors of transcription termination have been reported. The
first to be described is a 21.3-kDa protein encoded by gene psu of the satellite bacteriophage P4
(7). The second inhibitor is the product of gene yaeO from Escherichia coli, which has been
shown to reduce termination in the Rho-dependent bacteriophage terminator tL1 and upstream
the autogenously regulated gene rho (8).
We have solved the crystal structure of the YaeO from Vibrio cholerae 0395 (Vc-YaeO) at 1.8Å
atomic resolution and quantified the interaction with N-terminal part of Rho. It also shows
interaction with oligonucleotides and dNTPs which is a new finding.
References:
1. Richardson J. P., and Greenblatt J. (1996) in Escherichia coli and Salmonella typhimurium:
Cellular and Molecular Biology (Neidhardt, F. C., ed) pp. 822. American Society for
Microbiology Press, Washington, D.C.
2. Brendel V., Hamm G. H., and Trifonov E. N. (1986) J. Biomol. Struct. Dyn. 3, 705.
3. Opperman T., and Richardson J. P. (1994) J. Bacteriol. 176, 5033.
4. Platt T. (1994) Mol. Microbiol. 11, 983.
5. Richardson, J. P. (1996) J. Biol. Chem. 271, 1251.
6. Brennan C. A., Dombroski A. J., and Platt T. (1987) Cell 48, 945.
7. Linderoth N. A., and Calendar R. L. (1991) J. Bacteriol. 173, 6722.
8. Pichoff S., Alibaud L., Gue´dant, A., Castanie´ M. P., and Bouche´ J. P. (1998) Mol.
Microbiol. 29, 859.
A unique function of DTD to correct mischarging of glycine by alanyltRNA synthetase
Komal Ishwar Pawar, Katta Suma, Satya Brata Routh, Ayshwarya Seenivasan, Shobha P.
Kruparani and Rajan Sankaranarayanan*
CSIR - Centre for Cellular and Molecular Biology,Hyderabad 500007. suma@ccmb.res.in, sankar@ccmb.res.in
During translation of the genetic code, misacylated tRNA species generated by nearly half of the
twenty aminoacyl-tRNA synthetases (aaRSs) are removed by dedicated editing modules of
aaRSs present in either cis or trans form. For example, the cis-editing domain of alanyltRNAsynthetase (AlaRS) removes non-cognate serine or glycine mischarged on tRNA
Ala
.
Glycine misacylation is significant because AlaRS activates glycine two times more than serine.
Here, we show that D-aminoacyl-tRNA deacylase (DTD), apart from decoupling D-amino acids
mischarged on tRNAs, corrects glycine mischarged on tRNA
Ala
. Our previous crystallographic
and biochemical studies established the crucial role of an invariant Gly-cisPro motif for DTD’s
enantioselectivity (1). Recently, we have solved the crystal structure of DTD from Plasmodium
falciparum with Gly3AA at 2.1 Å which reveals that DTD's chiral proofreading site is
completely porous to achiral glycine. Hence, L-chiral rejection is the only mechanistic design
principle on which DTD functions (2). Further, we found that DTD is more efficient in
deacylating Gly-tRNA
Ala
than AlaRS and its trans-editing domains, especially in the presence of
elongation factor Tu (EF-Tu). Moreover, DTD’s presence, unlike that of AlaRS and its transediting domains, does not allow the accumulation of Gly-tRNA
Ala
during aminoacylation by
AlaRS. We are currently trying to elucidate the phenomenon in vivo using E. coli as a model
system by expressing AlaRS and DTD in alaS and dtd knockout strains of E. coli. This will help
to ascertain the hitherto unknown role of DTD as a trans-editing factor of AlaRS.
References:
1. Ahmad S et al., Mechanism of chiral proofreading during translation of the genetic code. eLife
(2013) 2:01519.
Gly
2. Routh SB et al., Elongation factor Tu prevents misediting of Gly-tRNA
caused by the
design behind the chiral proofreading site of D-aminoacyl-tRNA deacylase. PLOS Biology
(2016)(In Press).
Analysis of interaction network of channel nucleoporins with
adapter ring of vertebrate nuclear pore complex
Kriti Chopra, Pankaj Kumar Madheshiya, Neha Mishra, Parshuram Sonawane
and Radha Chauhan National
Centre for Cell Science, Pune
Email: kriti@nccs.res.in, pankajabtc@gmail.com, radha.chauhan@nccs.res.in
Nuclear pore complexes (NPCs) are the largest macromolecular assemblies embedded
in the nuclear envelope and form the selectivity barrier for nucleo-cytoplasmic
transport. They are composed of ~30 proteins called nucleoporins (Nups). NPCs can
be subdivided into various region comprising of central channel (composed of Nup62,
Nup58, Nup54) that imparts permeability barrier and adapter ring (composed of
Nup93, Nup205, Nup188, Nup155, Nup35) which holds up the central channel at the
core of NPCs with extensive interaction with various nups of adapter ring and
membrane proteins. Despite of advances in this area of research, interactions among
these vertebrate proteins remain poorly understood and limits generating accurate
architecture of NPCs. Using various biochemical and structural methods in
combination with computational biology, we aim to identify interaction network of
the central channel nucleoporins with adapter ring. We predicted the structural
domains in Nup62, Nup58 and Nup54 as well as Nup93 (of adapter ring) and
generated various constructs harboring those domains. After overexpression and
purification using bacterial system, we observed that trimeric complex consisting of
most of the structured region of Nup62-Nup58-Nup54 is able to interact with the
various regions of Nup93 protein in vitro. Immunoprecipitation experiments in HEK293 cells with corresponding deletion constructs of Nup93 suggest its N terminal
region is essential for the central channel interactions. We used structure based
multiple sequence alignment using PROMALS3D to identify evolutionary
conservation of these regions across the vertebrates. Interestingly, we observed that
these structured domains central channel nups needed for Nup93 interactions are
highly conserved across in all vertebrates. Crystallization trials for these complexes
are in progress and we aim to get the molecular level interactions in these regions of
vertebrate NPCs. Using the correlated mutation analysis and machine learning
approaches we aim at identifying the interacting regions of the all pairs of proteins in
the eukaryotic NPC.
B 27
Structural studies on OXA-58 of Acinetobacter Baumannii revealing the active site
structural elements essential for carbapenem hydrolysis by this enzyme
1
1
2
2,3
Madhusudhanarao Katiki , Shivendra Pratap , Preet Gill , Dasantila Golemi-Kotra
1
and Pravindra Kumar
1
Department of Biotechnology, Indian Institute of Technology Roorkee,
2
Roorkee, Uttarakhand-247667, India.
3
Departments of Biology and Chemistry, York University, 4700 Keele Street, Toronto,
ON M3J1P3, Canada
The crystal structure of the OXA-58 CHDL of Acinetobacter baumannii, a multi-drug resistant
gram-negative bacterium that is not responsive to treatment with carbapenems which are the
usual antibiotics of choice for this bacterium, is determined to elucidate the structural elements
required for the catalysis of carbapenems by these enzymes. The crystal structure is obtained in
its native state and acylated state of its active-site serine by a 6α-hydroxymethyl penicillin
derivative which is a structural mimetic of a carbapenem. In addition, functional characterization
of several point mutation variants of the active site of OXA-58, as identified by the crystal
structure analysis, was done using enzyme kinetics. The structural studies revealed the formation
and presence of a hydrophobic bridge over the active site and kinetics studies confirmed the
mechanistic relevance of this structural element. This structural feature is suggested to stabilize
the hydrolysis-productive acyl-enzyme species, which is the intermediate formed during the
catalysis of carbapenem substrates of this enzyme. Furthermore, a strong evidence is provided
that the hydroxyalkyl group of carbapenems samples different orientations in the active sites of
CHDLs, and the optimum orientation for catalysis depends on the topology of the active site
allowing proper closure of the active site. These combined studies propose that CHDLs use the
plasticity of the active site to drive the mechanism of carbapenem hydrolysis toward efficiency.
Structural and functional characterization of Type ISP RestrictionModification Enzymes
1
1
Mahesh Kumar Chand , Vanessa Carle and Saikrishnan Kayarat
1
B 29
1
Biology Department, Indian Institute of Science Education and Research, Pune 411008, India.
E-mail: mahesh.chand@students.iiserpune.ac.in
Bacterial survival depends on the defense mechanisms that protect them against the invading
bacteriophages. Restriction-modification (R-M) systems are one of such defense mechanisms that bacteria
employ to restrict the attack of foreign DNA. It cleaves foreign DNA by its restriction subunit whereas
protects host DNA by modification subunit. R-M enzymes can be divided into four types based on the
nature of substrate and co-factor requirements i.e. Type I, Type II, Type III and Type IV. NTP dependent
R-M enzymes (Type I and Type III) were discovered in 1960s; because of its complex nature we are still
unable to understand its exact mechanism of action. Recently a new subclass of Type I R-M enzymes has
been identified known as Type ISP (Single Polypeptide) R-M enzymes, containing functional domains
(target recognition, methyltransferase, ATPase and nuclease domain) in a single polypeptide chain. Using
Type ISP R-M enzyme (LlaBIII) we have been carrying out structural studies to gain mechanistic insights
into functioning of these enzymes. LlaBIII is 180kDa protein with N terminal Mrr nuclease domain, SF2
helicase like domain, N6-adenine methyltransferase and C terminal TRD (target recognition domain)
(1,2). It recognizes 6bp target sequence 5’-TnAGCC-3’ and translocates on dsDNA by utilizing energy
from ATP hydrolysis. When two translocating enzymes collide in head-to-head orientation, each of them
nicks one strand of DNA leading to a dsDNA break (2). Crystal structure of LlaBIII bound to 28bp
dsDNA shows interaction of helicase domain with DNA molecule through a unique loop (3). Mutagenic
study of loop residues shows that the loop plays a crucial role in the enzymatic activity of LlaBIII. The
results from these studies will be discussed.
References:
1. Smith, R.M., Josephsen, J., and Szczelkun, M.D., “An Mrr-family nuclease motif in the single
polypeptide restriction-modification enzyme LlaGI”, Nucleic acids research, 37,
(2009),7231-7238.
2. Sisakova, E., van Aelst, K., Diffin, F.M., and Szczelkun, M.D., “The Type ISP RestrictionModification enzymes LlaBIII and LlaGI use a translocation-collision mechanism to cleave nonspecific DNA distant from their recognition sites”, Nucleic acids research, 41, (2013), 10711080.
3. Chand, M.K., Nirwan, N., Diffin, F.M., van Aelst, K., Kulkarni, M., Pernstich, C., Szczelkun,
M.D., and Saikrishnan, K., “Translocation-coupled DNA cleavage by the Type ISP restrictionmodification enzymes”, Nature chemical biology, 11, (2015), 870-877.
Structural and functional studies of Eal, a c-di-GMP phosphodiesterase, from
Vibrio cholerae 0395
Malti Yadav & Udayaditya Sen*
Crystallography and Molecular Biology division, Saha Institute of Nuclear Physics, 1/AF Bidhan
Nagar, Kolkata- 700064 , India
Email: malti.yadav@saha.ac.in,udayaditya.sen@saha.ac.in
Eal domain proteins are the major phosphodiesterases for maintaining the cellular concentration
of second-messenger cyclic di-GMP in bacteria. c-di-GMP is a global second messenger which
controls a range of different cellular functions in bacteria at transcriptional, translational, and
post-translational level. c-di-GMP binds to various receptor proteins or riboswitches and
regulates biofilm formation, motility, virulence, antibiotic production, progression through the
cell cycle and other cellular functions in a wide variety of organisms. The intracellular level of cdi-GMP is controlled by the opposing action of two different groups of enzymes. The
diguanylate cyclases containing the GGDEF domain produce c-di-GMP from two molecules of
GTP, whereas specific phosphodiesterases (PDEs) associated with EAL or HD-GYP domains
hydrolyze the cyclic molecule c-di-GMP to linear 5-pGpG, which is subsequently hydrolyzed
into two GMP molecules. Here we discuss the biochemical and structural aspects of EAL
domain
protein
from
Vibrio
cholera
0395.
EAL
domain
containing
c-di-GMP
phosphodiesterases (PDEs) protein (30kDa) from Vibrio cholerae 0395 was purified by Ni-NTA
affinity chromatography. High resolution crystal structures of free EAL domain (2.4Å) and EAL
domain in complexed with its substrate and metal ions involved in catalysis or in enzyme
inhibition at different pHs (1.95 Å, 2.3 Å) provide a detailed understanding of the mechanism of
the EAL-domain c-di-GMP phosphodiesterases. An understanding of PDE activation is
important, as biofilm dispersal via c-di-GMP hydrolysis has therapeutic effects on chronic
infections.
Plant GET3- Deciphering the modus operandi
1, §
B 31
1, ♯
Manu. M. S
and Sureshkumar Ramasamy
1
Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune§
411008 Presenting author’s mail id: ms.manu@ncl.res.in
♯
Corresponding author’s mail id: s.ramasamy@ncl.res.in
Tail anchored (TA) proteins are membrane proteins with single pass transmembrane domain
at C-terminal region and a functional N- terminal cytosolic domain. Since targeting signal for
these proteins is located in the C-terminal transmembrane region, signal recognition particle
(SRP)-mediated protein targeting mechanism would fail in this scenario. These TA proteins
are targeted by the specialized machinery called Guided Entry of Tail Anchored protein
(GET) pathway. The combined and efficient functioning of GET pathway components
(GET1, GET2, GET3, GET4 and GET5) and its accessory proteins ensure the precise
delivery of TA proteins. Knocking out of GET3, the ATPase, causes temperature sensitive
growth in yeast, embryological lethality in mouse etc. The mechanistic basis of this pathway
is investigated considerably in Saccharomyces spp. Unlike yeast, presence of several
isoforms of GET3 and missing of several pathway components makes the pathway complex
in plant systems. To understand this mechanism, we selected Arabidopsis thaliana as model
organism. Out of the four isoforms, AtGet3L and AtGet3S are being characterized in our
study. The AtGet3∆L (C-terminal truncated) and AtGet3S are successfully purified and
crystallized. Crystals of AtGet3∆L diffracted up to 1.9Å with unit cell parameters as a= 59.2,
b= 66.9, c= 99, α= 90, β= 97.7 and γ= 90. The refinement of AtGet3∆L and crystallization
trials of AtGet3S is in progress. By structural and functional characterization of these
proteins, the modus operandi of GET pathway in plant system could be revealed.
Towards stability optimization of a recombinant leptospirosis vaccine scaffold
from comparative biophysical analysis of homologous antigenic domains
1
2
2
Mohd Akif , Christopher P. Ptak , Ching-Lin Hsieh and Yung-Fu Chang
1
2
Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad
1
500046, India
2
Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New
York 14853
masl@uohyd.ernet.in
Several surface proteins express during leptospiral infection and among them is a family of
Leptospira immunoglobulin-like (Lig) proteins, which have been identified as vaccine
candidates and promising markers for typing pathogenic isolates. The Lig family of proteins
includes LigA, LigB and LigC, possesses large extracellular multiple immunoglobulin-like
repeat domains (13 in LigA, 12 in LigB and LigC). Production of multi-domains recombinant
proteins and their optimal potency as vaccine, storage, handling and heat stability are matter of
great concern. We demonstrate here thermo-stability of each domain of LigA and LigB proteins.
Unfolding of the domains was monitored by measuring tryptophan fluorescence showed that the
terminal domain (domain 13) of LigA (LigA13) is the most stable domains among all and its
melting temperature (Tm) was observed as high as 65˚C. Interestingly, the domain 10 of LigB
(LigB10) displayed almost similar Tm as LigA13. Further, unfolding of the destabilizing mutant
of stable domain and chimeric domains generated by swapping N- and C-terminal regions of the
highest and lowest stable domains, provides an insight into the determinants responsible for
stability. The understanding of stability of Lig protein domains would provide information about
an optimal vaccine scaffold. Moreover, improvement in the stability of individual domain of Lig
proteins would limit unfolding dynamics, a factor that can disrupt crystal packing.
B 33
Heterogeneous behavior of metalloproteins towards metal ion binding
and selectivity: insights from molecular dynamics studies
*
Monika Chandravanshi, Shankar Prasad Kanaujia
Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam
- 781039, India
e-mail: chandravanshi.monika@gmail.com
* Corresponding author, e-mail: spkanaujia@iitg.ernet.in
Metalloproteins require metal ions as cofactors for their catalytic activities and structural
complexities. Many of them bind only to a specific metal, while others bind to multiple
(different) metal ions. In this study, we used molecular dynamics (MD) simulations to
investigate whether a cognate metal (bound to the structure) can be replaced with other similar
metal ions. We have chosen seven different proteins bound with cognate metal ion
2+
2+
2+
(phospholipase A2 (Ca ), sucrose phosphatase (Mg ), pyrazinamidase (Zn ), cysteine
2+
2+
2+
dioxygenase (CDO) (Fe ), plastocyanin (Cu ), monoclonal anti-CD4 antibody Q425 (Ba ),
2+
and synaptotagmin 1 C2B domain (Sr ). Although, the crystal structure of proteins bound with
cognate metals are available, the mechanistic behavior of pocket during metal binding and
selection is not yet available. Thus we used molecular dynamic (MD) simulation to get requisite
information upon metal binding. In this study, 49 MD simulations each of 50 ns were performed
to analyze each trajectory independently. The simulation results displays that cognate metal ion
can be replaced by similar metal ions. However, some proteins are stricted to their cognate metal
2+
2+
ions. Interestingly, two proteins cysteine dioxygenase (Fe ) and plastocyanin (Cu ) do not
exhibit binding affinity to any metal ion. Moreover, the study reveals that the active-site
topology in some apo form of protein remains rigid, whereas some require cognate metal ions for
their active-site stability. Thus it will be interesting to verify the results experimentally, which
will further help in designing novel active sites for proteins to sequester toxic metal ions.
Cloning, expression, purification and preliminary crystallographic studies of a
ribokinase super-family Pyridoxal kinase from Lactobacillus plantarum WCFS1
1
2
3
2
Mukesh Saran , Desigan Kumaran , Stephen K. Burley , Subramanyam Swaminathan , Ashima
1*
Bagaria .
1
2
Department of Physics, Manipal University Jaipur-303007, INDIA
Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
3
SGX Pharmaceuticals, Inc., San Diego, California, 92121, USA
*
Correspondence: ashima.bagaria@jaipur.manipal.edu
Pyridoxal kinase belongs to ribokinase super-family and plays a key role in the synthesis of the
active co-enzyme pyridoxal-5’-phosphate (PLP), by catalyzing the phosphorylation of the
precursor vitamin B6 in the presence of Zn
2+
and ATP. Herein, we report the cloning,
preliminary crystallizationa and data collection of a pyridoxal kinase, from Lactobacillus
plantarum WCFS1. The target gene for the full-length putative peptidase from L. plantarum was
cloned into E. coli in the pSGX (3) vector. Protein expression/purification utilized previously
published protocols, which are described in detail in PepcDB (pepcdb.pdb.org). Mass
spectrometry analyses documented that none of the purified proteins had undergone degradation
or post-translational modification (data not shown). The most suitable crystal form that has been
obtained belongs to the orthorhombic system in space group C2221. The protein was labeled
with selenium and the single wavelength anomalous diffraction (SAD) data from native crystals
were obtained at atomic resolution (1.3Å) using NSLS Beamline X29 (National Synchrotron
Light Source, Brookhaven National Laboratory).
Cross talk between the two functional domains in Formylglycinamide
- ribonucleotide amidotransferase
Nandini, Ajay S. Tanwar, Ruchi Anand
Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076,
India
Email address: Presenting author: contact.nansha@gmail.com; 134033018@iitb.ac.in
Supervisor: ruchi@chem.iitb.ac.in ; ruchi1975@gmail.com
Pathway providing purine nucleotides for the synthesis of DNA and RNA in various
organisms, is the most important target for the development of anticancer,
1
antimicrobial and antiviral drugs . FGAR-AT from Salmonella typhimurium encoded
by PurL gene (StPurL) is a 143 kDa enzyme which catalyzes the fifth step of purine
biosynthesis, have a single polypeptide chain (composed of glutaminase, FGAM
synthetase, N- terminal and a linker domain) and is characterized by a cys-his-glu
2
catalytic triad present in glutaminase domain . In this domain, glutamine to glutamate
conversion occurs and the released ammonia travels through an intramolecular
pathway to the other active site in FGAM synthetase domain thereby converting
2
FGAR to FGAM . Though its crystal structure and the pathway releasing ammonia
3
from one active site to another , has been determined, the mechanism of cross-talk
between the two functional domains remains elusive. Here, we report mutational
studies performed at the regions proximal to the glutaminase active site, where
ammonia is produced and at the end of the channel, where it is consumed. Results
showed that these regions are highly sensitive to perturbations. Surprisingly, certain
mutations in the mouth of channel increased the overall catalysis. However, any
perturbations at the end of the channel showed drastic loss in FGAM production. In
addition, there is a disordered catalytic loop in the FGAM synthetase domain which is
4
hypothesized to interact with catalytic N-terminal domain . Our studies showed that
the shortening of this dynamic catalytic loop, shielding FGAR/ATP, has a profound
effect on the distal glutaminase activity. Therefore, it appears that a relay mechanism
is triggered by the conformational changes in the FGAR catalytic loop that transmits
signal for the progress of the reaction from one active site to another.
References
1. Zhang, Y.et.al. (2008) Cellular and molecular life sciences : CMLS 65, 3699-3724.
2. Anand, R.et.al. (2004) Biochemistry 43, 10328-10342.
3. Tanwar, A. S.et.al. (2015) ACS Chemical Biology 10, 698-704.
4. Tanwar, A. S.et.al. (2012) Acta Crystallographica Section D 68, 627-636.
B 35
Characterization of Cra from Enterohemorrhagic E. coli to elucidate its structureactivity relationship
1
2
1
Neetu , Dinesh Yernool , Pravindra Kumar
1
2
Department of Biotechnology, Indian Institute of Technology Roorkee, India; Department of
Biological Sciences, Purdue University, USA
Enterohemorrhagic E. coli (EHEC) is a human pathogen responsible for bloody diarrhea and
hemolytic uremic syndrome (HUS). Upon treatment with conventional antimicrobial drugs, the
organism releases bacterial toxin by SOS response. In EHEC, most of the virulent genes are
grouped into pathogenicity island called the Locus of enterocytes effacement (LEE). LEE operon
products facilitate bacterial attachment and effacing lesion in human intestine and subsequent
colonization. Catabolite repressor/activator protein (Cra), a transcriptional regulatory protein,
helps in microbial pathogenesis and survival. Cra in coordination with KdpE (transcription
factor) plays a crucial role in the regulation of LEE operon. Cra is also involved in regulation of
carbon metabolism. Double-knockout of cra and kdpe are not able to attach and colonize in the
intestine thus proving to be a potential drug target. Structure of Cra complexed with DNA or
KdpE or all its effector molecules will help in elucidating the regulatory mechanism. Structural
analysis of active site of Cra will help in designing possible inhibitor molecules. Herein, we are
reporting the expression, purification and crystallization of Cra protein.
Reactive centre loop tripeptides of Pin-II serine protease inhibitors
as insect control agents against Helicoverpa armigera
B 37
Nidhi Saikhedkar, Ashwini Bhoite, Kiran Kulkarni and Ashok P. Giri
Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India-411008
Potato type II protease inhibitors (PIs) are involved in plant defence by inhibiting serine
proteases present in the midgut of insects. Functional units of PIs (Inhibitory Repeat
Domains; IRDs) mediate the interaction with target proteases by forming multiple noncovalent interactions through their reactive centre loop (RCL). The RCL is composed of
variable tripeptide sequences, and is the hotspot of IRD-protease interaction. TO investigate
the role of these RCL tripeptides in isolation of the 55-aa IRD scaffold, six peptides were
synthesized and evaluated for inhibitory function in vitro and in vivo against insect pest,
Helicoverpa armigera. PRN, PRY and TRE adversely affected insect growth and
development. The structures of peptides in complex with serine protease (trypsin) gives
further insights into the molecular mechanism of inhibition, and suggests that the tripeptides
might be the minimum requirement for inhibitory activity of PIs. The specific inhibitory
activity at alkaline midgut pH, retention and stability in insect gut makes them remarkable
pest control molecules.
Thioredoxin reductase-thioredoxin (TR-Trx) from Mycobacterium leprae:
Structural and Functional studies
Nitin Bayal
National Centre for Cell Science, SP Pune University campus, Ganeshkhind, Pune MH
411007
Email: nitinb@nccs.res.in
Leprosy is one of the most detrimental human diseases caused by Mycobacterium leprae,
which infects macrophages and Schwann cells, thereby causing inflammation in peripheral
nerves, eyes and upper respiratory tract followed by irreversible loss of sensation, poor
eyesight and ultimately loss of body parts. During infection, host immune response activates
the macrophages, which engulf the bacteria, which in turn generates reactive free radicals.
Upon phagocytosis, M. leprae uses its thioredoxin system in defense against reactive
oxygen/nitrogen species from the host. Therefore, it is essential to understand the mechanism
of the thioredoxin system of the bacterium to combat its pathogenicity. Although typical
components of a thioredoxin system (TR-Trx) constitute Thioredoxin reductase (TR),
thioredoxin (Trx) and NADPH, M. leprae uniquely encodes a single 49-kDa fusion protein
from a single gene that is reported with the dual activity of thioredoxin and its reductase.
This unique hybrid Trx system in M. leprae interferes with the host response against the
pathogen. Thus, this might be a potential mechanism by the pathogen in dealing with the
oxidative stress within human macrophages. Therefore, we are proposing to pursue detailed
structural and functional studies on this unique hybrid enzyme to comprehend its mechanism.
Structural Characterization of Podocin and Assessment of Nephrotic
Syndrome Associated Podocin Mutants
B 39
#
NSK Mulukala, Anil Kumar Pasupulati
Department of Biochemistry, University of Hyderabad, India
#
Email: sandeep2k9@yahoo.com, pasupulati.anilkumar@gmail.com
Podocytes are terminally differentiated epithelial cells that play critical role in renal filtration
ensuring almost protein-free ultra-filtrated urine. Adjacent podocytes form a size, shape and
charge selective adherent junction called slit-diaphragm (SD), which forms the fulcrum of
glomerular filtration. Mutations in podocyte proteins were reported to cause podocytes
effacement, disruption of glomerular filtration barrier and heavy proteinuria (Nephrotic
Syndrome). NPHS2 that encodes podocin was found to have most mutations among the genes
that are involved in the pathophysiology of NS. Podocin, an integral membrane protein
belonging to stomatin family, is expressed exclusively in podocytes and is localized to slitdiaphragm (SD). Mutations in podocin are known to be associated with steroid resistant
nephrotic syndrome (SRNS) and rapid progression to end-stage renal disease (ESRD), thus
signifying its role in maintaining the SD integrity and podocyte function. The structural
insights of podocin are not known and the precise mechanism by which podocin contributes
to the architecture of SD is yet to be elucidated. However, recently we predicted a model for
human podocin and identified N- and C-terminal intrinsically unstructured regions. Our
findings provide an understanding of how podocin interacts with other SD components. Also,
analysis of intra-protein interactions in wild type podocin and in some of its mutants that are
associated with idiopathic NS altered the innate intra-protein interactions affecting the native
structure of podocin and its ability to form critical complex with sub-podocyte proteins.
Attempts are being made to express recombinant podocin to solve its high resolution
structure.
Structure of multiple sugar binding transport ATP-binding protein from
Pyrococcus horikoshii
a
b
N. Omantheswara , K. J. Pampa and N. K. Lokanath
a
a*
b
Department of Studies in Physics, Department of Studies in Biotechnology, University of
Mysore, Manasagangotri, Mysuru 570 006, India.
Email: lokanath@physics.uni-mysore.ac.in
In the transport machinery of living cells, binding proteins play a vital role, especially in
bacteria. The crystal structure of multiple sugar binding transport ATP-binding protein from
Pyrococcus horikoshii was determined using X-ray diffraction method. The overall fold of
this protein was resolved into large domain and small domain. The large domain of the
protomer consists of two thick arms (arm I and arm II) which resemble ‘L’ shape. The ATPbinding pocket is identified, which is near to the arm I. ATP molecule is docked into the
active site, which interacts with residues of the large domain. The catalytic residues Ser41,
Gly42, Lys45, Thr47, and Asp167 are highly conserved in multiple sugar binding transport
ATP-binding protein family. The invariant residue Asp167 interacts with the γ-phosphate of
ATP molecule. From the analysis of 3-D structure, inter-subunit hydrophobic interactions
were found to be important for the protein oligomerization and thermostability.
Structural analysis of interaction network of channel nucleoporins with
adapter ring of vertebrate nuclear pore complex
B 41
Parshuram Sonawane, Pankaj Kumar Madheshiya, and Radha Chauhan*
National Centre for Cell Science, SP Pune University campus, Ganeshkhind, Pune MH 411007
Email: radha.chauhan@nccs.res.in
Nuclear pore complexes (NPCs) are the largest macromolecular assemblies embedded in the
nuclear envelope and form the selectivity barrier for nucleo-cytoplasmic transport. They are
composed of ~30 proteins called nucleoporins (Nups). NPCs can be subdivided into various
region comprising of central channel (composed of Nup62, Nup58, Nup54) that imparts
permeability barrier and adapter ring (composed of Nup93, Nup205, Nup188, Nup155, Nup35)
which holds up the central channel at the core of NPCs with extensive interaction with various
nups of adapter ring and membrane proteins. Despite of advances in this area of research,
interactions among these vertebrate proteins remain poorly understood and limits generating
accurate architecture of NPCs. Using various biochemical and structural methods in combination
with computational biology, we aim to identify interaction network of the central channel
nucleoporins with adapter ring. We predicted the structural domains in Nup62, Nup58 and
Nup54 as well as Nup93 (of adapter ring) and generated various constructs harboring those
domains. After overexpression and purification using bacterial system, we observed that trimeric
complex consisting of most of the structured region of Nup62-Nup58-Nup54 is able to interact
with the various regions of Nup93 protein in vitro. Immunoprecipitation experiments in HEK293 cells with corresponding deletion constructs of Nup93 suggest its N terminal region is
essential for the central channel interactions. We could successfully co-express and purify the
quaternary complex and crystallization trials for these complexes are in progress and we aim to
get the molecular level interactions in these regions of vertebrate NPCs.
Abstract
Lieshmania donovani is an intracellular pathogen, within macrophages, for the therapeutic
purposes we need to target curtail protein of the pathogen. The Guanine deaminase, a key
enzyme in nucleotide metabolism of salvage pathway, catalyzes the hydrolytic deamination of
guanine to xanthine, since there is no de novo pathway in Leishmania.
The structure and mechanism identification of GDA could be novel target for therapeutic
purposes. To investigate whether this enzyme can serve as a potential drug target against the
Leishmania pathogen, using computational approach. It has found that the crucial differences
between catalytic residues of Ld GDA as compared to bacterial and human GDA, indicated an
altogether new mechanism of action of the LdGDA enzyme.
For the structure determination we need to crystalized the enzyme, the enzyme cloned in pet
28a vector protein which expressed and purified using BL21 host cell initial hits were observed.
By Pankaj Singh Parihar
I.D.No-53033
Under the supervision of
Dr. J Venkatesh Pratap
Molecular & Structural Biology Division
Cdri –Lucknow india
Characterization of phosphoserine phosphatase from E. histolytica.
B 43
Poonam Kumari
School of Life Sciences, Jawaharlal Nehru University, New Delhi
Amoebiasis continues to be a major cause of morbidity and mortality in children in developing
countries, caused by the protozoan parasite Entamoeba histolytica. E. histolytica an enteric
protozoan parasite, pseudopod forming that causes hemorrhagic dysentery. In the process of
infection E. histolytica trophozoites are exposed to various reactive oxygen and nitrogen species,
where L-cysteine act as a major antioxidant stress defense molecule. L-cysteine also essential for
the structure, stability and also has a role in survival, growth, attachment and motility. Unlike
mammals, which relies on the reverse transsulfuration pathway for cysteine synthesis, in E.
histolytica cysteine synthesized de novo using serine as a precursor. Since for the cysteine
synthesis this is the only known pathway in E. histolytica, being a crucial pathway this should be
carefully regulated. In this work, we are focusing on the phosphoserine phosphatase (PSP)
enzyme, a rate limiting enzyme of serine biosynthesis pathway. PSP hydrolyzes O-phospho-Lserine through a stepwise Mg
2+
dependent phosphotransfer mechanism. To characterize it, we
have crystallize PSP and structure of this enzyme from E. histolytica is similar to dPGM which is
distinct from other known classical PSPs and further we have also confirmed phosphatase
activity.
Structural and Functional Characterization of cystine-knot AMPAR modulating
protein (CKAMP44)
Pratibha Bharti and Janesh Kumar
National centre for Cell Science, Pune University Campus, Ganeshkhind road, Pune411007 Email: pbsandilya@gmail.com
The L-α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPARs) are
glutamate-gated ion channels that play a critical role in fast excitatory synaptic transmission
and are also of vital importance in activity dependent synaptic plasticity. These receptors are
known to assemble as heterotetramers of subunits GluA1-4. Although, AMPARs can
assemble and form functional receptors in heterologous expression systems, their kinetics
(desensitization and deactivation) are not similar to in vivo receptors. Also, modelling data
showed the presence of other bound proteins. Finally all the discrepancy was accounted for
by the discovery of stargazin (TARP γ2) as AMPAR auxiliary proteins which was found to
be able to shape diverse aspects of AMPAR functions.CKAMP44 is the most recent addition
to the list of auxiliary proteins.
CKAMP44 or cystine-knot AMPAR modulating protein with predicted molecular weight of
44 KDa (CKAMP44) modulates short-term plasticity at specific synapses by affecting the
gating kinetics of AMPARs. The structural characteristics of CKAMP44 modulation of
AMPAR and their mutual interaction will be studied. Various deletion constructs have been
made in mammalian expression systems and checked for their expression at the small scale.
Further attempts to purify the protein from large scale mammalian cultures are being made
for crystallization trials. Also for functional characterization of the protein whole cell
recordings will be carried out for CKAMP44 coexpressed with wild type AMPA receptors
and various domain swapped chimeras between GluR2 and GluR6 receptors to identify the
interaction hotspots in a CKAMP44-AMPA complex.
Structural Studies on central channel of the nuclear pore complex from
various species
B 45
Pravin Dewangan, Sangeeta Niranjan, Radha Chauhan*
National Centre for Cell Science, Pune University Campus, Ganeshkhind, Pune, India
411007.
Email: pravinsd@nccs.res.in, sangeeta.19apr@gmail.com, radha.chauhan@nccs.res.in
The transport channel which facilitates the bidirectional transport of macromolecules between
the nucleoplasm and cytoplasm in eukaryotes is called as the nuclear pore complex (NPC). It
is a multiprotein assembly embedded in the nuclear envelope. Vertebrate NPCs comprises of
~30 different proteins called as Nucleoporins (Nups) which are present in multiple copies to
give vertebrate NPC a molecular mass of 125 MDa. Although the overall architecture of the
NPC is conserved from yeast to mammals there is considerable difference in the sequence
identity of Nups from yeast to mammals. NPC can be subdivided into many smaller
subcomplexes based on the interactions of Nups. We are focusing on structural elucidation of
Nup62 subcomplex which comprises the central channel and is essential for the function of
NPC. On the basis of secondary structure predictions we have cloned various regions of
channel nucleoporins (Nup62, Nup54 and Nup58). We are trying to co-purify the structural
regions of these proteins in bacterial expression system to reconstitute Nup62-subcomplex
from Rat (Rattus norvegicus), Zebrafish (Danio rerio) and Hydra magnipapillata which will
be further subjected to crystallization trials & negative staining. We intend to study the
similarities and differences in the central channel Nup62-subcomplex from these species from
an evolutionary perspective. The collective knowledge about their biophysical, biochemical
and structural characteristics would help to understand the details of the central channel of
NPC.
Crystallographic Characterization of the First LPMO Protein from Plants
Prema G. Vasudev
Molecular and Structural Biology Division, Central Institute of Medicinal and Aromatic
Plants, Lucknow-226015
Email: premavasudev@cimap.res.in
Lytic polysaccharide monooxygenases (LPMO) are recently discovered enzymes that
catalyze the oxidative degradation of recalcitrant polysaccharides. LPMOs are abundantly
present as part of the polysaccharide degrading machinery in fungi and bacteria, which derive
their energy from degrading the dead biomass. They are classified under the Auxiliary
Activity (AA) family in the CAZy database. So far, four different classes of Copperdependent LPMOs are identified based on their sequence and activity, viz, AA9, AA10,
AA11 and AA13. We have structurally characterized a protein Tma12, isolated from the
edible fern Tectaria macrodonta, which shows significant insecticidal activity against
whitefly (LC50 1.9 μg/ml). Crystal structure determination of Tma12 revealed that the protein has LPMO-­‐like fold, with a Copper (I) bound to the N-­‐terminal Histidine residue. An N-­‐glycosylation at Asn134 residue was identified from the crystal structure. The
structural characterization of Tma12 provides the first example of an LPMO from plant
systems. The talk will focus on the structural comparison of Tma12 with other LPMO
structures available and its significance in the plant system.
In silico analysis suggests that PH0702 and PH0208 encode for
B 47
methylthioribose-1-phosphate isomerase and ribose-1,5-bisphosphate isomerase,
respectively, rather than aIF2Bβ and aIF2Bδ
Prerana Gogoi and Shankar Prasad Kanaujia
*
Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati,
Guwahati–781039, Assam, India;
Email: prerana@iitg.ernet.in, spkanaujia@iitg.ernet.in, spkanaujia@gmail.com
For decades, the process of protein translation in archaea has been considered to be closer to
eukaryotes than to bacteria. However, several homologues of eukaryotic proteins involved in
translation initiation have not yet been identified; one of them being the initiation factor, eIF2B,
consisting of five subunits (α, β, γ, δ and ε). Three genes (PH0440, PH0702 and PH0208) in
Pyrococcus horikoshii, a hyperthermophillic archaeon, have been proposed to encode for the α-,
β- and δ-subunits of aIF2B, respectively. Herein, we have taken up the task of annotating
PH0702 and PH0208 using bioinformatics methods. Interestingly, our in silico analysis revealed
that PH0702 and PH0208 would function as methylthioribose-1-phosphate isomerase and ribose1,5-bisphosphate isomerase, respectively, and not as aIF2Bβ and aIF2Bδ. Furthermore, an
examination of all eIF2B-like proteins from archaea revealed that majority of these proteins are
homologues of the α-subunit of eIF2B, although they lack the residues essential for their
functional activity.
Structural Insights From a Novel Dimeric Marine Cholyolglycine hydrolase from
Shewanella loihica PV-4
Pushparani D Philem, Asmita Prabhune and Sureshkumar Ramasamy
1
1, ♯
Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune- 411008
♯
Email: s.ramasamy@ncl.res.in
Cholyolglycine hydrolase (CGH) group of enzymes belongs to the Ntn hydrolases
enzyme super family and consist of two members, namely – penicillin V acylases and bile salt
hydrolases. Penicillin V acylases (PVA, EC 3.5.1.11) are industrially important enzymes mainly
used for the production of 6-aminopenicillanic acid (6-APA), a key intermediate in manufacture
of semi synthetic β-lactam antibiotics. Bile salt hydrolases (BSH, EC 3.5.1.24) on the other hand
are the bile salt deconjugating enzyme, a major player in probiotic preparations. However despite
their industrial popularity, so far the physiological roles of the CGHs are not well elucidated. We
here report the structure of a novel marine CGH (designated as SlpV) from Shewanella loihicaPV4. In contrast to previously reported CGHs, which are tetrameric in nature, SlpV exists in
dimeric state with significant differences in the interface and loop characteristics. Apo- SlpV
structure belongs to the space group of P1211 having unit cell parameters, a=58.98 , b= 67.14 ,
c= 99.05 ; a= 90.00, b= 98.15 , g= 90.00. The 1.8 Å structure of SlpV shows the presence of
typical of Ntn hydrolases enzyme super family αββα fold. All the active site residues were
conserved both sequentially and structurally. SlpV, despite showing the highest sequence
similarity to penicillin V acylase, was found inactive on penicillin V and other substrates of
closely related Ntn hydrolases. These findings may throw some lights on the unknown activity of
these family and further structure aided mutational and computational investigation might leads
towards the in-vivo role of CGHs. Thus the oligomeric and structural variations observed in this
enzyme could become the framework for the functional diversity and enzymatic regulation in
choloylglycine hydrolases family.
B 49
Structure-Function Analysis of Xanthomonas oryzae pv. oryzae Virulence Factor
CbsA
Rajkanwar Nathawat* , Sushil Kumar, Tayi Lavanya, Ramesh V. Sonti and
Rajan Sankaranarayanan†
Centre for Cellular and Molecular Biology, Hyderabad – 500007
rajkanwar@ccmb.res.in, †sankar@ccmb.res.in
Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight disease of rice. Xoo uses
cell wall-degrading enzymes like Cellulase, Esterase, Cellobiosidase, Xylanase, etc. as virulence
factors. CbsA protein has an N-terminal catalytic domain (Glycosyl hydrolase) and a C-terminal
fibronectin type 3 domain. Under laboratory conditions, Xoo-secreted CbsA is a truncated
protein having just the catalytic domain. The crystal structure of CbsA catalytic domain was
solved at 1.86 Å resolution. The structure reveals the presence of the catalytic tunnel being
enclosed by two loops, characteristic of a typical exoglucanase. Based on the structure, key
residues for catalysis were predicted. These residues are D99, S105, D148, Y93 and E367. Wild
type CbsA shows typical exoglucanase activity but surprisingly, the D99A mutant has some
features of endoglucanase activity also. To know if the enzymatic activity is required for its
ability to induce immune responses and for its role in virulence, biochemically inactive forms of
CbsA which abrogate the enzymatic activity will be generated. The C-terminal region of CbsA
has the fibronectin type 3 (FN3) domain. A deletion mutant of FN3 domain was generated in
Xoo to assess its role in virulence and this mutant was found to be deficient in virulence. To
understand the role of this domain in modulating the biochemical activity of CbsA, structural
studies (SAXS & X-ray crystallography) will be done with the full length CbsA protein.
Structure of tryptically produced iron-free C-lobe of lactoferrin and
its functional significance in the gut
Rastogi N, Singh A, Pandey SN, Bhushan A, Kaur P, Sharma S and Singh TP
Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
Lactoferrin, an iron binding glycoprotein having molecular weight ~ 80kDa. It is
widely distributed in body fluids such as milk, tears, saliva and mucosal & genital
secretions and also found in specific granules of neutrophilic leucocytes. It has two
similar N- and C-terminal molecular halves binding two Fe
3+
ions. The N- terminal
half, designated as N-lobe and C-terminal half as C-lobe have similar iron binding
properties. However, C-lobe is resistant to enzymatic degradation and prolongs its
physiological role in the digestive tract.The true C-lobe which was produced by
limited proteolysis of bovine lactoferrin using trypsin in two step process. In the first
step, two fragments of 21kDa and 45kDa were generated because two lysine residues,
Lys85 and Lys282 in the structure of iron-saturated lactoferrin were fully exposed.
The 45kDa fragment got further digested at the newly exposed site of Arg341
generating a 38kDa perfect C-lobe.On the other hand, the apolactoferrin was cut by
trypsin only at Arg341 which was exposed in the structure while the other two sites
with Lys85 and Lys282 are inaccessible. The purified iron saturated C-lobe was
crystallized at pH 4.0 and pH 6.8. The structure was determined with molecular
replacement method using coordinates of the C-terminal half of the intact
apolactoferrin and Proteinase K digested iron saturated C-lobe respectively. The
structural determination of 38kDa at pH 4.0 revealed that iron atom was absent and
iron binding cleft is wide opened as compared to previously determined structure of
iron saturated C-lobe. The structure obtained at pH 6.8 contained Fe
3+
at its active
site and suggests that His595 may be the first residue to dissociate from ferric ion
when the pH is lowered.
Cloning, Expression and Purification of Glycinamide Ribonucleotide
B 51
(GARS) synthetase from Pyrococcus horikoshii OT3
Ravi Guru Raj Rao¹, Kanagaraj Sekar² and Jeyaraman Jeyakanthan¹*
¹ Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block,
Alagappa University, Karaikudi-630 004, Tamil Nadu, India
²Supercomputer Education and Research Center, Indian Institute of Science,
Bangalore 560012, India.
E-mail: jjkanthan@gmail.com
De-novo and salvage are the two pathways, responsible for the purine nucleotides
syntheses. The enzyme Glycinamide ribonucleotide Synthetase catalyzes the step 2 of the
subpathway that synthesizes N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-Dribose 1-diphosphate. In cancer, De-novo pathway plays an important role in the cell
proliferation by supplying the huge demand of purine nucleotides. Hence inhibiting this pathway
is an important target to regulate the disoriented and uncontrollable cancer cell proliferation in an
organism. In this investigation, the gene Glycinamide ribonucleotide Synthetase (PH0323) is
amplified using PCR from P. horikoshii OT3 genome as template with appropriate primers
cloned in pETM11 vector using KpnI and NcoI restriction enzymes. The clone was transformed
in E.coli DH5α cells and colony PCR was performed to confirm the insert. Followed by double
digestion with KpnI and NcoI restriction enzymes to confirm correct orientation of the insert
gene, both this experiments validate that the gene was cloned successfully. This clone was
transformed in E.coli Bl21 cells, over expressed; induced IPTG and the cells were harvested by
centrifugation and sonicated. The lysate was loaded on to a His trap™ column (GE Healthcare)
which was purified using AKTA 10 purifier® (GE Healthcare) and subjected to further
purification, were the homogenous protein was obtained. The protein was screened using
Hampton crystal screen kit were Needle crystal was obtained in PEG Ion screen condition B-22,
further X-ray studies have to be done to solve the structure.
The structure of B. subtilis RecU Holliday Junction resolvase in complex with a
palindromic DNA fragment and its solution studies using SAXS and MD;
elucidating a novel inverted manhole ascent mechanism
1
2
3
2
1,4
Sagar Khavnekar , Svetlana Sedelnikova , Sylvia Ayora , John Rafferty , and Avinash Kale
1
UM-DAE Centre for Excellence in Basic Science, University of Mumbai, Vidhyanagari
Campus, Mumbai 400098, India
2
The Krebs Institute, Department of Molecular Biology and Biotechnology, University of
Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
3
Department of Microbial Biotechnology, Centro Nacional de Biotecnologia, CNB-CSIC, 28049
Madrid, Spain
4
To whom correspondence may be addressed: E-mail: avinash.kale@cbs.ac.in
Abstract
We have determined the crystal structure of the Holliday Junction (HJ) resolving enzyme RecU
from B. subtilis in complex with a 12 base palindromic DNA fragment. This structure shows the
“stalk” region and the essential N-terminal region (33 residues) previously unseen in our DNA
unbound structure. Ensemble optimised modelling (EOM) of small angle X-ray scattering
(SAXS) data has further confirmed the flexible nature of the N-terminal region of RecU.
Thermofluor studies indicate stabilization of RecU on binding to DNA duplexes and four arm
HJs.In our DNA bound structure we observe symmetric positioning of stalk region of RecU with
respect to its mushroom cap, in contrast to the asymmetric positioning of the stalk region
observed in an unbound structure of homologous B. stearothermophilus RecU. Molecular
dynamics simulations on RecU and its complex with HJ DNA support stabilization of RecU and
asymmetric to symmetric switching on binding to HJ. On the basis of our crystal structure and
MD simulation studies we propose an inverted manhole ascent mechanism for binding of RecU
to HJ. Our simulation studies with the RecU-HJ complex strongly support previously proposed
mechanism for phosphodiester bond cleavage.
Structure of a heterogeneous, glycosylated, lipid-bound, in vivo grown
protein crystal at atomic resolution from viviparous cockroach, Diploptera
punctata
Sanchari Banerjee1, Nathan P. Coussens2,3, François-Xavier Gallat4, Nitish
Sathyanarayanan1, Jandhyam Srikanth5 , Koichiro J. Yagi6, James S. S. Gray2, Stephen
S. Tobe6, Barbara Stay7, Leonard M.G. Chavas4,8,* and S. Ramaswamy1,2,5,*
1
Institute for Stem Cell Biology and Regenerative Medicine, Bellary Road,
Bangalore 560065, India.
2
Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa
City, IA 52246, USA.
3
National Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, MD 20850, USA.
4
Structural Biology Research Center, High Energy Accelerator Research Organization,
Tsukuba-city, 305-0801 Ibaraki, Japan.
5
C-CAMP, Bellary Road, Bangalore 560065, India.
6
Department of Cell and Systems Biology, University of Toronto, Toronto M5S 3G5,
Canada.
7
8
Department of Biology, University of Iowa, Iowa City, IA 52246, USA. Center
for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.
E-mail: sancharib@instem.res.in, ramas@instem.res.in
Macromolecular crystals for x-ray diffraction studies are typically grown in vitro from
pure and homogeneous samples; however, there are examples of protein crystals
identified in vivo. Recent developments in micro-crystallography techniques and the
advent of x-ray free-electron lasers have allowed for the determination of several protein
structures from crystals grown in cellulo. Here we report an atomic resolution (1.2 Å)
crystal structure of heterogeneous milk proteins grown inside a living organism in their
functional niche. These in vivo grown crystals were isolated from the midgut of an
embryo within the viviparous cockroach, Diploptera punctata. The milk proteins
crystallize in the space group P1, and a structure was determined by anomalous
dispersion from the native sulfur atoms. The data reveal glycosylated proteins that adopt
a lipocalin fold, bind lipids and organize to form a tightly packed crystalline lattice.
Notably, the crystalline cockroach milk proteins are highly heterogeneous with respect to
amino acid sequence, glycosylation and bound fatty acid composition. These data present
a unique example of protein heterogeneity within a single in vivo grown crystal at atomic
resolution.
B 53
Exploring Structural and Biochemical basis of Nup155 in NPC assembly
Sangeeta Niranjan, Radha Chauhan
Affiliation: National Centre for Cell Science
Email: sangeeta.19apr@gmail.com, radha.chauhan@nccs.res.in
Nuclear pore complexes (NPCs) are the gateways that regulate the nucleocytoplasmic trafficking
across the nuclear envelope. Nuclear Envelope (NE) fuses at multiple points to form pores
known as nuclear pore complex. NPC is a largest protein assembly in the eukaryotes and is
composed of 30 different nucleoporins averaged at 8, 16 or 32 copies per NPC, thereby making it
a ~112MDa assembly in vertebrates. We are focusing on structural elucidation of Nup155 and
hence its role in the NPC assembly. The yeast homologue, Nup157 and its paralog Nup170 were
found to be interacting with nucleic acids in a sequence independent manner and hence play a
role in chromatin organization. Various other Nups including Nup93, Nup35 and pore membrane
proteins (Ndc1, Pom121 and Gp210) shows interaction and a structural network with Nup155,
which results in NPC assembly. Studies on Xenopus Nup155 shows that a specific loop of
Nup155 β-propeller domain dips into the lipid bilayer and the positioning of Nup155 as a rodshaped connector is elucidated with the positioning of Nup205 and Nup188 into the questionmark shaped density in the cytoplasmic ring (CR) and nuclear ring(NR). In previous studies a
homozygous mutation is identified, R391H in Nup155 that co segregates with Atrial Fibrillation,
affects nuclear localization of Nup155 and reduces nuclear envelope permeability. We are trying
to purify Nup155 in bacterial as well as in mammalian expression system which will further
subjected to crystallization trials, cryo-EM and elucidation of the interaction network. This
collective knowledge would help to understand the details of NPC.
Structural studies on redox proteins of Mycobacterium tuberculosis
Sapna Sugandhi and Shekhar C. Mande
National Centre for Cell Science, Pune University campus, Ganeshkhind road
Pune 411007
Among all living systems, most of the systems are based on aerobic life style. But it
also has been described that Oxygen plays contrasting role, as it acts as a toxic
substance when comes in contact with other chemicals and forms Reactive Oxygen
Species (ROS), which are toxic to cell. Interestingly, Mycobacterium tuberculosis
(M.tb), the causative agent of Tuberculosis faces this oxidative stress in the host
environment, when it is phagocytosed by macrophages in the lungs and surprisingly it
easily overcomes this stress. Its survival in the oxidative stress depends hugely on its
ability for maintaining redox homeostasis. M.tb utilizes the Mycothiol and
Thioredoxin systems to maintain its intracellular redox state. Components of
Thioredoxin system are member of the pyridine nucleotide disulfide oxidoreductase
family of flavoenzyme. All members of Trx family have a conserved CXXC motif in
their active site. Here, NADPH acts as ultimate source of electron as it reduces
Thioredoxin reductase (TrxR) and then active TrxR reduces its partner. Absence of
Glutathione system makes the Thioredoxin system of great importance, since
inhibition of the activity of Thioredoxin system would potentially be lethal to the
bacteria. In this work, our goal is to understand the mechanism of electron transfer in
the redox pathway, which opens newer avenues for the development of novel
therapeutics. Therefore, we would try to capture TrxR along with its electron
acceptors to understand the molecular mechanisms through which M.tb withstands
oxidative stress. Till now, we have succeeded in obtaining intermediate complexes of
TrxR along with its electron acceptors and now hope to crystallize them soon.
B 55
Structure of PCNA (Proliferating cell nuclear antigen) from Leishmania
Donovan
Satyaprakash Yadav, Pradeep Sharma, Sujata Sharma, Punit Kaur and T. P. Singh
Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029
Proliferating cell nuclear antigen (PCNA) is an essential protein which is involved in
DNA replication, transcription and repair. Homologues of this protein are found in all orders
of life. The high level of conservation and essential nature of PCNA infers that it may be a
potential drug target for anti-cancer drugs in humans and also a potential anti-parasitic target.
The PCNA from Leishmania donovani (LdPCNA) was purified and crystallized. The crystal
of LdPCNA diffracted to 2.95 Å resolution and belonged to space group P212121, with unit0
cell parameters a = 132.4 Å b = 150.5 Å, c = 169.7 Å and α = β = γ= 90 . The molecular
replacement of LdPCNA was first performed using the structure of DmPCNA (PDB ID
4HK1), (Dianlin Cheng et al 2013) . The crystal structure described had a low resolution, it is
likely that this is the result of a high (~70%) solvent content of these crystals. The loose
crystal packing may be the result of the flexible loop domains. The structure of LdPCNA
shows a potential hexameric state it forms a symmetric dimer of the homotrimer in a head-totail manner. An interdomain connector loop (IDCL) links the N- and C-terminal domains.
Additionally, the N-terminal and C-terminal domains contact each other through hydrophobic
associations. A comparison of PCNA structures of four species indicates structural
differences. In this work the oligomeric state of LdPCNA has been determined to be
hexameric both in solution and in the crystal This work provides a structural basis for further
functional and evolutionary studies of LdPCNA.
.
Structural insight into the glycerophosphocholine binding protein, a
subunit of ABC transporter
Shankar Prasad Kanaujia*
Department of Biosciences and Bioengineering, Indian Institute of Technology
Guwahati,
Guwahati - 781039, Assam, India
E-mail: spkanaujia@iitg.ernet.in
Glycerophospholipid is a major component of membrane phospholipid and is
biosynthesized through de novo pathway using the byproducts such as glycerol-3phosphate (G3P), glycerophosphocholine (GPC), glycerophosphoethanolamine (GPE),
etc. of glycerophospholipid metabolism. During glycerophospholipid biosynthesis,
these byproducts are actively transported inside the cell by two major classes of
transporters namely ABC (ATP-Binding Cassette) and MFS (Major Facilitator
Superfamily). The UgpABCE transporter is a member of ABC transporter
superfamily, known for uptake of G3P and GPC. UgpB is a periplasmic component of
UgpABCE transporter which shows homology with periplasmic sugar binding
proteins. Thus, several periplasmic proteins belonging to UgpABCE transporter have
been annotated as sugar binding proteins; one of such genes is TTHA0379 from
Thermus thermophilus HB8. In this study, we have characterized TTHA0379 as a
UgpB protein which binds to GPC. In addition, we determined the crystal structure of
TTHA0379 in its apo form. The crystals diffracted to 2.0 Å resolution and belonged to
primitive monoclinic space group P21. To the best our knowledge, this is the first
crystal structure of UgpB protein from a thermophilic organism. Moreover, isothermal
titration calorimetry (ITC) experiments exhibit that GPC strongly (Kd = ~140 µM)
binds to TTHA0379. Furthermore, other putative ligands such as G3P and maltose
show no binding to TTHA0379. Thus, in this study, we designate TTHA0379 as a
GPC binding protein belonging to the UgpABCE transporter.
B 57
Structural and functional studies on YbeY
1
1
2
Shivam Shukla , Ravi Singh , Janesh Kumar , Shree Prakash Pandey
1
Indian Institute of Science Education and Research, Kolkata.
2
1
National Centre for Cell Science, Pune
YbeY is a strand specific metallo-endoribonuclease, belonging to UPF0054 family encoding
a 17-21kDa protein in bacteria. It is conserved in nearly all sequenced bacteria as well and is
a part of the minimal bacterial genome. Functionally it is involved in rRNA maturation and
ribosome biogenesis. Deletion of YbeY leads to defect in processing of 16S, 23S, 5S rRNA.
Its function in plants is currently unknown. We are interested in elucidating the structure of
plant YbeY which would help us understand its function in plants. YbeY from Arabidopsis
thaliana has been successfully cloned and expressed in bacterial expression system with MBP
as fusion construct and purified through several chromatographic steps and setup for
crystallization. Needle shaped crystals have been obtained and diffraction of crystals is
underway. In addition to its role in Arabidopsis thaliana, YbeY’s possible role in virulence of
Mycobacterium tuberculosis infection is also focus of the study.
Structural and functional aspects of Low Molecular Weight Protein
Tyrosine Phosphatase from Vibrio cholera 0395
B 59
Shramana Chatterjee, Seema Nath & Udayaditya Sen*
Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata-700064
Email: shramana.chatterjee@saha.ac.in ; udayaditya.sen@saha.ac.in
Protein phosphorylation on tyrosine residues has been considered as a post translational
modification on eukaryotes and also in bacteria (gram negative, gram positive) which creates
recognition motifs for protein intercalation and cellular localization that affects the protein
stability and regulate enzymatic activity. Protein tyrosine phosphatases (PTP) are a group of
enzyme that removes the phosphate groups from phosphorylated tyrosine residues. Depending on
the mechanism it can be classified into four subgroups, where class II contains only Low
Molecular Weight Protein Tyrosine Phosphatase (LMWPTP). All members of this superfamily
includes a small catalytic domain having amino acid sequence motif CX5R(S/T), which are
similar in structure. Structural and functional aspects of LMWPTP isoform B, from Vibrio
cholera 0395, have been characterized. Studies in solution show that it exits as a dimmer
inaccordance with its (VcLMWPTPB). The structure also shows contrasting surface properties
around the ligand (MOPS) bound active site. The enzyme kinetic assay using p-NPP, shows a
little bit higher activity of the wild type enzyme than the homologous ones. Active site catalytic
cysteine mutated with a serine (C12S) shows lesser activity than the wild type. Whereas a double
mutant (C12S-C17S), where both the active site and adjacent to active site cysteine implicated to
protect the enzyme from ROS, lacked phosphatase activity, which conveys that the cysteine
adjacent to active site also takes part in its enzymatic activity.
Structure insights of exogenous siderophores and heme uptake proteins
VcFhuD and VcHutB of Vibrio cholerae
1
1
2
1
Shubhangi Agarwal , Sanjay Dey , Biplab Ghosh and Jhimli Dasgupta
1
Post Graduate Department of Biotechnology, St. Xavier’s College, Kolkata, 30
Park Street, Kolkata 700016
2
Raja Ramanna Center for Advanced Technology, Near Rajendra Nagar,
Indore 452012
E-mail address: shubhangiagarwal2202@gmail.com, jhimli@sxccal.edu.
The periplasmic ligand binding proteins (PLBPs) deliver the bound ligand to the
inner-membrane localized, ABC (ATP binding cassette) transport system responsible for the
translocation of a variety of nutrients in the cells of both prokaryotes and eukaryotes. This
mechanism of nutrient acquisition across the inner membrane of pathogenic bacteria is
insufficiently understood at the molecular level. In this study we investigated the periplasmic
siderophore-iron binding protein (VcFhuD) and the periplasmic heme binding protein
(VcHutB) of Vibrio cholerae. We have determined the crystal structures of desferal bound
FhuD at 3.4Å, apo-FhuD at 2.5Å and apo-HutB at 2.4Å resolutions. These structures revealed
a common architecture of Type-III PLBPs possessing two lobes connected by a long helix
and with a central ligand binding cleft. In vivo growth assays showed that heme and ferric
siderophores are efficient iron sources capable of restoring the growth of V. choleare.
Superposition of holo-FhuD structure on the apo structure did not indicate any significant
alteration upon desferal binding. Fluorescence quenching studies showed that VcFhuD could
effectively bind exogenous siderophores both hydroxamate-type like desferal and
ferrichromes and catecholate-type like enterobactins. Spectroscopic binding studies and
native page analysis showed that up to two hemes can bind to VcHutB and considerable
conformational changes occur in VcHutB upon heme binding. Structural results revealed that
the larger central binding cleft of VcHutB can accommodate two stacked hemes that may
coordinate via Tyr65 and His164 side chains. Spectroscopic and native page studies on
tyrosine mutants VcHutB-Y65A and VcHutB-Y65F showed that His164 is the primary
binding site and reaches saturation in a concentration dependent manner of added heme.
Collectively, our results indicate that VcFhuD can bind both hydroxamate and catecholate
type exogenous siderophores while VcHutB binds two heme molecules primarily using
His164 although persistent binding takes place at Tyr65.
Design, Insilco analysis and synthesis of novel imidazole derivatives as
an anti-angiogenesis and anticancer agents
Dr. Someswar R. Sagurthi,
Dept. of Genetics & Biotechnology
Osmania University, Hyderabad, India 500007
E-mail: drsomeswar@osmania.ac.in
Based on earlier proven pharmacophore analogues of cancer a novel 2-(substituted 2Hchromen-3-yl)-5-aryl-1H-imidazoles (13-16) were rationally designed and synthesized.
Synthesized compounds (13–16) were screened in vitro for the inhibition of KRAS/Wnt
and their anti-angiogenesis properties. Among all the screened compounds, 16f was
found to be the most potent inhibitor of cancer with the highest selectivity. Furthermore,
in the anti-angiogenesis assay compound 16f showed potent activity in inhibiting the
VGF_ADSC/CFC Angiotube area. The molecular docking analysis also exhibited the
higher binding affinity of 16f with the KRAS, Wnt and VEGF ligands. Hence, 16f could
be considered as a lead structure in the development of a new series of antiangiogenesis/anticancer agents. Co-crystallization studies are in progress with 16f
compound.
1) Royal Society of Chemistry Adv., 2014,4, 56489-56501
2) Royal Society of Chemistry Adv., 2016, Accepted Manuscript
DOI: 10.1039/C6RA07507J
B 61
Structural studies on ppGBP provide evolutionary insights and basis for
structure-based sub-classification of periplasmic sugar binding proteins
Suman Pandey, Arnab Modak, Prashant, S. Phale and Prasenjit Bhaumik*
Department of Biosciences and Bioengineering, IIT Bombay, Mumbai- 400076, Maharashtra
sumanpandey0801@gmail.com, *pbhaumik@iitb.ac.in
Periplasmic substrate binding proteins (SBPs) bind specific ligand with high affinity and
mediate its transport into the cytoplasm via the cognate inner membrane ATP binding cassette
(ABC) proteins. Despite of very low sequence identity among the SBPs, the 3D fold is highly
conserved. Although at very low sequence identities, it is difficult to predict evolutionary
relatedness, but 3D structures and operonic arrangements indicate evolutionary patterns.
Based on the structural topology of central β-sheet core, SBPs were classified into three
classes where monosaccharide binding SBPs in class-I and oligosaccharide-binding SBPs in
class-II group. Later, structure based classification divided the SBPs into six clusters where
class-I and class-II sugar binding proteins were clustered into group A and D, respectively.
Here we report the first high resolution, (1.25 Å) crystal structure of periplasmic glucose
binding protein from Pseudomonas putida CSV86 (ppGBP) in complex with glucose. Crystal
14
structure, [ C]-glucose based cold chase experiment and SPR have shown ppGBP to be
glucose specific with no affinity for oligosachharides. The structure of ppGBP revealed it to
have an oligosaccharide-binding class-II fold but it binds only to monosaccharides as the
binding pocket is occluded by the presence of one helix and two loops. Upon loop deletion,
the mutant showed some affinity for maltose. We analyzed all the sugar binding SBPs in the
PDB and built homology models for monosaccharide binding class-II proteins. Structure
based phylogenetic tree grouped the monosaccharide and oligosaccharide binding class-II
proteins into two separate branches. With these observations we hypothesize that
monosaccharide binding class-II SBPs might have undergone structural modulation of sugar
binding pocket to accommodate only monosaccharide during their evolution. We can also sub
classify the class-II sugar binding SBPs into two sub classes, oligosaccharide and
monosaccharide binding proteins.
Reference
1. Modak, A., Bhaumik, P. and Phale, P. S. (2014) Periplasmic glucose-binding protein from Pseudomonas putida CSV86 –
identification of the glucose-binding pocket by homology-model-guided site-specific mutagenesis. FEBS J. 281, 365-375
2. Pandey, S., Modak, A., Phale, P. S. and Bhaumik, P. (2015) Cloning, purification, crystallization and preliminary X-ray
diffraction studies of periplasmic glucose binding protein of Pseudomonas putida CSV86. Adv. Biosci. Biotechnol. 6,164171.
3. Pandey, S., Modak, A., Phale, P. S. and Bhaumik, P. (2016) High resolution structures of periplasmic glucose binding
protein of Pseudomonas putida CSV86 reveal structural basis of its substrate specificity. J. Biol. Chem. 291, 7844-7857.
Design, Construction and Molecular Dynamics Studies of Ebola Viral
Proteins and identifying their potent antiviral.
B 63
Background: Ebola viruses (EBOVs) are enveloped, non segmented negative-strand RNA
viruses belonging to the family Filoviridae . Because filoviruses cause outbreaks of severe,
often lethal hemorrhagic fever, they are of concern as potential bioweapons and as an
emerging public health threat. Protein flexibility of viral proteins, are essential attribute
without which few proteins can carry out their biological functions. Nucleoprotein (NP) is
likely to involve in all steps of viral replication, including the formation of nucleocapsid like
structure, replication of the viral genome.Viralprotein(VP35) is an multifunctional protein
and plays important role in viral pathogenesis including viral mRNA synthesis and
replication.VP35 an essential component and interaction of VP35 with RNA polymerase is
essential for the mRNA synthesis. The Viralprotein (VP30) is an important factor regulating
viral transcription. It is an EBOV specific transcription factor and also helps in replication.
Without all these functional proteins the Ebola Virus cannot replicate and transcribe to
mRNA so making these proteins a good drug target. The RNA polymerase (L) proteins of
NNS(Non segmented Negative Strand) RNA viruses are thought to contain all catalytic
functions required for replication and transcription, such as polymerization, polyadenylation
and methylation.
Methodology: In order to know the stability of the structural proteins (NP, VP35, VP30, L
polymerase) molecular dynamics simulations was studied using GROMACS 5.0, and then
molecular docking studies were performed by iGemDock 2.1 with an existing antiviral.
Results: Molecular Dynamic Simulation of hypothetical models of viral proteins showed an
individual trajectories of length upto 10ns using potential energy functions, radius of
gyration, root mean square deviation, performed at temperature 300K to study the flexibility
of viral proteins. An anti viral drug Zidovudine was found to interact with the residues of
VP35, NP, VP30 and L polymerase whose interaction differs with viral proteins after
simulations. The differences were also observed in binding energies, and amino acid residues
interacting with these viral proteins.
Conclusion: The current study reveal that the proteins after MD simulations were more stable
and also the existing antiviral drug Zidovudine interacted with viral proteins involved in
replication, can be an alternate against Ebola disease.
Expression, Purification and Crystallization of Prokaryotic Glutamate receptor
Surbhi Dhingra, Dr. Janesh Kumar
National Centre for Cell Sciences, Pune
Email: dhingrasurbhi@gmail.com, janeshdubey@gmail.com
GluR0 from Synechocystis PCC 6803 is the first reported Glutamate receptor in the prokaryotes
which binds to glutamate and forms potassium-selective channels. It is related in amino-acid
sequence to both eukaryotic Glutamate receptors and prokaryotic potassium channels, thereby
forming connecting link between the prokaryotic potassium channels and the eukaryotic GluRs
(Chen G. et al. Nature, 1999). Hence, structural studies of full length GluR0 can provide insights
into the more complex eukaryotic Glutamate receptors. The objectives of the present research are
cloning, expression and purification of GluR0 and to perform biophysical characterizations and
crystallization. The study design consisted of construct optimizations to yield better behaving
protein for further studies and crystallization trials. We are able to purify protein from membrane
fraction in its tetrameric form as suggested by size exclusion chromatography. The crystallization
trials have given some positive hits and further optimizations are underway to get better quality
crystals.
B 65
Characterizations of Solute Binding Proteins by Differential
Scanning Fluorimetry and Crystallography
U. Yadava
1
1,2
2
2
3
, M.W. Vetting , N.F. Al Obaidi , J.A. Gerlt , S.C. Almo
2
2
Department of Physics, DDU Gorakhpur University, Gorakhpur, UP, 273009 INDIA Department of
Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461 USA 3Department of
Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
The uptake of exogenous solutes are mediated by transport systems embedded in the plasma membrane
and drive active transport even at µM to nM solute concentrations. In many of these systems a
periplasmic Solute-Binding Protein (SBP) is utilized to bind their cognate ligands with high affinity and
deliver them to the membrane bound translocator subunits. Active transport systems with SBP
components are traditionally divided into three main families based on their energetic coupling
mechanism, primary sequence and subunit composition: TRipartite ATP-independent Periplasmic
Transporters (TRAP), ATP Binding Cassette transporters (ABC) and Tripartite Tricarboxylate
Transporters (TTT). Knowledge of the cognate ligand for the SBP component of the transporter can
1
provide crucial data for functional assignment of co-located or co-regulated genes . In the present study,
the structural and functional characterizations of several solute binding proteins have been carried out.
Proteins were cloned from genomic DNA, expressed by autoinduction, and purified by a combination of
Ni-NTA and size exclusion chromatography. The purified SBPs were screened using differential scanning
fluorometry (DSF) and a > 400 compounds ligand library. Two of the SBPs exhibited DSF hits that were
novel for their respective transport family. Crystallization trials of proteins have been conducted with
their respective DSF ligand hits. Those SBPs that have structures determined and their respective
interactions with co-crystallized ligands will be presented. Co-crystallization with DSF determined
ligands resulted in structures of Avi_5305 in complex with D-glucosamine and D-galactosamine, the first
structure of an ABC SBP with an amino sugar.
Structure and function determination of an uncharacterized enzyme from
Mycobacterium smegmatis of the cytidine deaminase superfamily
1
Vandana Gaded and Ruchi Anand
1,2
2
Department of Chemistry, Indian Institute of Technology, Mumbai 400076, Maharashtra,
India.
Email: vandanagaded@gmail.com,vandanag@chem.iitb.ac.in,ruchi@chem.iitb.ac.in,
ruchi.ra62@gmail.com
Mycobacterial species are global threats possessing unique regulatory properties that assist
them in evading the immune system and emerging as multidrug resistant strains. To design
effective drugs against such pathogens, it’s necessary to target pathways that are important
for survival. As mycobacterial species has to recycle bases, nucleosides or nucleotides to
persist in the hostile environment offered by the host macrophages, targeting the nucleobase
salvage pathway can serve as promising drug targets (1). Here, we report the structural and
functional analysis of an uncharacterized deaminase from Mycobacterium smegmatis (Msd)
belonging to the cluster of orthologous group 0590 (COG0590) of the cytidine deaminase
(CDA) superfamily. We have determined the structure of Msd at 1.89Å using single
wavelength anomalous diffraction (SAD) phasing method. Structural analysis reveals that
although Msd possesses a typical cytidine deaminase (α/β/α) fold but it has a relatively larger
active site cavity, harbouring the unusual helix-loop conformation which is unique to this
enzyme. Using Berthelot’s reaction, we have screened Msd with a library of nucleobases and
their analogues, where ammeline (a triazine compound) was found to be the substrate with a
3
catalytic efficiency of 6.8 × 10 M
-1 -1
s . We have also determined the crystal structure of
Msd in complex with ammeline and investigated its binding profile using isothermal titration
calorimetry. Based on the large size of the catalytic cavity, docking with bulky triazines and
nucleobases were performed. The results show that benzoguanamine possess highest mean
binding energy and therefore its derivatives can serve as potent inhibitors.
References
1. Zilpa A.S.Q.et.al., (2010), Journal of Structural Biology, 169, 413–423
2. Bitra A,et.al. (2013), Biochemistry, 52, 3512-3522.
B 67
Understanding the activation mechanism of Plasmepsins from Plasmodium
falciparum and their structural studies to develop antimalarial inhibitors
1
1
2
3
Vandana Mishra , Ishan Rathore , Huogen Xiao , Ricky Yada , Prasenjit Bhaumik
1
1
Department of Biosciences and Bioengineering, Indian Institute of Technology
Bombay 400076, India.
2
Department of Molecular and Cellular Biology, University of Guelph, Ontario, N1G2W1,
Canada.
3
Faculty of Land and Food Systems, University of British Columbia, 248-2357 Main Mall
Vancouver, BC V6T 1Z4, Canada.
E-mail: vandanamishra@iitb.ac.in, pbhaumik@iitb.ac.in
Plasmodium falciparum is the causative agent of the most lethal form of malaria, killing
millions of people annually. Increasing emergence of drug-resistant parasites rapidly
necessitates the development of novel and effective anti-malarial inhibitors. A family of ten
different plasmepsins are identified in parasite which belong to pepsin-like aspartic protease
family. The four food vacuolar plasmepsins, PMI, II, IV and HAP engage in hemoglobin
degradation; therefore, are attractive drug targets to combat malaria. Recently, KNI series of
inhibitors are found to be very potent against food vacuolar plasmepsins. We have solved
crystal structures of mature plasmepsin II in complex with four different KNI inhibitors
(10395, 10742, 10772, 10333). These structures explain their unique binding mode and thus
leading a way for modifying these inhibitors for greater potency.
Plasmepsins are synthesized as inactive zymogens and undergo cleavage of their prosegments to generate active mature enzymes in acidic conditions. The mechanism of
activation of plasmepsin zymogen to its mature form is not well understood. Our study shows
that activation of PMI is not blocked by Pepstatin A (a potent aspartic protease inhibitor) and
therefore we hypothesize that active site of PMI zymogen is dispensable for its maturation in
contrary to earlier reported studies leading to a possibility of two alternative pathways that
plasmepsins follows for rapid maturation.
Discovery of new genetic variants from Vibrio cholera,
V. parahaemolyticus and V. corallilyticus
Vijaykumar Pillalamarri and Anthony Addlagatta*
Email: anthony@iict.res.in
Center for Chemical Biology,
Indian Institute of Chemical Technology, Hyderabad-500007, INDIA
Methionine Aminopeptidases (MetAPs) are the enzymes that specifically remove the
initiator methionine during protein synthesis. MetAPs are conserved from eubacteria, archaea
to eukaryotes. MetAPs are classified into Type1 and Type2 MetAPs, based on a 60 amino
acid insert in the catalytic region of Type2 MetAP. Type1 MetAPs further classified into
Type1a, Type1b, Type1c and Type1d based on the N-terminal extensions. Type1a
(EcMetAP) is prototype of all MetAP family of proteins, Type1a’ (SpMetAP) is a recent
discovery from our lab, identified a new insert in the Type1a MetAP. These MetAPs are
considered as potential pharmaceutical targets to treat various diseases like cancer,
rheumatoid arthritis, obesity and various microbial infections etc. as the knocking out of map
gene which codes for MetAPs is shown to be lethal to cell. Even though MetAPs are potential
drug targets the main problem associated with MetAPs is specificity as the active site where
the competitive inhibition is targeted is very much conserved in different isoforms across all
organisms. In a recent discovery from our lab showed a molecule specifically targeting
Streptococcus pneumonia MetAP without affecting human Type1 MetAP. This discovery
encouraged us to find more MetAPs with extra insertions in the catalytic site of MetAPs. In
the present study, exclusive genome wide search has resulted in new MetAPs in the species of
Vibrio. MetAPs with either no insert or two inserts or three inserts were identified. One each
from three classes of MetAPs (no insert, two inserts, and three inserts) were cloned expressed
and purified for further biochemical and structural characterization.
Exploring Hematopoietic Stem Cell Regulation at the Atomic Level
with ASRIJ
1
1
2
1*
Zenia Motiwala , Asmita Prabhune , Maneesha Inamdar , Kiran Kulkarni
1.
Division of Biochemical Sciences, CSIR- National Chemical Laboratory, Pune-411008
2. Laboratory of Stem Cell Biology and Vascular Biology, JNCASR,
Bangalore-560064 e.mail id: z.motiwala@ncl.res.in; ka.kulkarni@ncl.res.in
Asrij is an evolutionarily conserved Endosomal membrane protein containing a
novel OCIA domain. It is expressed in hematopoietic stem cells and is a key point of
control in hemocyte development pathways via. Notch Trafficking. It acts as a
Regulatory Switch to maintain stemness. Asrij is an important stem cell marker and
the OCIA domain is an oncogenic marker as well as a therapeutic target for Breast
cancer. The key interacting partners of Asrij are ARF-1 & STAT 3.
We aim to explore the structure of this membrane protein employing X-ray
crystallography. For this, the gene has been cloned in bacterial vectors and protein
expression has been optimized. Multiple chromatography techniques have been
employed for protein purification. Crystallization trials and detergent optimization are
currently in progress.
The structure- function data will give insight to hematopoietic stem cell
regulation and will also play a crucial role in development of treatment for blood and
breast cancers.
B 69
C1
Rapid crystallization of amino acids using biocompatible nucleant with
Nd:YAG laser
a*
a
a
a
a
A. Abdul Ajees , T. Shilpa , S. D. George , A. Bankapur , C. Santhosh , A. K.
b
a,b
Dharmadhikari , D. Mathur
a
Department of Atomic and Molecular Physics, Manipal University, Manipal 576 104, India.
b
Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005,
India
*Corresponding and presenting author: abdul.ajees@manipal.edu
Molecular structures define the properties and function of proteins and X-ray crystallography
is one of the primary tools used to obtain the 3D structure of the proteins. But the success of
this method relies on obtaining the good quality crystals. Protein crystallization is a tedious
and time consuming endeavor. In order to get the protein crystals many novel methods have
been proposed in the literatures. Among those methods, laser induced crystallization has been
recognized as one of the promising techniques to crystallize biomolecules. The interest is
especially due to the efficiency and versatility of this technique to produce crystals with lesser
time, increasing the probability of nucleation, wide applicability, polymorph selectivity, and
spatial-temporal controllability. Though this technique is recognized as promising technique,
it has few limitations such as high laser power requirement, limitations of solvent choice,
difficulty in controlling temperature, requirement of sophisticated lab arrangements, etc. To
overcome these limitations, we have proposed a new technique by combining laser with
nucleants. Recently we have successfully crystallized several amino acids with less laser
2
power (~20 mW/cm ) and less time (within 4 seconds) using different nucleants under laser.
Following this success, we have extended this work and crystallized 12 amino acids using
biocompatible nucleant. Here we report rapid crystallization of freshly prepared polar (LThreonine) and hydrophobic (L-Isoleucine) amino acids at less laser power using continuous
wave (λ= 1064nm) laser source with the usage of biocompatible nucleant. The reduction in
time scale and the laser power for crystallizations of L-Threonine (59 seconds, 20mW) and LIsoleucine (12 seconds, 20 mW) in presence of nucleants clearly demonstrates the role of
nucleants in laser induced crystallization technique. The outcome of the current experiments
may be applicable to tackle the crystallization problem existing in the protein crystallography.
Nucleant
L- Threonine crystals
a) L-­‐ threonine
0 sec
0 sec
Nucleant
59 sec
b) L-­‐Isoleucine acid
12 sec
110 sec
55 sec
L- Isoleucine crystals
Crystallization of L-Threonine and L-Isoleucine using laser. Representative time evolution of
crystallization L-Threonine (a) and L-Isoleucine (b) upon the irradiation of the 1064nm laser
onto the biocompatible nucleant.
C2
Synthesis of Heterometallic 3d-4f Complexes using new Multisite Coordination
Ligand
Amit Chakraborty, Prasenjit Bag and Vadapalli Chandrasekhar
National Postdoctoral Fellow
Dr. Rahul Banerjee group,
Physical/Material Chemistry Division,
CSIR-National Chemical Laboratory, Pune,
Dr. Homi Bhabha Road
Pune-411008, India
Heterometalic 3d-4f metalcomplexes are of interest in molecular magnetism.
1, 2
In general,
heterometallic complex are synthesized by serendipitous approach or rational design
approach. Typically rational design approach depends upon judicial choice of organic linker.
Compartmental ligands in general and Schiff-base ligands in particular are quite effective for
assembling such complexes. One of the compartments in such ligands can be specific for 3d
metal ions while the other compartment can be utilized for speicifically accommodating f3
block metal ions. We have utilized ferrocene to build new compartmental ligands which have
been used to synthesize the heterometallic complexes. The syntheses, structures,
electrochemical behavior and magnetic properties of these complexes will be presented.
References
[1] Chandrasekhar, V.; Pandian, B. M. Acc. Chem. Res.,2009, 42, 1047.
[2] Gatteschi, D.; Sessoli, R. Angew. Chem. Int. Ed. 2003, 42, 268.
[3] Chandrasekhar, V.; Chakraborty, A.;Sañudo, E. C. Dalton Trans., 2013,42,13436.
[4] Chakraborty, A.; Bag,P.; Riviere, E.;Mallah, T.;Chandrasekhar,V.; Dalton Trans., 2014,
43, 8921.
II
Potential Ferroelectric Response In {Cu L2}n Assemblies Derived From
C3
Pyridyl-functionalized Flexible Amino-P(V) Ligands
1
2
2
1,*
Anant Kumar Srivastava, P. Divya, B. Praveenkumar, and R. Boomishankar
1
Department of Chemistry, Indian Institute of Science Education and Research (IISER)
2
Pune-411008, Maharashtra, India; Piezoelectric Division, ARDE, DRDO, Pune - 411008,
Maharashtra, India.
E-mail: aksrivastava@students.iiserpune.ac.in; boomi@iiserpune.ac.in
Supramolecular metal-organic assemblies have gained recent attention as ferroelectric
materials due to their synthetic simplicity, flexibility and ease in device fabrication.
Nevertheless, synthesis of such metal-organic based ferroelectrics is still challenging because
of the strict requirement of a non-centrosymmetric polar packing arrangement. Noticeably,
we have synthesized dipodal ligands based on phenyl phosphonic diamide backbone,
1
2
3
PhPO(NHPy)2 (Py = 2-pyridyl (L ) or 3-pyridyl (L ) or 4-pyridyl (L )), that can generate
II
both centrosymmetric and noncentrosymmetric {Cu L2}n assemblies on reaction with nitrate
2
and perchlorate Cu(II) salts. Starting from L , we developed a family of anion driven
II 2
{Cu L 2}n based frameworks in discrete (centrosymmetric) and helical 1D-polymeric
1
(noncentrosymmetric) structures, whereas L yielded only discrete mononuclear
centrosymmetric complex. Interestingly, the presence of perchlorate or nitrate anions in the
2
packing cavities of the noncentrosymmetric 1D-helical assemblies (based on L ) played a
3
significant role in tuning their ferroelectric behavior. Further, by utilizing L , a new
II
noncentrosymmetric 2D-{Cu L2}n type material was synthesized, that gave a high remnant
2
polarization (Pr) value of ~28 µCcmˉ at room temperature, which is the highest among all
known metal-organic, organic, and polymeric ferroelectric materials. Temperature-dependent
II
dielectric measurements on the 2D {Cu L2}n assembly showed an unusual dielectric
II
anomaly peak at ∼40 °C due to the onset of desolvation. Furthermore, all the {Cu L2}n
assemblies displayed a high dielectric constant. The results mentioned here clearly
demonstrate that variation of ligand, anion, and framework topology can be used as a facile
approach for tuning the ferroelectric behavior in such metal-organic assemblies.
II
Figure. Representative {Cu L2}n assemblies derived from flexible Amino-P(V) Ligands.
References
1. Srivastava, A. K. et al. Chem. Mater. 2014, 26, 3811-3817.
2. Srivastava, A. K. et al. Chem. Mater. 2015, 27, 5222-5229.
3. Boomishankar, R.; Srivastava, A. K. Phosphorus, Sulfur, and Silicon and the Related
Elements 2016, 191, 618-623.
C4
Exploring the topological properties of electron density, electrostatic potential
and intermolecular interactions of Zidovudine via experimental charge density
analysis
†
†
‡
†
‡
†
I.Ancy , C.Kalaiarasi , Parthapratim Munshi and P.Kumaradhas *
Laboratory of Biocrystallography and Computational Molecular Biology
Department of Physics, Periyar University, Salem-636 011, India
Department of Chemistry, School of Natural Sciences, Shiv Nadar University,
UP 203207, India
ancy.annie42@gmail.com & kumaradhas@yahoo.com
Zidovudine (AZT) is the first approved nucleoside analogue reverse transcriptase inhibitor of
HIV-1. It is one of the potential inhibitor and over many years it is using as a mono therapy for
HIV treatment. Resistance development and side effects are the major problems of AZT. In
order to overcome these issues and to develop new drug, the detailed understanding of its
structure, intermolecular interactions, charge density distribution and the electrostatic
properties are very much essential. In the present study, we have performed an experimental
charge density analysis of AZT from the high resolution X-ray diffraction using HansenCoppens multipole model. AZT compound crystallizes in P21 space group with two molecules
in the asymmetric unit. A high angle X-ray diffraction intensity data set has been collected at
the low temperature 100K. The structure was determined by SHELXS software and further, an
aspherical multipole model refinement was performed up to octapole level using XD2006;
from the results, the structure, bond topological and electrostatic properties of the molecule
were determined. The molecular packing in the crystal is stabilized by weak and strong
intermolecular hydrogen bonding interactions. Notably, the intermolecular interactions,
N(2)−H(2)···O(1A), N(2A)−H(2A)···O(1), O(4A)−H(4A)···O(3A) and O(4)−H(4)···O(2A)
are forming strong intermolecular hydrogen bonding interactions in the crystal. The topological
analysis of electron density at the bond critical points (bcp) of the molecule was carried out to
2
determine the electron density ρbcp(r) and the Laplacian of electron density∇ ρbcp(r); these
parameters shows the charge accumulation and the charge concentration/depletion in the bonds
of AZT molecule. The electrostatic parameters such as atomic charges and the dipole moment
of the molecule were calculated. The electrostatic potential surface of the molecule has been
plotted, it displays large electronegative region around the azide and OH groups of the AZT
molecule. The detailed results will be presented.
Near-Infrared Luminescent Sn(IV) Complexes of N-Confused
C5
Tetraphenylporphyrin
a
Arghya Basu , Motoki Kitamura, Masatoshi Ishida, Yongsh Xie and Hiroyuki Furuta*
a
b
Physical and Material Chemistry Division, National Chemical Laboratory, Pune , India 411008.
b
Department of Chemistry and Biochemistry Graduate School of Engineering Kyushu
University,Japan 819-0395.
In recent times, Sn(IV) porphyrins have been attracting much attentions for development of
optoelectronic material applications such as light emitting diodes. The Sn(IV) cation
accommodates in the central porphyrin core and form stable octahedral complex possessing two
axially coordinated ligands. The optical properties of the Sn(IV) porphyrin complexes can thus
be fine-tuned by suitable choices of axially coordinated ligands. We herein report systematic
photophysical study of a series of Sn(IV) N-confused tetraphenyl porphyrin complexes in which
a pyrrolic ring connected to the surrounding meso-carbons at the α- and β-positions. The Sn(IV)
complexes prepared are indeed near IR luminescent and the effect of axial anions on their
photophysical properties of these complexes were examined by various spectroscopic and
theoretical techniques.
References
1. Y. Xie, T. Morimoto, H. Furuta, Angew. Chem. Int. Ed., 2006, 45, 6907.
2. A. Basu, M. Kitamura, S. Mori, M. Ishida, Yongsh Xie and Hiroyuki Furuta J. Porphyrins
Phtalocyanines., 2015, 19, 361..
th
Special isssue on the ocassion of 65 birthday of Prof. Fukuzumi
C6
Decoding the Morphological Diversity in Two Dimensional Crystalline Porous
Polymers by Core Planarity Modulation
a
Arjun Halder and Rahul Banerjee
a
b
Junior Research Fellow, D-108, Polymers and Advanced Materials Laboratory, CSIR
National Chemical Laboratory, Pune-411008, Maharashtra
a.halder@ncl.res.in
b
Scientist, D-105, Polymers and Advanced Materials Laboratory, CSIR National Chemical
Laboratory, Pune-411008, Maharashtra
r.banerjee@ncl.res.in
Two new chemically stable triazine and phenyl core based crystalline porous polymers
(CPPs) have been synthesized via a single step template free solvothermal route. Unique
morphological diversities are observed for these CPPs [2,3-DhaTta (ribbon) and 2,3-DhaTab
(hollow sphere)] by simply altering the linker planarity. A detailed time dependent study is
performed and a significant correlation is established between molecular level structures of
building blocks with morphology of CPPs. Moreover, a DFT study has been taken into
account for calculating the interlayer stacking energy, which reveals that the extent of
stacking efficiency is responsible for governing the morphological diversity in these CPPs.
C7
Structure of bacterial ribosome decoding site RNA containing
conformation-sensitive fluorescent ribonucleoside
a
b
b,
Ashok Nuthanakanti, Mark A. Boerneke, Thomas Hermann, * and Seergazhi G.
a,
Srivatsan *
a
Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi
Bhabha Road, Pashan, Pune 411008, India
b
Department of Chemistry and Biochemistry, University of California, San Diego, 9500
Gilman Drive, La Jolla, CA 92093, USA
Bacterial ribosome and its RNA components, which play important roles in protein synthesis
process, are attractive targets for antibiotics such as natural aminoglycosides, macrolides,
1
tetracyclines and the synthetic oxazolidinoes. In particular, ribosomal decoding site (A-site)
RNA motif is of unique significance as it monitors the cognate codon-anticodon interaction
and is also a target for aminoglycoside antibiotics. A-site motif, present in the 16s rRNA,
forms a conserved internal loop which signals the binding of cognate tRNA with mRNA
condon via conformational change at the nucleotide level.
2
We have developed a
conformation-sensitive dual-labeled ribonucleoside analog, which enables the monitoring of
aminoglycoside antibiotic binding to A-site RNA by fluorescence and X-ray crystallography.
The 5-selenophene-modified uridine analog is fluorescent and also contains Se atom, which
3
serves as anomalous dispersion phasing agent in X-ray crystallography analysis. When
incorporated into A-site and titrated with aminoglycoside antibiotics (e.g., paraomomycin and
neomycin), the probe reports the binding event with enhancement in fluorescence intensity,
which further enabled the estimation of binding constant. We have also obtained the X-ray
crystal structure of the selenophene-modified A-site RNA, which provides the structural basis
of the sensing ability of the modified nucleoside (see Figure). The development,
photophysical characterization and incorporation of the nucleoside analog into bacterial
decoding site will be discussed in this presentation. Furthermore, fluorescence binding assay
and structure of A-site RNA containing 5-selenophene-modified uridine will be presented.
Figure: Secondary structure of the bacterial A-site RNA motif containing 5-selenophenemodified uridine. 3-D structure of the same.
References
1. T. Hermann, Biopolymers 2003, 70, 4‒18.
2. J. M. Ogle, V. Ramakrishnan, Annu. Rev. Biochem. 2005, 74, 129‒177.
3. M. G. Pawar, A. Nuthanakanti, S. G. Srivatsan, Bioconjugate Chem. 2013, 24, 1367‒1377.
C8
Anion Induced Potentially High Ferroelectric Polarization in a Luminescent
[Zn6L8]
12+
Octahedral Cage
Ashok Yadav, Pillutla Divya, Anant Kumar Srivastava, Alexander Steiner, B. Praveenkumar,
and Ramamoorthy Boomishankar*
Department of chemistry, Indian Institute of Science Education and Research,
Pune, Maharashtra-411008
boomi@iiserpune.ac.in and ayadav@students.iiserpune.ac.in
Metal-organic hybrid materials exhibiting ferroelectric, multiferroic and piezoelectric properties
have gained extensive research interest in the recent years as materials for applications such as
non-volatile computing devices, capacitors, micro-electro-mechanical systems (MEMS), fieldeffect transistors (FETs), telecommunication signal processing units, ultrasonic medical imaging
devices and as light absorbing layers in FE solar cells. Employing a tripodal ligand
3
[PS(NH Py)3] (TATP), two axially symmetric octahedral noncentric [M6L8]
12+
type cage
molecules having nitrate (1) and perchlorate anions (2) were synthesized. The cage-assembly of
1 containing nitrate anions was crystallized in the polar tetragonal space group I4 and the cage 2
having perchlorate anions was crystallized in the nonpolar cubic space group I-43d. Ferroelectric
measurements on the polar structure of 1 gave a high remnant (Pr) and saturation (Ps)
-2
polarization values of 29.2 and 22.7 µCcm , respectively. Also, 1 exhibits a bright blue coloured
fluorescent emission at room temperature. These results show for the first time that nonpolar
cages having axial symmetry can be used a platform for obtaining potential ferroelectric
materials depending upon the anions present in them.
References
[1] T. Hang, H.Y. Ye, R.G. Xiong, Chem. Soc. Rev. 2011, 40, 3577.
[2] P. Jain, V. Ramachandran, R.J. Clark, H.D. Zhou, B.H. Toby, N.S. Dalal, H.W. Kroto, A.K. Cheetham, J. Am.
Chem. Soc. 2009, 131, 13625.
Novel multicomponent crystals of L-tryptophan with three isomers of
C9
pyridinedicarboxylic acids
Babulal Das*
Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati-39, Assam, India
dasbld@iitg.ernet.in
Multicomponent crystalline materials derived from various therapeutic agents or APIs have been
1
explored towards the development of drug formulations as well as in other applications . Amino
acids like many APIs are also known for potential salt and co-crystals formers which find many
2
applications in pharmaceutical industry . Tryptophan “an essential amino acid” is required for
normal functioning in humans and also acts as an important intrinsic fluorescent probe to
estimate the nature of microenvironment. The current work explores multicomponent crystals of
L-tryptophan with three isomers of pyridinedicarboxylic acids (PDA) where the structural
changes, binding ability and variation of fluorescence properties of L-tryptophan upon
3
interacting with these PDAs are discussed . The co-crystal of zwitterionic L-tryptophan with 2,6PDA shows strong charge assisted hydrogen bonding leading to a three dimensional closed
packed network structure. The amino acid shows higher binding affinity towards 2,6-PDA
among the three isomers. The solid state fluorescence intensity of L-tryptophan has been
quenched marginally in these crystals due to π – stacked arrangement.
Figure. (a) Asymmetric unit of L-tryp/2,6-PDA cocrystal, (b) Emission spectrum of the cocrystals
References
1. Stahl, P.H.; Wermuth, C.G. (Eds.), “Handbook of Pharmaceutical Salts, Properties, Selection
and Use”, Wiley-VCH, New York, 2008.
2. Tilborg, A.; Norberg, B.; Wouters, J. Eur. J Med. Chem. 2014, 74, 411-426.
3. Das, B. J. Cryst. Growth 2016, 447, 67-72.
Control Sulfathiazole Polymorph Nucleation on Functionalized Surface
C 10
Basanta Saikia, Pranita Bora and Bipul Sarma*
Department of Chemical Sciences, Tezpur University, Nappaam-784028, Assam,
India E-mail: sarmabipul@gmail.com
Sulfathiazole, an antimicrobial drug has total five polymorphs recognized. Concomitant
polymorphism is observedfrequentlyif crystallization environment is notprecisely maintained.
Control polymorph nucleation experiments using self-assembled mono layers (SAMs) are
successful in this instance to generate single phase. Using equivalentdrug solution
concentration and identical solvents lead to different pure polymorphic forms in
SAMsurfaces of different functionality. Hence, the translation of chemical functionality
effect fromthe surfaces directs the nucleation of specific polymorph and reported.
(i)
(ii)
Figure 1 Optical microscope image of sulfathiazole (i) concomitant polymorphs from normal
crystalization (ii) square prismatic polymorph IV generated from Functionalized SAM.
References
1. Abu Bakar, M. R.; Nagy, Z. K.; Rielly, C. D.; Dann, S. E. Int. J. Pharm.2011, 414,
86.
2. Hiremath, R.; Basile, J. A.; Varney, S. W.; Swift, J. A. J.am. chem. soc. 2005, 127,
18321.
3. Yang, X.; Sarma, B.; and Myerson, A.S.Cryst. Growth Des.2012,12, 5521.
C 11
Encapsulation of a Keggin Cluster Anion in ZIF-8 Cage: A Supramolecular
Host-Guest System having potential to act as a Water Oxidation Catalyst
Subhabrata Mukhopadhyay, Joyashish Debgupta, Chandani Singh and Samar K. Das*
School of Chemistry, University of Hyderabad, Hyderabad 500046, India
Contact: 0-40-2301-1007
skdsc@uohyd.ernet.in and Chandanisingh3@gmail.com
We have recently explored a metal organic framework (MOF)-based highly efficient
water oxidation catalyst (WOC) with a mono-nuclear Co(II)-aqua complex in its active
site.[1] This prompted us to design a system with reversible Co(III)/Co(II) red-ox couple
in its active site, which can be synthesized at room temperature with less expensive
starting materials and may behave as WOC.[2,3] Thus we choose a cobalt-centered
Keggin compound, K6[CoW12O40] · 16H2O, a well-known polyoxometalate (POM)based system, which has recently been explored in the context of photophysics.[4] This
Keggin cluster anion [CoW12O40]
6-
degrades in neutral as well as in basic solution,
thereby reducing its possibility to function as a catalyst. In order to have a stable system
based on this Keggin anion, we have encapsulated this POM cluster anion into void
2
spaces of ZIF-8, a zeolite type framework having well-defined cages, capable of
encapsulating this Keggin cluster anion. Keeping parity with our expectation, this
encapsulation enhances the stability of POM anion to a great extent in neutral- as well as
in basic pH-solution. Importantly this host-guest system acts as an efficient
electrocatalyst for water oxidation. This encapsulation strategy increases the flexibility of
the central tetrahederal Co
2+
ion to actively participate in water oxidation, which was
never shown before for a Keggin anion. We have performed detailed kinetics for this
electrocatalytic water oxidation. We have observed that higher loading level of the
Keggin anion works better than the lower loading.
Figure A: pXRD pattern of POM1@ZIF-8 (different loading). Fig. B: UV-Vis spectra of POM1@ZIF-8,
POM1 and ZIF-8, Fig. C: CV of POM1 and POM1@ZIF-8 in 0.5 M H2SO4. Fig. D: CV of POM1@ZIF-8
in 0.1 M KNO3.
References
[1] Manna, P.; Debgupta, J.; Bose, S.; Das, S. K.; Angew. chem. Int. Ed ,2016, 55, 2425
[2] Li, R.; Ren, X.; Zhao, J.; Feng, X.; Jiang, X.; Fan, X.; Lin, Z.; Li, X.; Hu, C.; Wang,
B., J. Mater. Chem. A, 2014, 2, 2168.
[3] Baker, L. C. W.; McCutcheon, T. P.; J. Am. Chem. Soc., 1956, 78, 4503.
[4] Glass, E. N.; Fielden, J.; Kaledin, A. L. ; Musaev, D. G.; Lian, T.; Hill, C. L., Chem.
Eur. J. 2014, 20, 4297.
C 12
Low overpotential electrocatalytic water splitting with noble metal3
free nanoparticles supported in a sp N-rich flexible COF
Dinesh Mullangi,, Ramanathan Vaidhyanathan
*
Department of Chemistry, Indian Institute of Science Education and Research,
Pune 411008, India
dinesh.mullangi@students.iiserpune.ac.in and vaidhya@iiserpune.ac.in
Covalent Organic Frameworks (COFs) are highly ordered crystalline porous materials, have
attracted a great deal of research interest due to their chemical diversity, high surface area and
1
tenable functionalities . Presence of pre-designed nitrogen rich functional groups in COFs make
them capable of strongly interacting with active metal nanoparticles to form excellent
2
heterogeneous catalysts and therefore avoid metal NPs leaching. Here, we formed highly
3
flexible tetrahedral sp nitrogen rich COF which can serve as ideal supports for nanoparticles for
electrocatalytic water splitting. This flexibility gives rise to structural changes which generate
mesopores capable of confining very small (<2 nm) non-noble-metal-based nanoparticles (NPs).
This dispersed small-size NPs in the mesopores of the COF enables high access to the
catalytic sites resulting exceptional activity toward the Oxygen Evolution Reaction (OER)
−2
from alkaline water with overpotential of 258 mV at a current density of 10 mA cm . The
overpotential observed in the COF-nanoparticle system is the best in class, and is close to the
current record of ≈200 mV. Also, it possesses outstanding kinetics (Tafel slope of 38.9 mV
−1
dec ) for the reaction. These values surpass most of the reported Ni/Co-based electrocatalyst in
their supported as well as unsupported forms. DFT modeling shows the interaction between the
3
hexagonal Ni(OH)2 NPs having sandwiched between the sp nitrogens of the adjacent COF
layers. This interaction could be crucial to maximizing their synergistic interactions for active
catalyst.
References
1. (a) Côté, A. P.; Benin, A. I.; Ockwig, N. W.; Matzger, A. J.; O’Keeffe, M.; Yaghi, O. M.
Science 2005, 310, 1166.(b) Feng, X.; Ding, X.; Jiang, D.; Chem. Soc. Rev. 41, 6010–6022
(2012).
2. Mullangi, D.; Nandi, S.; Shalini, S.; Sreedhala, S.; Vinod, C. P.; Vaidhyanathan, R. Scientific
Reports. 5, 10876 (2015).
3. Mullangi, D,; Dhavale, V,; Shalini, S,; Nandi, S,; Collins, S,; Woo, T,; Kurungot, S,;
Vaidhyanathan, R. Advanced Energy Materials. 1600110. doi:10.1002/aenm.201600110 (2016)
C 13
Colour Cocrystal Polymorphism: Cocrystals of Furosemide with Pyridines
a
a
a
a
Ekta Sangtani, Sanjay K. Sahu, Shridhar H. Thorat, Rupesh L. Gawade, Kunal K. Jha,
b
Parthapratim Munshi, and Rajesh G. Gonnade*
a
b
a
b
CSIR-National Chemical Laboratory, Pune 411008, India. Department of Chemistry, Shiv
Nadar University, UP 201314, India. Email ID- e.sangtani@ncl.res.in; rg.gonnade@ncl.res.in
Pharmaceutical cocrystals are gaining tremendous interest in recent times because of their
potential to alter the physicochemical properties of active pharmaceutical ingredients (APIs)
along with preventing polymorphism of APIs. The added complexity of two or more components
for cocrystallization increases the structural specificity and reduce the potential to show
polymorphism. However, compunds that are more prone to exhibit polymorphism are more
1
likely to form cocrystals and can produce polymorphism in cocrystals too. Furosemide (FS), a
loop diuretic drug showed polymorphism and also forms cocrystals. Its cocrystals with
nicotinamide yielded five polymorphic cocrystals. This suggests that FS has the ability to show
conformational tuning even in cocrystals which is eventually manifested into cocrystal
polymorphism. In a quest to further investigate conformation polymorphs of FS in cocrystals, we
carried out its cocrystallization with 4,4′- bipyridine (4BPY), 2,2′-bipyridine (2BPY), and 4aminopyridine (4AP). Interesting, FS with 4BPY exhibited colour cocrystal polymorphism (dark
orange and light yellow) with coformer 4, 4’-bipyridine (4BPY) albeit both the API and the
cocrystal former are colourless. Cocrystallization of FS with 2BPY and 4AP gave colorless
cocrystals and did not exhibit polymorphism. The significant colour difference between the two
cocrystals dimorphs of FS and 4BPY could be attributed to the different π-stacking patterns and
hydrogen bonding interactions between molecules of FS and 4BPY in their cocrystal structures.
1.
2.
Aitipamula, S.; Chow, P. S.; Tan, R. B. H. CrystEngComm 2014, 16, 3451–3465.
Sangtani, E .; Sahu, S.K .; Thorat, S.H .; Gawade, R.L .; Jha, K.K .; Munshi, P .; Gonnade, R.G.
Cryst.Growth Des,2015 ,15 ,5858-5872.
2
C 14
Structural transformations of coordination polymers on the counter anion exchange
and metal-metathesis
Fayaz Baig, Kumari Suman and Madhushree Sarkar*
Department of Chemistry, Birla Institute of Technology and Science, Pilani, Pilani Campus,
Rajasthan, India. Tel: +91-1596-515679
fayazbaig2012@gmail.com and msarkar@pilani.bits-pilani.ac.in
Crystal engineering of Coordination-polymer (CP)s is attracting much attention since past two
decades for their potential applications in the areas of gas storage, molecular sensing, separation,
catalysis, etc. The cogent design of CPs can be in principle controlled through the judicious
selection of metal nodes and the organic linkers. In contribution to this we analyzed the ways to
design stable and flexible CPs that can show structural transformations in response to the
external stimulus such as counter anions, guest molecules. For this reason in our current work we
synthesized the CPs with bispyridyl-bisamide ligands with alkyl group in the spacer. Amide
functional group is a promising functional group for its ability to provide stable and flexible
network geometries with softer but network directing hydrogen bonding interactions and the
alkyl group in the spacer generates the dynamic nature to the CPs due to its conformational
changes. The main focus in this work is to determine the different CPs with the response of
ligand to the respective metal nodes, effect of different types of counter anions in directing the
flexible alkyl chain of CPs to adopt different conformations there by affecting the guest inclusion
properties and the metal-metathesis to get CPs with desired network geometry.
Counter anion exchange
Metal-metathesis
References
1. Suman, K.; Rajni kant; Gupta, V. K.; Sarkar,* M. Dalton Trans., 2013, 42, 8492-8497.
2. Suman, K.; Baig, F.; Rajni kant; Gupta, V. K.; Mandal, S.; Sarkar,* M. RSC Adv., 2014, 4,
36451-36457
C 15
Synthesis and crystal structure of (Z) 2-(4-chlorophenyl)-N’-hydroxy
acetamidine
a
b
b
a*
M. K. Hema , Sushma , K. M. Lokanatha Rai and N. K. Lokanath ,
a
b
Department of Studies Physics, Department of Studies in Chemistry, University of Mysore,
Manasagangotri, Mysuru 570 006, India.
*Correspondence e-­‐mail: lokanath@physics.uni-­‐mysore.ac.in
Abstract
The title compound, 2-(4-chlorophenyl)-N’-hydroxy acetamidine (C8H9OCl) was synthesized
from 4-chlorobenzyl cyanide, hydroxylamine hydrochloride and characterized by various
spectroscopic techniques and finally the structure was confirmed by X-Ray diffraction
studies. The title compound crystallizes in the monoclinic crystal system with the space group
P21 with unit cell parameters are a = 7.4949(10) Å, b = 5.3891(8) Å, c = 10.7292(15) Å, β =
0
3
91.35(6) , Z = 2 and V=433.24(11) Å . The structure exhibits both inter and intra-molecular
hydrogen bonds of the type O-H...N and N-H...N, which accounts for the stability of the
molecule. The structure adopts a Z-conformation with respect to the C=N bond. Hirshfeld
surface analysis for visually analyzing intermolecular interactions in crystal structures
employing molecular surface contours and 2D fingerprint plots have been used to examine
molecular shapes.
Keywords: Crystal structure; Oximes; Monoclinic crystal.
C 16
Topological characterization of electron density, electrostatic potential and
intermolecular interactions of 2-nitroimidazole: An experimental and
theoretical study
†
†
‡
†
C. Kalaiarasi , Mysore S.Pavan and P.Kumaradhas *
Laboratory of Biocrystallography and Computational Molecular Biology
Department of Physics, Periyar University, Salem-636 011, India
‡
Solid State and Structural Chemistry Unit, Indian Institute of Science,
Bangalore-560 012, India
kalaiphy90@gmail.com and kumaradhas@yahoo.com
An experimental charge density distribution of 2-nitroimidazole was determined
from high resolution X-ray diffraction and Hansen-Coppens multipole model. The 2nitroimidazole compound was crystallized and high angle X-ray diffraction intensity
data set has been collected at low temperature 110(2) K. The structure was solved and
further, an aspherical multipole model refinement was performed up to octapole level;
the results were used to determine the structure, bond topological and electrostatic
properties of the molecule. In the crystal, the molecule exhibits a planar structure and
forming weak and strong intermolecular hydrogen bonding interactions with the
neighboring molecules. The Hirshfeld surface of the molecule was plotted, which
explores different types of intermolecular interactions and their strength. The
topological analysis of electron density at the bond critical points (bcp) of the molecule
was performed, from that the electron density ρbcp(r) and the Laplacian of electron
2
density∇ ρbcp(r) at the bcp’s of the molecule have been determined; these parameters
are showing the charge accumulation and the charge concentration/depletion of the
nitroimidazole bonds in the crystal. The electrostatic parameters like atomic charges and
the dipole moment of the molecule were calculated. The electrostatic potential surface
of molecule has been plotted, it displays large electronegative region around the nitro
group. All the experimental results were compared with the corresponding theoretical
calculations performed using Crystal09.
Investigations on synthesis, growth and physical properties of
C 17
AgGa0.5In0.5S2 single crystals for Mid-IR application
N. Karunagaran* and P. Ramasamy
Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603110,
India karthickkaruna@gmail.com
The I-III-VI2 ternary semiconductor of AgGaInS2 single crystal has been
grown by Bridgman technique. Indium was substituted at Gallium site in chalcopyrite
AgGaS2 structure. The growth of AgGaInS2 single crystal is two steps. First synthesis of
the polycrystalline material from the starting elements is achieved using melt temperature
oscillation method. Secondly the synthesized material is employed to grow a single
crystal. The crystal AgGaInS2 crystallize with chalcopyrite structure in the space group I42d with unit cell parameters a = b = 5.831 Å, c = 10.876 Å. The synthesized AgGaInS2
polycrystalline charge was confirmed by powder XRD.
Thermal property of AgGaInS2 was analyzed using differential scanning
calorimetry (DSC) technique. The melting point is 896°C and solidification temperature
862°C. The grown crystal was subjected to IR transmission. The transmission in the IR
region is 65%. The band gap energy of the AgGaIns2 single crystal is 2 eV. The
stoichiometric composition of AgGaS2 single crystal was confirmed using energy
dispersive spectrometry (EDS).
C 18
Structural analysis of dihydropyrimidine based organic compounds
1
2
1
Keshab M. Bairagi , Katharigatta N. Venugopala and Susanta K. Nayak *
1
Department of Chemistry, Visvesvaraya National Institute of Technology (VNIT), Nagpur,
Maharashtra-440010, India
2
Department of Biotechnology and Food Technology, Faculty of Applied Sciences, Durban
University of Technology, Durban 4001, South Africa
k100bairagi@gmail.com and nksusa@gmail.com
Dihydropyrimidine (DHPM) is the product of combination of an aldehyde, β-ketoester and urea
under acid catalysis which is well known as Biginelli reaction, was reported by Pietro Biginelli in
1
1983. This one-pot condensation reaction of DHPM products shows interesting pharmacological,
2
calcium channel modulation, antiviral, antibacterial activities and antimicrobial. Further, DHPM
molecules are potentially inhibitor of dihydrofolate reductase, which restricts the thymidine supply to
folate cycle for the inhibition of DNA biosynthesis and influence of cell proliferation, which may be
3
a mechanism to inhibit multidrug resistance tuberculosis(MDR-TB). Recently, our work by some of
the authors on hydrochloride salt of DHPM molecules exhibit promising antitubercular agents
4
against multidrug resistance tuberculosis. In order to evaluate the role of non-covalent interactions
in the molecular assembly of DHPM molecules, a series of compounds were synthesized with
various functionalized aldehyde compounds, the functional groups such as hydroxy, methoxy,
pyridine and/or, chloro. It is interesting to note that the DHPM derivatives prefer dimer formation
through two types of N-H···O hydrogen bonds whereas the three-dimension molecular packing is
decided by the preference of additional non-covalent interactions (hydrogen and/or halogen bonding)
involving the functional substituent's of aldehyde group in DHPM molecule. The biological activity
of these DHPM molecules is under progress to evaluate structure-function relationship.
References
(1)
Kappe, C. O. Eur. J. Med. Chem. 2000, 35 (12), 1043–1052.
(2)
Acharya, B. N.; Rao, G. B. D.; Kumar, D.; Kumar, P.; Kaushik, M. P. Med. Chem. Res. 2014, 24
(4), 1763–1775.
(3)
Then, R. L. J. Chemother. 2004, 16 (1), 3–12.
(4)
Narayanaswamy, V. K.; Nayak, S. K.; Pillay, M.; Prasanna, R.; Coovadia, Y. M.; Odhav, B.
Chem. Biol. Drug Des. 2013, 81 (2), 219–227.
C 19
Crystal and Molecular docking studies of 3-hydroxy-2-((2-hydroxy-4, 4dimethyl- 6-oxocyclohex-1-enyl) (4-methoxyphenyl) methyl)-5,5dimethylcyclohex-2-enone with focal adhesion kinase inhibitors
K S Kiran
1*
1, 2*
2
3
, M K Kokila , Guruprasad R , Prashantha Karunakar
4
Department of physics, School of Engineering and Technology, Jain University, Bangalore,
Karnataka, India
2
Department of physics, Bangalore University, Bangalore, Karnataka, India
3
Scientific Director, Durga Femto Technologies & Research, Bangalore, Karnataka, India
4
Department of Biotechnology, PES University, Bangalore, Karnataka, India.
*Corresponding author: Email: kiranxrd@gmail.com
ABSTRACT
In the present study crystal structure of 3-hydroxy-2-((2-hydroxy-4, 4-dimethyl-6-oxocyclohex1-enyl) (4-methoxyphenyl) methyl)-5, 5-dimethylcyclohex-2-enone was determined using single
crystal X-ray diffraction. Further the structural feature was extrapolated to molecular docking
studies with focal adhesion kinase (FAK) domain using Autodock to study its anticancerous
property. The compound exhibited considerable bacterial inhibition of lower to moderate
concentrations. We conclude that these derivatives can be used in medicine and have enormous
potential as pharmaceutical agents due to their biological activities. The above titled receptor
gain functional and structural insights into their mechanism of inhibition and explore its potential
as an anticancer agent.
Keywords: Bis cyclohexyl diols, Docking, Focal adhesion kinase, anticancer therapy target.
C 20
Synthesis and Crystallographic analysis of fluoro substituted arylidene derivatives
of thiazolopyrimidines
Krishnamurthy M.S. and Noor Shahina Begum*
Department of Studies in Chemistry, Bangalore University, Bangalore- 560 001,
India. noorsb@rediffmail.com and krishnams8@rediffmail.com
In the field of modern medicinal chemistry it has been found that the fluorinated heterocyclic
compounds are of much interest. The study of the influence of aromatic C-F group in directing
crystal packing is a significant area of current research. A number of efforts were made to
synthesize a series of fluoro-substituted arylidene derivatives of thiazolopyrimidines. Elemental
analysis, IR, NMR, mass spectral techniques were used to characterize these compounds. These
compounds were subjected to biological evaluation and were found to have significant activity
against the tested microorganisms. The structures were determined by single crystal X-ray
diffraction method. The crystal packing and molecular structures were mainly stabilized by
intramolecular C-H···S hydrogen bonding and a variety of intermolecular C-H···F, C-H···O, CH···N, C-H···π and π-π interactions leading to the formation of the supramolecular network. It
has been shown that C-H···F interactions can be as important as C-H···O and C-H···N hydrogen
bonds in stabilizing the structure and they have significant ability to direct and alter the
molecular packing.
ORTEP Diagrams
2b
2c
2m
R
1
O
2j
2e
O
O
N
N
2i
S
R2
2g
2f
C 21
Unraveling Charge-transfer Mechanism in Organic NLO Materials via Experimental and
Theoretical Charge Density Analysis
Kunal Kumar Jha, Sanjay Dutta and Parthapratim Munshi*
Department of Chemistry, School of Natural Science, Shiv Nadar University, Tehsil Dadri, Uttar Pradesh201314. E-mail: kk703@snu.edu.in, parthapratim.munshi@snu.edu.in
The understanding of nonlinear polarization mechanism and their relation to the structural characteristics
of nonlinear optical (NLO) materials have been utmost importance considering a surge in the information
technology and industrial applications. Some investigations in search of NLO materials have been carried
out on organic molecule scaffolds such as nitro stilbene having π-eˉ donor (D) acceptor (A) substituent
which facilitates intermolecular charge-transfer; leading to the generation of good frequency conversion
materials [1]. Absence of center of symmetry in a crystal is a must for a material to exhibit second
harmonic generation (SHG). The intermolecular interactions such as C ̶H•••O, C ̶H•••π, C ̶H•••N etc.
present in such D–π–A systems act as a channel for intermolecular charge-transfer. Moreover, the
presence of non-centric crystal fields further facilitates the charge-transfer and hence the dipolar
interactions - leads to the enhancement of dipole moment [2]. In order to elucidate the ambiguity in
charge-transfer mechanism in organic NLO materials, we have considered a series of such compounds for
quantitative analysis using experimental and theoretical charge density analysis [3]. Here we report the
case of (Z)-3-(4-(dimethylamino)phenyl)-2-(4-nitrophenyl)acrylonitrile (NNDM-CNS), a cyano
substituted nitro stilbene derivative (Figure 1), which belongs to the family of D–π–A chromophore and
crystalized in non-centrosymmetric space group, Pn. The presentation will highlight the discussion on
detailed charge density distribution of the molecule, its one-electron properties and correlation of these
results with its NLO behavior. Here we would like to investigate how charge-transfer mechanism can be
understood through charge density analysis.
Figure 1: Static deformation electron density map of NNDM-CNS
References:
1. H. Zhang; Q. Liao; X. wang, Z. Xu; H. Fu. Nanoscale. 7, 2015, 10186.
2. R. S. Gopalan; G. U. Kulkarni; C. N. R. Rao. ChemPhysChem. 1, 2000, 127
3. N. K. Hansen; P. Coppens. Acta Cryst. A34, 1978, 909.
C 22
Powder X-ray diffraction pattern analysis of Hydronium adipate
*
Dr.A.Sinthiya P.Lalitha
Department of Physics, SrimadAndavan Arts and Science College , Trichy 620
005. r.brightson2010@gmail.com
Department of Physics, SrimadAndavan Arts and Science College , Trichy 620 005.
lallipons86@gmail.com
slow evaporation method was used for the synthesis of Hydroniumadipate in
tetragonal crystal system and it was characterized by the powder X-ray diffraction pattern.
Using the X-ray broadening, the crystallite sizes and lattice strain on the peak broadening
were studied by Williamson-Hall plot. The result of mean particle size showed that the
particle size increases with the decrease in breadth (in degrees) with mosaic defect. The size
and strain are analysed using warren-averbach method.
Key words: Hydronium, adipic acid, Williamson-Hall plot, Warren-Averbach.
Warren - Averbach analysis:
Reciprocal Histogram profile:
Strain and size coefficient
Size coefficient
Strain coefficient
strain versus column lengths plot
Log-normal distribution:
References
1.http://www.invista.com/en/brands/adipure.html
2. Warren, B.E. X-ray Diffraction, Addison-Wesley, Reading, 1969.
3. Balzar, D. J. Res. NIST, v. 98, n. 3, p. 321-353, 1993; Balzar, D. CroaticaChemicaActa, v.
69 p. 3, p. 1069-1115, 1996.
4. Enzo, S.; Fagherazzi, G.; Benedeti, A.; Polizzi, S. J. Appl. Cryst., v. 21, p. 536-542, 1988.
1
C 23
Single Crystal Growth, Structural and Physical Characterizations of novel
superconductors and topological insulators
Luminita Harnagea, Giri M, Prachi Telang, Surjeet Singh
luminita@iiserpune.ac.in
We will present our results of the single crystal growth experiments using the hightemperature solution growth and chemical vapour transport methods. Experiments were
carried out on the iron based superconductors; and layered chalcogenides which are expected
to show interesting topological and thermoelectric properties. Specific examples that we will
present include: Superconducting SrFe2As2 co-doped with transition metals Co and Mn at the
Fe site; SnSe which exhibits a record high thermoelectric figure-of-merit exceeding 2.5 above
750 K; SnSe doped with Bi and Zn; and layered VSe2 and VS2. The grown crystals were
rigorously characterized using powder x-ray diffraction, x-ray Laue diffraction, scanning
electron microscope and the associate energy dispersive x-rays analysis for composition
determination. Some interesting doping effects on the physical properties will be presented
briefly.
C 24
Synthesis and Computation of crystallite shape in Silk Films using X-ray
diffraction data
1
1
1
2
1
Mahadevaiah , Thejas Urs.G , M.B.Nanda Prakash , G.K.Gowtham and R.Somashekar *
1
UPE Project, Center for Materials Science, University of Mysore, Vijnana
Bhavan, Manasagangotri, Mysore, Karnataka, India – 570 006.
2
Yuvaraja College, University of Mysore, Mysore 570005. rs@physics.uni-mysore.ac.in
o
We have synthesized silk films by silk fibers using 9.3M lithium bromide solution at 80 C. We
have recorded X-ray powder diffraction data for these films. Using peak fit software; we have
identified nearly fifteen reflections and computed FWHM for these Brags reflections. Using an
in-house program, we have calculated crystallite size and strain for each of these Bragg
reflections. After identifying Miller indices (hkl), we have calculated three dimensional shape of
the crystallite region in these silk films, which is for the first time defined for a polycrystalline
material.
Keywords: Crystallite size, strain, XRD
C 25
Facile formation of core-shell silicon@mesoporous TiO2 heterostructure
and their photoelectrochemical property
†§
Manas Pal,
†
†
†
†
†
Hao Wu, Yunke Jing, Gengfeng Zheng *, and Dongyuan Zhao *
Department of Chemistry, Laboratory of Advanced Materials, Shanghai Key Laboratory of
Molecular Catalysis and Innovative Materials, Collaborative Innovation Center of
Chemistry for Energy Materials (iChEM), Fudan University, Shanghai 200433, P. R. China.
§
Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India. E-mail: manas_chem@yahoo.com (M. P); dyzhao@fudan.edu.cn (D. Z)
Core-shell p-Si@mesoporous n-TiO2 hetero-nanostructure has been successfully fabricated
using facile extended Stöber method. Silver (Ag) metal-assisted chemically wet etched p-type
silicon nanowires (Si NWs) were used as the core, and layer-controllable mesoporous n-type
anatase TiO2 was grown as the shell to successfully fabricate such core-shell p/n type hybrid
nanostructures. As synthesized material was well characterized using different techniques,
which reveal that the TiO2 shell was composed of aggregated crystalline TiO2 nanoparticles
with the diameters of ~15 nm, where the TiO2 coating thickness was tuned ~50 nm. The
interstitial pores of these nanoparticles were observed with average pore sizes of 4~8 nm. The
core-shell structured p-Si@mesoporous n-TiO2 hybrid materials were demonstrated as
photocathodes for the solar-driven photoelectrochemical (PEC) production of H2 at the
semiconductor/electrolyte interface. These results clearly present a cost-effective and facile
method for the fabrication of various semiconducting p/n type hybrid core–shell
nanostructures, which may bring new design opportunities of device configuration for
energy-conversion/storage as well other applications.
Reference
1. L. J. Lauhon, M. S. Gudiksen, D. L. Wang, and C. M. Lieber, Nature 2002, 420, 57–61.
2. W. Li, J. P. Yang, Z. X. Wu, J. Wang, B. Li, S. S. Feng, Y. H. Deng, F. Zhang, and D. Y.
Zhao, J. Am. Chem. Soc. 2012, 134, 11864–11867.
3. Y. C. Wang, J. Tang, Z. Peng, Y. H. Wang, D. Jia, B. Kong, A. A. Elzatahry, D. Y. Zhao,
and G. F. Zheng, Nano Lett. 2014, 14, 3668–3673.
C 26
Crystallite shape computation in four different varieties of cotton fibers using Xray powder diffraction data.
Manju V V
1
2
1,*
1
2
, Divakara S , Thejas Urs G , Somashekhar R
2,3,4
Department of Physics, Vidyavardhaka college of Engineering, Mysuru-570002
Center for Material science, University of Mysore, Vijnana Bhavan, Mysuru-570006,
3
Department of Physics, Regional College of Education, Mysuru570006. *Email: manjuvv10@vvce.ac.in
4
Email:rs@physics.uni-mysore.ac.in
Abstract
Four different varieties of cotton fibers were obtained from farmers and used after cleaning the
fibers physically. X-ray powder diffraction data for these fibers was obtained using imaging plate
system (Dip-3200) with dimension440×240!!!. With the available software, scanning was
carried out along the equator to obtain Intensity versus two-theta and then corrected for
instrumental broadening and Lorentz polarization factors. Using peak-fit program, we have
identified and separated 16 Bragg reflections and from FWHM of these (hkl) reflections, we
have estimated the crystallite size and strain corresponding to various [hkl] directions. From
these data we have suggested a novel method to compute crystallite shape in these cotton fibers
and it is reported for the first time.
C 27
Structure, charge density distribution and the electrostatic properties of
Andrographolide molecule - An experimental and theoretical study
†
‡
†
S. Manjula , C.Kalaiarasi, Mysore S.Pavan and P.Kumaradhas *
†
Laboratory of Biocrystallography and Computational Molecular Biology
Department of Physics, Periyar University, Salem-636 011, India
‡
Solid State and Structural Chemistry Unit, Indian Institute of Science
Bangalore-560 012, India
manjusimba@gmail.com & kumaradhas@yahoo.com
Abstract
Andrographolide is an emerging anti-Hepatitis C viral agent, which blocks the viral replication
by up-regulation of Nrf2-Haeme oxygenase-1 pathway. An experimental charge-density analysis
of Andrographolide has been performed to understand its structure and electronic properties in
the solid state. Andrographolide crystallizes in P21 space group. A high-resolution X-ray
intensity data set has been collected at the low temperature (100 K). The structure was solved by
direct methods using SHELXS97 and refined by SHELXL97. Further, an aspherical multipole
model refinement was carried out using XD2006 software to explore the bond topological and
electrostatic properties of andrographolide molecule. The molecule exhibits a strained geometry
and the structure is stabilized by O‒H···O and C‒H···O types of hydrogen bonding interactions
in the crystal. The topological properties of electron density of andrographolide are determined,
reveals, the charge density distribution of the molecule. The electrostatic properties of the
molecule such as atomic charges, molecular dipole moment and the electrostatic potential are
determined. The topological analysis of electron density of non-covalent bonds has been carried
out, which shows the strength of intermolecular interaction of andrographolide with the
neighboring molecules in the crystal. The dipole moment of the molecule has been calculated
and compared with the corresponding theoretical value. The electrostatic potential surface of the
molecule shows the strong electropositive and negative regions of the molecule. The
experimental results were compared with the corresponding theoretical charge-density analysis
performed using CRYSTAL09.
C 28
Crystallite Shape For Wild Silks Using X-ray Powder Diffration Data
1,**
M B Nandaprakash
1,3
2
, S S Mahesh and R Somashekar
3*
Department of Studies in Physics, University of Mysore, Manasagangotri, Mysuru 570006, India
2
3
Department of Physics, Acharya Institute of Technology, Bangalore 560090, India
Department of Physics, RIE, University of Mysore, Manasagangotri, Mysuru 570006, India
*Corresponding Author: rs@physics.uni-mysore.ac.in
**: npphysics10@gmail.com
Abstract
For the varities of wild silks, we have recorded X-ray powder diffraction data. Using peak fit
and separation softwares, we have separated nearly 44 reflections and computed FWHM for these
Bragg reflections. Using Inhouse program, we have calculated crystallite size and strain for each
one of these reflection. After identifying (hkl) miller indices we have computed shape of the
crystallite region in wild silks for the first time.
C 29
Crystal Structure of (2-Amino-thiazol-4-yl)-acetic acid hydrazide
1
2
3
Pallavi. G.B , Ramakrishna Gowda, K.V Arjuna Gowda, Mahantesha Basanagouda
4
1
P.G Department of Physics, Bharathi College, K M. Doddi, Mandya Dist - 571 401,
Karnataka.
2
Department of Physics, Govt. College for Women, Kolar - 563 101, Karnataka, India.
3
Department of Physics, Govt. College for Women, Mandya-571 401, Karnataka,
4
India. P.G Department of Chemistry, P.C Jabin Science College, Hubli-580 031,
Karnataka, India.
kvarjunagowda@gmail.com
Compound (C5H8N4OS) has been grown by slow evaporation technique using
ethanol, thin plate like single crystals suitable for X-ray diffraction was obtained. The
three dimensional intensity data was collected using a crystal of size 0.35 × 0.20 × 0.25
mm mounted Enhance Mo Kα X-ray Source' (λ = 0.71073 Å) at 293 K temperature. The
data was collected using ω and φ scans mode was in the 2θ range 1.08 to 25°. Among
7518 measured reflections of which 1364 reflections with I > 2σ (I). With h -5 to 5, k 22 to 22, l - 9 to 9. The crystals of the compound crystallize in Monoclinic with space
group P21/c having 4 molecules in the unit cell of dimensions crystal system a =
3
4.96850(10), b = 18.8795(5), c = 8.2913(2) Å, β= 91.448(2) and V= 777.50(3) A˚ .
Multi-scan absorption was carried out using SADABS. The calculated absorption
-1
coefficient was 0.363 mm . The parameters at the end of final refinement were R (F) =
2
0.0303, wR(F ) = 0.0829. The minimum and maximum electron densities from
-3
difference Fourier map are 0.269 and -0.278e.A respectively.
The molecule adopts L shaped conformation. The packing is consolidated by a
very weak NHN and NHO hydrogen bonds.
Figure. ORTEP diagram of the title molecule with 40% probability displacement
ellipsoids with-H atoms.
C 30
Reinvestigation of δ-, η- phase region in the gold-cadmium binary
system: synthesis, crystal structure analysis and thermal stability
1,2
2
Partha Pratim Jana * Sven Lidin
1
Department of Chemistry, Indian Institute of Technology Kharagpur, India -721302
2
Centre for Analysis and Synthesis, Department of Chemistry, Lund University,
Lund, Sweden, Box 124, SE-22100
E-mail: ppj@chem.iitkgp.ernet.in
Cadmium rich phases deserve chemical interest due to its intricate phase relation and
structural complexity. Many cadmium based binary complex intermetallic structures are yet
to be uncovered. Recently, we have been focusing on the Cd-rich phases in the Au−Cd binary
system.
Figure1. Au−Cd phase diagram.1
According to previous reports the existence of δ- phase (δ-, δ´- and δ´´, Au3Cd5) domain in
Au-Cd binary system was known. Among them δ- and δ´- phases correspond to the γ-brass
type phase (Cu5Zn8 type). The structure of the δ´´-phase was not known.1-3 The structure of
Au3Cd5 was previously reported, but the structural refinement led to the residual (R) value of
10%. The existence of η-phase in Au-Cd system was previously mentioned as η-AuCd5 but
the structure was not known to date before our current study .1In this presentation, we will
discuss about the existence, homogeneity range, thermal stability and complete crystal
structure of δ´´- and η-phases, and Au3Cd5 in the Au-Cd binary system.
[1] Okamoto, H.;Massalski, T.B. Bulletin of Alloy Phase Diagrams Vol. 7, No. 1, 1986.
[2] Alasafi, K. M.; Schubert, K. J. Less-Commom Met.1979, 65, 23-28.
[3] Alasafi, K. M.; Schubert, K. J. Less-­‐Common Met. 1977, 51, 225-­‐233. Anomalous volume collapse in pyrochlore Iridate Eu2Ir2O7 upon
C 31
isovalent doping of Bi at the Eu site
Prachi Telang, Kshiti Mishra, Surjeet Singh
Department of Physics, Indian Institute Of Science Education and Research, Pune
411008 prachi.telang@students.iiserpune.ac.in , surjeet.singh@iiserpune.ac.in
Pyrochlore iridates A2Ir2O7 display strong structure-property correlation with changing Asite ionic radius. To carefully study the effect of A-site radius on the properties, a series of
compounds with composition (Eu1-xBix)2Ir2O7 was synthesized where Eu
replaced by bigger Bi
3+
3+
was gradually
ion. Using Rietveld refinement of the powder x-ray diffraction data,
we observed an unexpected collapse of the unit cell volume for Bi concentrations as low as 2
%; for higher doping concentrations (i.e, > 5%), the volume exhibits the expected linear
increase. This anomalous trend appears to be unique to the iridates, since analogously
prepared and studies Bi doped pyrochlore stannate Eu2Sn2O7 exhibit the expected linear
increment in the unit cell volume with increasing dopant concentration. Other physical
properties, namely resistivity and the linear term in the low-temperature specific heat also
exhibit anomalies coinciding with the collapsed state, suggesting a change in the electronic
density of states at the Fermi level. These observations are significant since the title
compound Eu2Ir2O7 has been proposed to be a Weyl semimetal.
.
C 32
Crystal structure of Diethyl 2, 6-dimethyl-4-(naphthalen-1-yl)-1,4
dihydropyridine-3,5-dicarboxylate
Prasad N.L. and Noor Shahina Begum*
Department of Studies in Chemistry, Bangalore University, Bangalore- 560 001,
India. noorsb@rediffmail.com and nlprasad27@gmail.com
1,4-Dihydropyridines (1,4-DHPs) are an important class of chemicals widely used as drugs or
their precursors. 1,4-Dihydropyridine compounds are prescribed for the treatment of
hypertension and heart defibrilation. Dihydropyridines (DHPs), in particular 4-aryl-substituted
1,4-dihydropyridines (Hantzsch esters), have been recognized as an important class of organic
calcium channel modulators for the treatment of cardiovascular diseases. Herein, we report the
crystal structure of the “Diethyl 2,6-dimethyl-4-(naphthalen-1-yl)-1,4 dihydropyridine-3,5
dicarboxylate” compound. The compound crystallizes in the monoclinic space group P21 with a=
3
8.7072(2) Å, b= 9.8740(2) Å, c= 11.221(2) Å, β= 95.307(6)°, V= 960.6 (3) Å , Z=2.
The crystal structure of the compound C23H25NO4, is stabilized by intermolecular CH···O and N-H···O interactions.
Fig.1: ORTEP diagram.
Fig.2: Crystal packing diagram.
C 33
Single crystal growth in travelling-solvent floating-zone method of Spin
Chains SrCuO2, Sr2CuO3 and Spin Ladders Sr14Cu24O41
Rabindranath Bag, Koushik Karmakar and Surjeet Singh*
Indian Institute of Science Education and Research,Pune.
*Email: surjeet.singh@iiserpune.ac.in
Developments in travelling solvent floating zone (TSFZ) method associated with an image
furnace over last 2 decades has made it possible to grow large and high-quality single crystals
of incongruently melting compounds that cannot otherwise be grown in sufficiently large
size. Since the flux-method, which is the only other viable growth method for obtaining
crystals of incongruent melting compounds, is often faced with problem of flux inclusion in
the grown crystal. Even smallest amount of flux or the crucible material incorporated in the
crystal is undesirable when studying the effect of dilute doping. Flux growth is also
undesirable in view of the size of the grown crystals, which is often small –not suitable for
such experiments as inelastic neutron scattering (INS) where the low-energy spin excitations
can be probed with unprecedented accuracy.
We show here our results of TSFZ growth of incongruently melting cuprates: Sr2CuO3,
SrCuO2 and Sr14Cu24O41 doped with various types of dopants in very dilute quantities to
probe the low-energy spin excitations using INS. We have grown crystals of these
compounds using TSFZ method with dilute doping of Co, Ni and Zn at the Cu-site. We show
that novel ground states and spin excitation, not present in the pristine compounds, can be
induced by dilute doping in these quantum magnets. The study is a part of a larger research
program on low-dimensional quantum magnets in our research group at IISER Pune.
K.Karmakar et al. Crystal Growth and Des. 14(3), 1184-1192, (2014).
2. K. Karmakar et al. Crystal Growth Des. 15(10), 4843-4853, (2015).
3. K. Karmakar at al. Phys. Rev. B 91(22), 224401, (2015).
4. R. Bag et al. Journal of Cryst. Growth. (2016) (unpublished).
5. K. Karmakar et al. arXiv:1602.03677 (2016).
1.
C 34
2D COF as Heterogeneous Catalyst for Control Oxidation of Benzyl Alcohols
Rajiv Khatioda, Dhrubajyoti Talukdar, Basanta Saikia and Bipul Sarma*
Department of Chemical Sciences, Tezpur University, Napaam-784028, Assam, India
E-mail: sarmabipul@gmail.com
A two dimensional covalent organic framework (COF) with carboxamide functionality has been
synthesized and characterized by thermal analysis, spectroscopic techniques and X-ray
diffraction. The porosity and rigidity of the material was confirmed with BET surface analyzer.
The material was then subjected as a catalyst for the oxidation of substituted benzyl alcohols to
their corresponding aldehydes. Remarkable selectivity as heterogeneous catalyst is reported. The
results are further supported by DFT calculations.
CH2OH
R
CHO
B
H
TB
P
T
ly
s
t
a
t
a
C
R
Zero Yield
70 - 90 % Yield
Figure 1. Pore size distribution of Scheme 1. Oxidation of benzyl alcohols. synthesized
COF.
Reference:
1. Ding, S. Y.; Gao, J.; Wang, Q.; Zhang, Y.; Song, W. G.; Su, C. Y.; Wang, W. J. Am.
Chem. Soc. 2011, 133, 19816.
2. Wu, Y.; Xu, H.; Chen, X.; Gao, J.; Jiang, D. Chem. Commun. 2015, 51, 10096.
3. Khatioda, R.; Talukdar, D.; Saikia, B.; Sarma, B. (Manuscript in preparation, 2016).
C 35
Crystal Structure of 7, 8-Benzocoumarin-4-acetic acid
1
2
3
N.Ramprasad , Ramakrishna Gowda, K.V Arjuna Gowda, Mahantesha
4
Basanagouda
1
Department of Physics, Govt. First Grade College, Mulbagal, Kolar Dist - 563 131,
Karnataka.
2
Department of Physics, Govt. College for Women, Kolar - 563 101, Karnataka, India.
3
Department of Physics, Govt. College for Women, Mandya-571 401, Karnataka,
4
India. P.G Department of Chemistry, P.C Jabin Science College, Hubli-580 031,
Karnataka, India.
rkgowdaphy@gmail.com
Compound (C15H10O4) has been grown by slow evaporation technique using
ethanol thin plate like single crystals suitable for X-ray diffraction was obtained. The
three dimensional intensity data was collected using crystal of size 0.35 × 0.20 × 0.25
mm mounted Enhance Mo Kα X-ray Source' (λ = 0.71073 Å) at 293 K temperature. The
data was collected using ω and φ scans mode was in the 2θ range 2.64 to 26.96°.
Among 2001 measured reflections of which 1356 reflections with I > 2σ (I). With h -15
to 14, k -10 to 10, l - 22 to 22. The crystals of the compound crystallize in orthorhombic
with space group Pbca having 8 molecules in the unit cell of dimensions crystal system
3
a = 13.4231(4), b = 8.9892(3), c = 18.8407(6) Å and V= 2273.37(12) A˚ . Multi-scan
absorption was carried out using SADABS. The calculated absorption coefficient was
-1
2
0.612 mm . The parameters at the end of final refinement were R (F) = 0.0441, wR (F )
= 0.1375. The minimum and maximum electron densities from difference Fourier map
are 0.8843 and 0.9832 e.A
-3
respectively.The fused-ring system of the title compound
[systematic name:2-(2-oxo-2H-benzo[h]chromen-4-yl) acetic acid], C15H10O4, is
almost planar (r.m.s. deviation = 0.031 A ˚) and the Car—C—C O (ar = aromatic)
o
torsion angle for the side chain is 134.4 (3) . In the crystal,
molecules are linked by OHO hydrogen bonds,
generating [100] C(8) chains, where the acceptor
atom is the exocyclic O atom of the fused-ring
system. The packing is consolidated by a very
weak CHO hydrogen bond to the same acceptor
atom.
Figure: ORTEP diagram of the title molecule with 40% probability
displacement ellipsoids with-H atoms.
C 36
Investigation of binding behavior of p-sulfonatocalix[4]arene with quinoline in the
solid state
,
a
a
a a
Rupali Thorave , Ankita Jadhav , Asmita Jarange , Dipalee Malkhede * Department
of Chemistry Savitribai Phule Pune University, Ganeshkhind-411007, Pune, India.
Quinoline nucleus occurs in several natural compounds (Cinchona Alkaloids) and
1
pharmacologically active substances for new drug development, displaying a broad range of
biological activity. Single crystal structure for p-SC4-Q system is present in flattened cone
conformation. The quinoline molecule is encapsulated in the cavity of p-sulfonatocalix[4]arene
by one face to face π-π interaction between them and two CH- π interactions (distances are 2.516
A
0
and 2.5 A
0
respectively). p-sulfonatocalix[4]arene (p-SC4) is becoming increasingly
important in the field of supramolecular chemistry and crystal engineering. Therefore, in the
present study we have estimated a complete study of biologically important quinoline and psulfonatocalix[n]arenes using NMR and single-crystal data which supported location of
complexation. The presence of hydrogen bonding due to the hydroxyl group at lower rim of
calixarenes and hydrogen bonding due to -SO3 at upper rim through water molecule strongly
govern for stability of complexation as observed in single crystal.
(a) p-SC4
(b) Quinoline
Figure: Crystal structure of p-SC4 with Quinoline
References
1.
O. Shkurenko, K. Suwinska, A. W. Coleman, Cryst. Eng. Comm., 2008, 10, 821-823.
2.
B. Lesniewska, O. Danylyuk. K. Suwinska, T. Wojciechowski, A. W. Coleman,
CryEngComm., 2011, 13, 3265-3272.
3.
F. Perret, A. N. Lazar, A. W. Coleman, Chem. Commun., 2006, 2425-2438.
C 37
Synthesis, Growth and Characterzation of 2-((1H-benzo[d]imidazol-2-yl)
amino)-1-phenylethan-1-one (C15 H13 N3 O) single crystal
K. Saiadali Fathima and K. Anitha
School of Physics, Madurai Kamaraj University, Madurai-625021, India
fathimaphy8@gmail.com
Benzimidazoles and its derivatives play an important role in analysis of several biological
reactions as antibacterial, pharmaceutical products and polymers. In this work, the synthesis,
growth and vibrational spectra of the title compound (C15 H13 N3 O) were reported. The
novel organic material (C15 H13 N3 O) was synthesized and single crystals were grown by
slow evaporation solution growth technique. The cell parameter and crystal system were
determined using single crystal X-Ray diffraction method. It belongs to monoclinic system
ο
1
with cell parameter a= 9.719 (4) Å, b= 21.556 (9) Å, c= 9.847(4) Å, β= 95.09 Å. In H
NMR, CH2 band appeared at 3.65ppm and
13
C NMR, carbonyl (C=O) appeared at 195ppm.
+1
-1
The mass spectrum shows a molecular peak (m ) at 252.12 m/z. The FTIR (400-4000 cm )
-1
and FT-Raman (500-4000 cm ) of title compound shown that the γ(C=N) and γ(C=O) bands
were shifted to higher wavenumber. The absorptions of crystal was studied by UV-Vis
spectrum showed a band at 277 nm due to π-π* transition and a band at 515nm due to n-π*
transition. Using these chacterizations the structure of the title compound was conformed.
Further the antimicrobial activity of complex against klebsiella pneumonia, bacillus subtilis
and MRSA pathogens was investigated. So the complex molecule inhibits both Gram positive
and Gram negative bacterial. It can be a lead compound in future since it’s having
antimicrobial activity due to the presence of imidazole moiety.
Supramolecular Self-Assembled Motifs
Sakharam B. Tayade, Avinash S. Kumbhar
C 38
*
Department of Chemistry, Savitribai Phule Pune University, Pune-411007,
India. askum@chem.unipune.ac.in and tayadesb@gmail.com
Supramolecules are formed by the intermolecular interactions such as hydrogen bonds, π-π
interactions, van der Waals interactions, cation-π interactions and metal-ligand coordination
bonds. Weak intermolecular forces have been intentionally used in for connecting coordination
compounds into a wide variety of extended networks. Metallosupramolecules are constructed
mainly by coordination bonds between metal ions and ligands, together with intermolecular
interactions. The goals for construction of metallosupramolecular networks are to obtain the
materials that show specific or multifunctional properties such as molecular adsorption,
separation processes, catalysis, sensor technology and opto-electronics. Following this rationale,
we have exploited the use of a self-complimentary motif bipyridine-glycoluril (BPG) which is
capable of coordinating with metal ions as well as to generate self-assembled supramolecular
synthons. Concurrent with our interest in the supramolecular synthons, and to explore the
variations in the structures and their applications formed by using different metals and ancillary
ligands, herein, we present potential of BPG ligand to act as versatile tecton which forms a
supramolecular self-assembled frameworks of different metals.
References
1. M. S. Deshpande, A. S. Kumbhar, V. G. Puranik Cryst. Growth Des., 2008, 8, 1952.
2. V. A. Kawade, A. S. Kumbhar, A. Erxleben, P. Pachfule, R. Banerjee CrystEngComm, 2011, 13, 5289.
C 39
Quinoline-Based Reversible Turn-on Fluorescent Probe: Detection of Acids in
Solution and Vapor-state
Samir. R. Shaikh, R. L. Gawade, P. V. Joshi,A. L. Chandanshiv and R. G. Gonnade
Center for Materials Characterization, CSIR-National Chemical Laboratory, Pune - 411
008, India.
E-mail: sr.shaikh@ncl.res.in
Designing of effective alarming system for the detection of toxic volatile chemicals
into our environment is one of the major research objective. Hazardous chemicals are mostly
acidic toxins such as nerve agents, blood chocking agents and leaked acid vapors or mist in
the industries. To date many methods have been reported for detecting acidic toxins in
solution and solid-state, however, turn-on fluorescent organic probes are advantageous due to
their rapid and naked eye response to the analyte. Extensively conjugated 8a-azoniaacridine is
widely used as fluorescent probe for the detection of small chemicals and biomolecules. Most
of these fluorescent organic conjugated compounds consists of acid responsive component
(ARC) and fluorescent component (FC).
Designing Strategy Combinatorial approach was adopted to design fluorescent
organic compounds containing ARC and FC to favour insitu generation of acid responsive
8a-azoniaacridine salts. In the present study we have successfully designed and synthesized
quinoline-benzophenone conjugated system for detecting acid vapors and analysed by
relevant characterisation tools and methods.
C 40
Supramolecular π-π and C-H--π interactions in Mn(II) and Zn(II) coordination
solids involving pyrazolyl and bipyridyl ligands.
Sanjib Chetry, Anshuman Gogoi and Manjit K. Bhattacharyya*
Department of Chemistry, Cotton College, Guwahati-781001, Assam, India
Author email: snjbchetry@gmail.com
*Corresponding author email: manjitbhattacharyya@yahoo.com
Abstract
Noncovalent interactions between the molecules are weak intermolecular forces that
plays a pivotal role in biological systems and governs the physicochemical properties of
molecular systems in condensed phase.
1,2,3
Pyrazole and bipyridyl ligands are a good
candidate in building supramolecular systems because they effectively incorporate their
nitrogen moiety for coordination with metal ions, and may provide supramolecular interaction
sites for molecular recognition
4,5
.
Two new coordination solids, [Zn(Hdmpz)2Cl2] (1) and [Mn(bpy)(C6H5COO)2(H2O)]
(2) [bpy = 2´,2´-bipyridyl and Hdmpz = 3,5-dimethylpyrazole] have been synthesized and
characterized by FT-IR, UV-vis and single crystal XRD techniques. Weak interactions viz π-
π stacking, C-H···π contact, C-H···Cl and N-H···Cl hydrogen bonding interactions stabilizes
the supramolecular architectures of the compounds. The structure, thermal stability,
bioactivity and magnetic behavior of the compounds have been investigated.
Fig1: Crystal structure of 1
Fig 2: π-π and C-H···π stacking interactions in 2
References:
1. Netto, Adelino V. Godoy., Frem, Regina C.G., Mauro, Antonio E., Almeida, Eduardo T. de., Santana, Anderson M.,
de Souza, Jaime Jr., Santos, Regina H.A.; Inorganica Chimica Acta. 2003, 252.
2. Seth, Saikat Kumar., Saha, Indranil., Estarellas, Carolina., Frontera, Antonio., Kar, Tanusree., Mukhopadhyay, Subrata.;
Cryst. Growth Des. 2011, 3250.
3. Jin, Shou-Wen., Ye, Xiang-Hang., Jin, Li., Zheng, Lu., Li, Jing-Wen., Jin, Bin-Peng., Wang, Da-Qi.; Polyhedron. 2014,
382.
4. Guerrero, Miguel., Pons, Josefina., Bardia, Mercè Font., Calvet, Teresa., Josep, Ros.; Polyhedron .2010, 1083.
5. Ye, Bao-Hui., Tong, Ming-Liang.,Chen, Xiao-Ming.; Coordination Chemistry Reviews. 2005, 545.
C 41
Molecular self-assembly in [2]catenanes obtained via the mechanical
interlocking of D-shaped macrocycles
Shobhana Krishnaswamy and Dillip Kumar Chand
Department of Chemistry, Indian Institute of Technology, Madras 600036, India.
E-mail: cy14ipf04@smail.iitm.ac.in, dillip@iitm.ac.in
[2]Catenanes are mechanically interlocked molecules with intriguing structures and potential
1
2
applications as molecular machines. Transition metal driven self-assembly can be used for
the synthesis of such interlocked species due to well defined metal-ligand coordination
bonding which, when combined with simple synthetic procedures results in supramolecules in
3
high yield. Suitable pyridyl appended ester or amide ligands (L1), a linear pyridyl spacer
(L2) and cis-protected Pd(II) units [Pd(L′)(NO3)2] (L′ = ethylenediamine; tetramethyl
ethylenediamine; 2,2′-bipyridine; 1,10-phenanthroline) when combined in water yield a
concentration dependent equilibrating mixture of the macrocycle [Pd2(L′)2(L1)(L2)](NO3)4
and the [2]catenane [Pd2(L′)2(L1)(L2)]2(NO3)8. Reaction in DMSO yielded the
4
corresponding macrocycle as the sole product. A comparison of the crystal structures and
molecular packing of the [2]catenanes (2) and the D-shaped macrocycle (1) will be presented.
References
1. B. Champin, P. Mobian and J.-P. Sauvage, Chem. Soc. Rev., 2007, 36, 358-366.
2. N. B. Debata, D. Tripathy and D. K. Chand, Coord. Chem. Rev., 2012, 256, 1831-1945.
3. M. Fujita, Acc. Chem. Res., 1999, 32, 53–61.
4. S. Prusty, S. Krishnaswamy, S. Bandi, C. Baby, J. Luo, J. S. McIndoe, G. S. Hanan and D.
K. Chand, Chem. Eur. J., 2015, 21, 15174-15187.
C 42
Self-Exfoliated Guanidinium-Based Ionic Covalent Organic Nanosheets (iCONs)
a
a
Shouvik Mitra, Rahul Banerjee *
a
Physical/Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, 411008,
India.
Abstract
Covalent organic nanosheets (CONs) have emerged as functional two dimensional materials for
versatile applications. Although π-π stacking between layers, hydrolytic instability, possible
restacking prevents their exfoliation on to few thin layered CONs from crystalline porous
polymers. We anticipated rational designing of a structure by intrinsic ionic linker could be the
solution to produce self-exfoliated CONs without external stimuli. In an attempt to address this
issue, we have synthesized three self-exfoliated guanidinium halide based ionic covalent organic
nanosheets (iCONs) with antimicrobial property. Self-exfoliation phenomenon has been
supported by molecular dynamics (MD) simulation as well. Intrinsic ionic guanidinium unit
plays the pivotal role for both self-exfoliation and antibacterial property against both grampositive and gram-negative bacteria. Using such iCONs we have devised mixed matrix
membrane which could be useful for antimicrobial coatings with plausible medical benefits.
C 43
Molecular Salt Hydrate of an Anticancer Drug Gefitinib and a Loop Diuretic Drug
Furosemide: An Alternative for Multidrug Treatment
Shridhar H. Thorat, Sanjay Kumar Sahu, Manjusha V. Patwadkar, Manohar V. Badiger and
Rajesh G. Gonnade*
Center for Materials Characterization, CSIR-National Chemical Laboratory, Pune - 411 008,
India.
E-mail: sh.thorat@ncl.res.in
Constant and consistent attempt to develop active pharmaceutical ingredient (API)
cocrystals with suitable cocrystal excipient is gaining widespread research interest because of its
exploitation in tuning the physicochemical properties of an API. Multi API cocrystals have
potential relevance in the context of delivery of combination drug that can be experimented to
prevail over the issues associated with traditional combination drugs. Gefitinib, an anticancer
drug used in treatment of lung cancer has some serious side effects such as diarrhea, rash, acne,
dry skin, nausea, vomiting, and interstitial lung disease. To overcome the effect of kidney
toxicity and hypertension caused by gefitinib, there is a need of combination drugs therapy. We
chose furosemide, a loop diuretic drug used for the treatment of hypertension and edema as
cocrystal former. A 1:1 monohydrate salt of gefitinib and furosemide has been prepared by
solution crystallization. The cocrystal crystallized in triclinic P-1 space group. The remarkable
stability of the salt hydrate could be attributed to the strong hydrogen bonding interactions in the
crystal structure. The release of water from the lattice at 140°C produced new anhydrous salt that
has better solubility and dissolution rate than salt hydrate. The drug–drug molecular salt may
have some bearing on the treatment of patient suffering from anticancer and hypertension.
A single-ligand ultra-microporous MOF for pre-combustion CO2 capture
C 44
and hydrogen purification
Shyamapada Nandi, Phil De Luna, Thomas D. Daff, Jens Rother, Ming Liu,
*
William Buchanan, Ayman I. Hawari, Tom K. Woo, and Ramanathan
Vaidhyanathan
*
Email of the presenting author: shyamapada.nandi@students.iiserpune.ac.in
Email of the corresponding authors: vaidhya@iiserpune.ac.in & twoo@uottawa.ca
Abstract: Metal organic frameworks (MOFs) built from a single small ligand typically have
high stability, are rigid, and have syntheses that are often simple and easily scalable.
However, they are normally ultra-microporous and do not have large surface areas amenable
to gas separation applications. We report an ultra-microporous (3.5 and 4.8 Å pores) Ni-(4pyridylcarboxylate)2 with a cubic framework that exhibits exceptionally high CO2/H2
selectivities (285 for 20:80 and 230 for 40:60 mixtures at 10 bar, 40°C) and working
capacities (3.95 mmol/g), making it suitable for hydrogen purification under typical
precombustion CO2 capture conditions (1- to 10-bar pressure swing). It exhibits facile CO2
adsorption-desorption cycling and has CO2 self-diffusivities of ~3 × 10
−9
2
m /s, which is two
orders higher than that of zeolite 13X and comparable to other top-performing MOFs for this
application. Simulations reveal a high density of binding sites that allow for favorable CO2CO2 interactions and large cooperative binding energies. Ultra-microspores generated by a
small ligand ensure hydrolytic, hydrostatic stabilities, shelf life, and stability toward humid
gas streams.
References:
1) Nandi et al. Sci. Adv. 2015; 1:e1500421
2) Herm et al. J. Am. Chem. Soc. 2011; 133, 5664.
C 45
Relieving Geometrical frustration through doping in the
Dy1-xCaxBaCo4O7 Swedenborgites
1
1
1,2
Soumendra Nath Panja , Jitender Kumar , Shanu Dengre, & Sunil Nair
1
Department of Physics, Indian Institute of Science Education and Research,
2
Centre for Energy Science, Indian Institute of Science Education and
Research, Dr. Homi Bhabha Road, Pune, Maharashtra-411008, India
Email: soumendra.panja@students.iiserpune.ac.in ; sunil@iiserpune.ac.in
The geometrically frustrated antiferromagnetic Swedenborgite DyBaCo4O7 is investigated by
a combination of X-ray diffraction, magnetization and dielectric measurements. Systematic doping in
the series Dy1-xCaxBaCo4O7 causes a lifting of the geometrical frustration resulting in a structural
transition from a Trigonal P31c to an orthorhombic Pbn21 symmetry at x = 0.4. This structural
transition can also be accessed as a function of temperature, and all our orthorhombic specimens
exhibit this transition at elevated temperatures. In line with previous reports, the temperature at
which this structural transition occurs scales linearly with the mean ionic radii of the A site ion.
However, CaBaCo4O7 which has an equal number of Co
2+
and Co
3+
ions clearly violates this
quasilinear relationship, indicating that charge ordering could also play a critical role in stabilizing
the orthorhombic distortion in this system. Using thermoremanent magnetization measurements to
circumvent the problem of the large paramagnetic background arising from Dy
the phase diagram of the Dy1-xCaxBaCo4O7 series.
3+
ions, we chart out
C 46
Phosphoric Acid Loaded Covalent Organic Frameworks as Proton
Conducting Materials
Suman Chandra, Tanay Kundu and Rahul Banerjee.
Physical/Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi
Bhabha Road, Pune 411008, India.
E-mail id: sg.chandra@ncl.res.in.
Two new chemically stable functional crystalline covalent organic frameworkds (COFs)
(Tp-Azo and Tp-Stb) were synthesized using the Schiff base reaction between
triformylphloroglucinol (Tp) and 4,4′-azodianiline (Azo) or 4,4′-diaminostilbene (Stb),
respectively. Both COFs show the expected keto-enamine form, and high stability towards
boiling water, strong acidic, and basic media. H3PO4 doping in Tp-Azo leads to
immobilization of the acid within the porous framework, which facilitates proton
conduction in both the hydrous (σ = 9.9×10
−4
−1
Scm ) and anhydrous state (σ = 6.7×10
−5
−1
Scm ). This report constitutes the first emergence of COFs as proton conducting
materials.
(a) Schematic of H3PO4 doping in COFs. Proton conductivity of PA@Tp-Azo in (b)
anhydrous and (c) hydrous conditions. (d) Proton conductivity of PA@Tp-Stb in
hydrous conditions. (e) Arrhenius plot for PA@Tp-Azo in hydrous conditions.
References
(1) Kandambeth, S.; Mallick, A.; Lukose, B.; Mane, M. V.; Heine, T.; Banerjee, R. J.
Am. Chem. Soc. 2012, 134, 19524.
(2) Chandra, S.; Kundu, T.; Kandambeth, S.; BabaRao, R.; Marathe, Y.; Kunjir, S.M ; Banerjee, R. J. Am. Chem. Soc. 2014, 136, 6570. (3) Xu, H.; Jiang, D. Nature Chemistry.2014, 6, 564. C 47
Quantitative Analysis of Hydrogen Bonding in Proteins: A Charge Density Database
Transfer Approach
a
b
a
Suman Kumar Mandal , Benoit Guillot and Parthapratim Munshi ,*
a
Department of Chemistry, School of Natural Science, Shiv Nadar University, Dadri, Uttar Pradesh201314, INDIA.
b
Laboratoire de Cristallographie, Institut Jean Barriol, Université de Lorraine, 34 Cours
Léopold, 54000 Nancy, France
E-mails: sk225@snu.edu.in; parthapratim.munshi@snu.edu.in
The function of a protein is determined by its structure. During the folding process, the nonpolar side
chains get buried due to hydrophobic effects and the main-chains form N-H···O=C hydrogen bonds.
Experimental1 and theoretical2 evidences claim that the electrostatic energy term of hydrogen bonding
energy predominates during the folding to stabilize protein. The major hydrogen bonding in globular
protein occurs between the main-chain N-H and C=O groups, which are the key building blocks of both
a-helix and β-sheet structures. Knowledge of such hydrogen bonding networks and the local
electrostatics in proteins is essential for proper thermodynamic modeling, prediction of protein folding
pathways and binding interactions. Research in the area of protein charge density analysis has recently
been stimulated particularly with the interest in the topological analysis of hydrogen bonds, proteinligand interactions and their electrostatics.3 In this presentation we will discuss the energetics involved
in the formation of N-H···O=C hydrogen bonds present in the a-helices and β-sheets. The estimates are
based on the studies of several high-resolution X-ray protein structures as deposited in the Protein Data
Bank and their charge density models constructed via ELMAM-2 database4 transfer. The results from
this novel approach revealed the unusual trend in the variation of electrostatic energies with the
variation of H-bonds and their angles and also with the bonding electron densities.
References:
1. Rose, G. D., Fleming, P. J., Banavar, R. J., Maritan, A. Proc. Natl. Acad. Sci., 2006, 103, 16623.
2. Kyte, J. Structure in Protein Chemistry (Garland Science, New York, 2007).
3. Fournier B, Bendeif EE, Guillot B, Podjarny A, Lecomte C, Jelsch C. J. Am. Chem. Soc, 2009, 131,
10929–10941.
4. S. Domagala, B. Fournier, D. Liebschner, B. Guillot and C. Jelsch, Acta Cryst. 2012, A68, 337-351
C 48
Supramolecular Engineering of Guest-Adaptable Porous Organic Frame
Work for Ammonia and Reaction Intermediates Trapping
Suresh Madhu, R.G. Gonnade, Tamal Das, Kumar Vanka, Gangadhar J. Sanjayan
*
Organic Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr.
HomiBhabha Road, Pune 411008, India.
E-­‐mail: m.suresh@ncl.res.in, gj.sanjayan@ncl.res.in
Abstract
We report a novel class of multiple hydrogen bonded hexaphenylbenzene (HPB)-based
supramolecular sponge which is shown to trap a variety of guest molecules including
ammonia and reaction intermediates in its crystal lattice. The porous frame work is formed
via co-operative interplay of hydrogen bonding and backbone rigidity of HPB. Out of all
multiple hydrogen bonding sites present in the HPB core, some are involved in the porous
network formation and the rest participate in the capture of guest molecules. The nature of the
network and porosity depend on the solvent system and condition which are used for
crystallisation (adaptive porosity). The structural and spongy nature of the materials were
unambiguously characterised using single crystal X-ray crystallography. The ammonia
holding ability of the HPB has been characterised by TGA, IR, and other experiments.
Further, the type of binding and interactions between the host and guest molecules (ammonia)
in the presence of methanol, dioxane were investigated by employing density functional
theory (DFT).
C 49
In situ cryocrystallography of low melting halogen-bonded complexes
1,2
Susanta K. Nayak
1
1
1
, Giancarlo Terraneo , Pierangelo Metrangolo and Giuseppe Resnati
1
NFMLab, Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”,
Politecnico di Milano, IIT-CNST@POLIMI, via L. Mancinelli 7, Milan-20131, Italy
2
Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur
440010, Maharashtra, India (Current affiliation)
nksusa@gmail.com; sknayak@chm.vnit.ac.in
In situ cryocrystallisation technique offers a unique opportunity to crystallize low
melting compounds at low temperature. Boese, Guru Row and others have proven the
potential of this technique in the study of weak and elusive interactions.
1–4
In the last decade
halogen bond (XB) has emerged as an effective and useful non-covalent interaction of wide
use in several fields of supramolecular chemistry which occurs when there is evidence of a net
attractive interaction between an electrophilic region associated with a halogen atom in a
5
molecular entity and a nucleophilic region in another, or the same molecular entity. In
particular, the robust C-X•••N XB (X = I, Br or Cl) supramolecular synthons have been
frequently used in the crystal engineering of organic co-crystals. However, it was observed
from the Cambridge Structural Database (CSD), C-X•••O (X = Br or Cl) interactions are
typical weak XBs to influence the crystal packing and this XB synthon can be hardly surmised
from these structures as most of them obtained serendipitously and/or involve quite complex
3
and random molecules. This presentation will highlight the importance of the ability of CBr•••O supramolecular synthons to promote molecular recognition and self-assembly
processes using in situ cryocrystallization technique in low melting adducts formed by some
commonly used solvents containing a carbonyl, sulphinyl or phosphoryl moiety with the liquid
dibromoperfluoroarene or dihaloperfluoroalkanes .
6,7
References
(1) Chopra, D.; Row, T. N. G. J. Indian Inst. Sci. 2013, 87 (2), 167.
(2) Choudhury, A. R.; Winterton, N.; Steiner, A.; Cooper, A. I.; Johnson, K. A. J. Am.
Chem. Soc. 2005, 127 (48), 16792–16793.
(3) Kirchner, M. T.; Bläser, D.; Boese, R. Chemistry 2010, 16 (7), 2131–2146.
(4) Yufit, D. S.; Howard, J. A. K. CrystEngComm 2010, 12 (3), 737–741.
(5) Desiraju, G. R.; Ho, P. S.; Kloo, L.; Legon, A. C.; Marquardt, R.; Metrangolo, P.;
Politzer, P.; Resnati, G.; Rissanen, K. Pure Appl. Chem. 2013, 85 (8), 1711–1713.
(6) Nayak, S. K.; Terraneo, G.; Forni, A.; Metrangolo, P.; Resnati, G. CrystEngComm 2012,
14 (13), 4259–4261.
(7) Bertolotti, F.; Cavallo, G.; Metrangolo, P.; Nayak, S. K.; Resnati, G.; Terraneo, G.
Supramol. Chem. 2013, 25 (9-11), 718–727.
C 50
Three Oxime Ethers: Structural Characterization with Single- and PowderCrystal X-ray Diffraction and Molecular Electrostatic Potential Calculations
Tanusri Dey and Alok Kumar Mukherjee
Department of Physics, Jadavpur University, Kolkata 700032, India
E-mail: tobli.ju@gmail.com
Crystal structures of three oxime ether derivatives, (E)-3-methoxy-4-(prop-2-ynyloxy)benzaldehyde-O-prop-2-ynyl-oxime (C14H13NO3) (1), benzophenone-O-prop-2-ynyl-oxime
(C16H13NO) (2) and (E)-2-chloro-6-methylquinoline-3-carbaldehyde-O-prop-2-ynyl-oxime
(C14H11ClN2O) (3), have been determined using single-crystal X-ray diffractometry with MoKα
radiation (λ = 0.7107 Å) for 1 and X-ray powder diffraction with CuKα radiation (λ = 1.5418 Å)
for 2 and 3. While compounds 1 and 3 crystallized in C2/c and P1 space groups, respectively,
having one molecule in the asymmetric unit, that of 2 crystallized in space group P21 with two
molecules in the asymmetric unit. The DFT optimized molecular geometry in 1-3 agrees closely
with that obtained from the crystallographic analysis. The nature of intermolecular interactions in
1-3 has been analyzed through Hirshfeld surface and two dimensional fingerprint plot
description. The crystal packing in 1-3 is influenced by weak hydrogen bonds and π···π
interactions, which assemble molecules into supramolecular framework. Hydrogen bond based
interactions in 1 and 3 have been complemented by calculating the molecular electrostatic
potential (MEP) surfaces. Hirshfeld surface analyses of 1-3 as well as a few related oxime ether
derivatives retrieved from the Cambridge Structural Database (CSD) indicate that about 60% of
the Hirshfeld surface areas in these compounds are due to H···H and C···H contacts.
Final Rietveld plots of C16H13NO (2) and C14H11ClN2O (3)
C 51
Solvent Induced Unusual 2D to 3D Transformation in a Zn(II)-Framework
via SC-SC Fashion
Vivekanand Sharma, Dinesh De and Parimal K. Bharadwaj*
Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016
Email: vivekshr@iitk.ac.in; pkb@iitk.ac.in*
Metal-organic frameworks (MOFs) are a class of hybrid supramolecular solid
1
materials comprised of organized organic linkers and metal cations. They have great
contemporary interest not only owing to the fact that their fascinating variety of architectures
and topologies but also their extensive application in gas storage, catalysis, separation and
2
drug delivery. Single-crystal-to-single-crystal (SC-SC) structural transformations in MOFs
have received considerable attention in recent years for the development of new and useful
3
materials that may not be accessible ab initio. Although it occurs rarely, in spite of this, one
of the primary goal of crystal engineering is to obtain this astonishing phenomenon. It opens a
door to understand the structure-function relationship happens at the molecular level.
However, the researches on the SC-SC transformations in MOFs are still limited since it is
difficult to retain single crystallinity after the solid-state rearrangement.
Here, we have synthesized a 2D layered Zn(II)-framework using a novel
dicarboxylate ligand and hexamine co-linker having [Zn3(COO)6] SBU. An unprecedented
linker substitution reaction is observed which facilitates the formation of a 3D framework
from a 2D framework. During this substitution reaction the trinuclear [Zn3(COO)6] SBU has
been changed to a mononuclear SBU. This transformation takes place without losing
crystallinity and can be observed directly via X-ray crystallography.
References
1. Zhou, H. C.; Long, J. R.; Yaghi, O. M. Chem. Rev. 2012, 112, 673−674.
2. Furukawa, H.; Cordova, Kyle E.; O’Keeffe, M.; Yaghi, Omar M. Science 2013, 341,
1230444
3. Deria, Pravas.; Mondloch, Joseph E.; Karagiaridi, Olga.; Bury, Wojciech.; Hupp, Joseph
T.; Farha, Omar K. Chem. Soc. Rev., 2014, 43, 5896-5912
C 52
Surface studies of Ag-In-Gd 1/1 quasicrystalline approximant
1,2
T. P. Yadav
1
3
1
1
, S. S. Hars , R. Tamura , R. McGrath and H. R. Sharma
1
Hydrogen Energy Centre, Department of Physics, Institute of Science, Banaras Hindu
University,
Varanasi-221005, India
2
Surface Science Research Centre and Department of Physics, The University of
Liverpool,
Liverpool, L69 3BX, UK
3
Department of Materials Science and Technology, Tokyo University of Science, Noda,
Japan. E-mail: yadavtp@gmail.com
Quasicrystalline approximant are intermetallics whose compositions and structural units are
similar to those of a quasicrystal, but possess a periodically repeating unit cell. Therefore,
approximant may be take part in a crucial role in understanding of the structures of
quasicrystas because of their similarity. The surface study of approximant can provide insight
into the influence of quasiperiodic order structure. The Ag-In-RE (RE=Yb, Gd and Tb) has
attracted great attention because of the lack of chemical disorder in the structure and the large
number of related approximants that have been found. The basic building block of Ag-In-Gd
1/1 approximants is the same as of the Cd6Yb approximant; this is the rhombic
triacontahedral (RTH) cluster. The single-grain Al-In-Gd crystals have been grown using
self-flux method and in the first instance, to determine the optimum sample preparation
parameters for 1/1 Ag-In-Gd quasicrystalline approximant was carried out. Following
successful preparation, the surface structure of the sample was investigated using low energy
electron diffraction (LEED) and scanning tunneling microscopy (STM). Finally comparisons
with the theoretical bulk model for the approximant were made. STM data confirms that
icosahedral clusters are positioned upon lattice points throughout BCC structure of the Ag-InGd approximant. The data also suggests cluster preservation on the sample surface.
Furthermore, it appears that the symmetry within the icosahedral clusters may have an impact
upon the formation of surface structures. The evidence supporting this conclusion will be
discuses and presented.
Keywords: Quasicrystal, Approximant, Intermetallics, Surface structure
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Visit us at www.bio-rad.com
10/14/14 10:33 AM
protein crystallization
dispensing - effortlessly
simple
fast
accurate
mosquito® LCP, mosquito® Crystal and dragonfly®
The crystallographers’ favourite robots ensure easy automation of your protein crystallization
and optimization drop set-ups.
For more information please email crystallography@ttplabtech.com
ttplabtech.com/crystallography