Department of Crystallography - Center for Biocrystallographic

Department of Crystallography - Center for Biocrystallographic

CONFERENCE
MULTIDISCIPLINARY APPROACH TO STRUCTURAL BIOLOGY
FROM MACROMOLECULES TO CELLS
Poznan Science Center
Wieniawskiego 17/19, Poznan, Poland
March 6–7, 2015
Department of Crystallography - Center for Biocrystallographic Research at the Institute
of Bioorganic Chemistry, Polish Academy of Sciences in Poznan organises on 6-7
March 2015 a conference “Multidisciplinary Approach to Structural Biology. From
Macromolecules to Cells”. The meeting will bring together representatives of leading
Polish research institutions dedicated to various aspects of structural biology and using
state-of-the-art techniques. The purpose of the conference is to take stock of structural
biology in Poland, as well as a presentation of our research community and
infrastructure to the European consortium “Instruct”, with the prospect of joining the
consortium.
“Instruct” provides researches with access to modern infrastructure and expertise
throughout Europe and encourages multi-disciplinary approach in order to build an
integrated model of the cell. Presently, “Instruct” has 2618 members and 16 Instruct
Centres in 11 countries. It also provides short-term internships for young scientists in
leading research laboratories.
“Instruct” will be represented by its director, prof. David Stuart from Oxford University,
and representatives from other member states.
For detailed information about “Instruct” please go to: http://www.structuralbiology.eu
Organising Committee
Wojciech Rypniewski, Mariusz Jaskólski, Michał M. Sikorski
Department of Crystallography – Center for Biocrystallographic Research
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
Contact: wojtekr@ibch.poznan.pl and mmsik@ibch.poznan.pl
MULTIDISCIPLINARY APPROACH
TO STRUCTURAL BIOLOGY
FROM MACROMOLECULES TO CELLS
Poznan Science Center
Wieniawskiego 17/19, Poznań, Poland
March 6 – 7, 2015
Invited Speakers
Prof. David Stuart - special Instruct guest - Oxford University, London, UK
Prof. Marek Figlerowicz - Director of the Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznań, Poland
Dr. Krzysztof Brzeziński - University of Bialystok, Białystok, Poland
Dr. Honorata Czapińska - International Institute of Molecular and Cell Biology, Warszawa, Poland
Prof. Michał Dadlez - Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
Dr. Grzegorz Dubin - Jagiellonian University, Kraków, Poland
Prof. Tadeusz Holak - Jagiellonian University, Kraków, Poland
Dr. Agnieszka Kiliszek - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
Prof. Maciej Kozak - Adam Mickiewicz University, Poznan, Poland
Prof. Paweł P. Liberski - Medical University of Lodz, Łódź, Poland
Prof. Barbara Nawrot - Department of Bioorganic Chemistry, Polish Academy of Sciences, Łódź, Poland
Dr. Izabela Sierocka - Adam Mickiewicz University, Poznań, Poland
Joanna Śliwiak - Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznań, Poland
Dr. Anna Urbanowicz - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
Prof. Krzysztof Woźniak - Warsaw University, Warszawa, Poland
Dr. Mirosław Zarębski - Jagiellonian University, Kraków, Poland
Organized by:
Institute of Bioorganic Chemistry
Polish Academy of Sciences
Poznan, Poland
Department of Crystallography
Center for Biocrystallographic Research
Conference web page: www.ibch.poznan.pl/pl/main-pl/ogloszenia/konferencje/
Sponsors:
LKB Biotech
MULTIDISCIPLINARY APPROACH TO STRUCTURAL BIOLOGY
FROM MACROMOLECULES TO CELLS
PROGRAMME
Friday, March 6, 2015
08:30 – 8:45
Wojciech Rypniewski - General remarks
08:45 – 9:00
Marek Figlerowicz - Director of the Institute - Research at the Institute of Bioorganic Chemistry
09:00 – 9:30
David Stuart - special Instruct guest
09:30 – 10:00
Maciej Kozak - Polish synchrotron SOLARIS and its potential in Bio-SAXS applications
10:00 – 10:30
Honorata Czapińska - Structural studies of restriction-modification systems
10:30 – 10:50
Coffee break
10:50 – 11:20
Krzysztof Woźniak - Crystallography beyond Independent Atom Model
11:20 – 11:50
Michał Dadlez - Approach to structures of difficult protein targets by hydrogen-deuterium
exchange/mass spectrometry analysis - new clothes for the old emperor
11:50 – 12:20
Tadeusz Holak - Monitoring the Antagonist-Protein and Protein-Protein Interactions with NMR
Spectroscopy: Inhibitors of the p53-Mdm2 Interaction
12:20 – 12:50
Barbara Nawrot - Synthetic oligonucleotides as molecular tools for applications in cell biology
12:50 – 14:00
Lunch
14:00 – 14:30
Paweł P. Liberski - Prions, prionoids and misfolded proteins
14:30 – 14:50
Mirosław Zarębski - Subcellular Cytometry - Quantitative 3-D Analysis of Discrete Subcellular
Structures and Events
14:50 – 15:10
Grzegorz Dubin - Structural and functional analysis of Spl proteases form S. aureus
15:10 – 15:30
Joanna Śliwiak - Protein-ligand- interactions - structural and biophysical studies
15:30 – 15:50
Agnieszka Kiliszek - Crystallographic studies of toxic RNA
15:50 – 16:10
Izabela Sierocka - High-throughput platforms for RNA analyses in the Institute of Molecular
Biology and Biotechnology at the Faculty of Biology, Adam Mickiewicz University, Poznan
16:10 – 16:30
Coffee break
16:30 – 16:50
Anna Urbanowicz - TROSPA from Ixodes ricinus - the first intrinsically disordered protein involved
in specific vector-microbe recognition
16:50 – 17:10
Krzysztof Brzeziński - Structural and biochemical characterization of archaeal type S-adenosyl-Lhomocysteine hydrolases
17:10 – 18:00
Discussion
POSTERS
POSTER
NUMBER
AUTHOR(S)/ AFFILIATION
TITLE
PROTEINS
1
Aleksandra Pawela, Joanna Banasiak
Department of Natural Products Biochemistry,
Group of Plant Molecular Physiology, IBCh, PAS
Poznań, Poland
ABA transport as an essential regulatory factor
in nodulation process
2
Wanda Biała, Michał Jasiński
Department of Natural Products Biochemistry
Group of Plant Molecular Physiology, IBCh, PAS
Poznań, Poland
Functional analysis of MtABCG transporters in search of endogenous substrates
3
Karolina Jarzyniak
Department of Natural Products Biochemistry,
Group of Plant Molecular Physiology, IBCh,
PAS Poznań, Poland
Unravelling the role of Medicago truncatula
ABCG/PDR transporters in nodulation
4
Dominik Lewandowski
Department of Molecular and Systems Biology,
Institute of Bioorganic Chemistry, Polish
Academy of Sciences, Poznań, Poland
TROSPA - an intrinsically disordered protein
involved in the tick colonization by Borrelia
5
Aleksander Tworak
Department of Molecular and Systems Biology,
Institute of Bioorganic Chemistry, Polish
Academy of Sciences, Poznań, Poland
Dicer-like proteins in Medicago truncatula, a
model legume plant
6
Michał Taube, Artur Jarmołowski, Maciej Kozak
Department of Macromolecular Physics, Faculty
of Physics, Adam Mickiewicz University,
Poznań, Poland
Structural studies of the plant HSP90-SGT1ADP complex in solution
7
Przemysław Wieczorek
Department of Gene Expression, Faculty of
Biology, Adam Mickiewicz University, Poznań,
Poland
Structural study of the human SGT1 protein in
solution
8
Mateusz Bajczyk
Department of Gene Expression, Adam
Mickiewicz University, Poznań, Poland
Novel proteins interacting with the SERRATE
protein in Arabidopsis thaliana
9
Weronika Andrzejewska
Department of Macromolecular Physics, Faculty
of Physics, Adam Mickiewicz University,
Poznań, Poland
The study of complexation process between
cationic gemini surfactants and DNA using
structural and spectoscopic methods.
Witold Gospodarczyk
Department: Macromolecular Physics
Department, Faculty of Physics, Adam
Mickiewicz University, Poznań, Poland
Microfluidic system for amyloids formation
analysis
10
1
11
Marta Grzechowiak
Protein Engineering Laboratory, Department of
Crystallography – CBB, Institute of Bioorganic
Chemistry, PAS, Poznań, Poland
Inorganic pyrophosphatase (PPase) from a
higher plant
12
Miłosz Ruszkowski, Joanna Śliwiak, Agnieszka
Ciesielska, Jakub Barciszewski, Michał Sikorski,
Mariusz Jaskólski
Protein Engineering Laboratory, Department of
Crystallography – CBB, Institute of Bioorganic
Chemistry, PAS, Poznań, Poland
Specific plant hormone binding proteins with
PR-10 fold - structural and thermodynamic
studies
NUCLEIC ACIDS
13
Ewelina Małecka
Department of Biochemistry, Adam Mickiewicz
University, Poznań, Poland
14
Agnieszka Stefaniak
Department of Structural Chemistry and Biology
of Nucleic Acids, Institute of Bioorganic
Chemistry, PAS, Poznań, Poland
RNA Chaperone activity of retroviral proteins
15
Magdalena Małgowska
Institute of Bioorganic Chemistry, PAS, Poznań,
Poland
Distinctive structural motifs of RNA Gquadruplexes composed of AGG, CGG and
UGG trinucleotide repeats
16
Tadeusz Kuliński
Department of Chemical Biology, Institute of
Bioorganic Chemistry, PAS, Poznań, Poland
Structural propensities of RNA motifs
17
Jolanta Lisowiec
Department: Department of Structural Chemistry
and Biology of Nucleic Acids, Institute of
Bioorganic Chemistry, PAS, Poznań, Poland
Structural Determinants of Alternative Splicing
Regulations of the MAPT pre-mRNA
18
Marta Szabat
Department of Structural Chemistry and
Biology of Nucleic Acids, Institute of Bioorganic
Chemistry, PAS, Poznań, Poland
Thermodynamic and structural features of
beta-L-RNA
19
Anna Pasternak, Kotkowiak Weronika
Department of Structural Chemistry and Biology
of Nucleic Acids, Institute of Bioorganic
Chemistry, PAS, Poznań, Poland
Unlocked nucleic acids: implications of
increased conformational flexibility for
RNA/DNA triplex formation
The unique mode of binding of bacterial
sRNAs to the distal side of the Hfq protein
VIRUSES
20
Aleksander Jan Strugała
Department of molecular and systems biology,
Institute of Bioorganic Chemistry, PAS,
Poznań, Poland
BMV- and RCNMV- based virus like particles as
carriers of biologically active substances.
21
Agata Groszewska
Department of Biochemistry, Institute of
Molecular Biology and Biotechnology, Faculty
of Biology, Adam Mickiewicz University,
Poznań, Poland
Competition among sRNAs for access to Hfq
affects the rates of association and dissociation
of the complex of DsrA sRNA with rpoS mRNA
22
Daria Sobańska
Department of Biochemistry, , Faculty of
Biology, Adam Mickiewicz University, Poznan,
Poland
The rates of sRNA association to mRNA
correlate with Hfq-dependent translation
repression.
2
23
Joanna Mazur
Department of Biochemistry, Institute of
Molecular Biology and Biotechnology, Faculty
of Biology, Adam Mickiewicz University,
Poznań, Poland
The role of Mg2+ ions for E.coli sRNA MgrR
binding to eptB mRNA and to the Hfq protein.
NUCLEOTIDE ANALOGUES
24
Dorota Magner
Dept of Structural Chemistry and Biology of
Nucleic Acids, Institute of Bioorganic
Chemistry, PAS, Poznań, Poland
SNP alleles expression differentiation on mRNA
level using modified antisense oligonucleotides
25
Lucyna Budźko
Department of Molecular and Systems Biology,
Institute of Bioorganic Chemistry, PAS,
Poznań, Poland
Deamination of methylated and non-methylated
cytidines by human AID
26
Grzegorz Framski
Institute of Bioorganic Chemistry Polish
Academy of Sciences, Poznan, Poland
New applications of 6-alkyl-2,3dihydrofurano[2,3-d]pyrimidin-2(1H)-one and 6alkyl-2,3-dihydropyrrolo[2,3-d]pyrimidin2(3H,7H)-one nucleosides: anticancer properties
27
Dagmara Sara Baraniak
Institute of Bioorganic Chemistry Polish
Academy of Sciences, Poznań, Poland
Synthesis and Cytotoxic Evaluation of Novel
Proparagyl Derivatives of 5-Fluoro-2’deoxyuridine Nucleosides
28
Justyna Gołębiewska
Department of Nucleic Acids Chemistry,
Institute of Bioorganic Chemistry Polish
Academy of Sciences, Poznań, Poland
Studies on the synthesis and biological
properties of nucleosid-5’-yl phosphoramidates.
29
Agnieszka Szymańska-Michalak
Institute of Bioorganic Chemistry, Polish
Academy of Sciences, Poznań
Cell cycle arrest, apoptosis and anti-proliferative
activity of new 3'-O-acyl-2'-deoxy-5-fluorouridine
derivatives
30
Krystian Kołodziej
Group of Nucleotide Stereochemistry, Institute
of Bioorganic Chemistry, Polish Academy of
Sciences, Poznań, Poland
The Loss of TEAH+ Cation From Certain
Nucleotide Analogues
31
Magdalena Materna
Department: Department of Nucleic Acids
Chemistry, Institute of Bioorganic Chemistry
Polish Academy of Sciences, Poznań, Poland
N-Oxides in the synthesis of nucleotide
analogues
3
ALPHABETICAL LIST OF PARTICIPANTS
1. Andrzejewska Weronika
2. Bajczyk Mateusz
3. Banasiak Joanna
4. Baraniak Dagmara S.
5. Barciszewski Jakub
6. Barciszewski Jan
7. Bejger Magdalena
8. Belter Agnieszka
9. Biała Wanda
10. Boryski Jerzy
11. Brzeziński Krzysztof
12. Brzęk Aleksandra
13. Budźko Lucyna
14. Czapik Tomasz
15. Czapińska Honorata
16. Dadlez Michał
17. Daenke Susan
18. Dubin Grzegorz
19. Fedoruk-Wyszomirska Agnieszka
20. Femiak Iwona
21. Figlerowicz Marek
22. Framski Grzegorz
23. Gawron Marian
24. Gdaniec Zofia
25. Gołębiewska Justyna
26. Gospodarczyk Witold
27. Groszewska Agata
28. Grzechowiak Marta
29. Handschuh Luiza
30. Holak Tadeusz
31. Imiołczyk Barbara
32. Jarzyniak Karolina
33. Jasiński Michał
34. Jaskólski Mariusz
35. Kamel Karol
36. Kasperska Alina
37. Kasprzak Joanna
38. Kiliszek Agnieszka
39. Kołodziej Krystian
40. Koralewska Natalia
41. Kotkowiak Weronika
42. Kozak Maciej
andrzejewskaw@gmail.com
mateusz.bajczyk@amu.edu.pl
joaban@ibch.poznan.pl
baraniak@man.poznan.pl
agent007@ibch.poznan.pl
Jan.Barciszewski@ibch.poznan.pl
mbejger@poczta.onet.pl
abelter@ibch.poznan.pl
wanda.biala@up.poznan.pl
jboryski@ibch.poznan.pl
k.brzezinski@uwb.edu.pl
brzek.aleksandra@amu.edu.pl
budzko@man.poznan.pl
ttomek.czapik@gmail.com
honorata@iimcb.gov.pl
michald@poczta.ibb.waw.pl
grzegorz.dubin@uj.edu.pl
agaw@ibch.poznan.pl
iwofem@ibch.poznan.pl
marekf@ibch.poznan.pl
Grzegorz.Framski@ibch.poznan.pl
mgawron@ibch.poznan.pl
zgdan@ibch.poznan.pl
justynagolebiewska-91@tlen.pl
w.gospodarczyk@gmail.com
a.grosz@amu.edu.pl
grzecha@o2.pl
luizahan@ibch.poznan.pl
tadeusz.holak@uj.edu.pl
barim@ibch.poznan.pl
kjar@up.poznan.pl
jasinski@ibch.poznan.pl
mariuszj@amu.edu.pl
kamel@ibch.poznan.pl
alinakas@ibch.poznan.pl
jkasp@amu.edu.pl
kiliszek@ibch.poznan.pl
krychu@man.poznan.pl
nataliak@man.poznan.pl
kawecka.weronika@gmail.com
mkozak@amu.edu.pl
43. Krzywda Szymon
44. Kuliński Tadeusz
45. Lewandowski Dominik
46. Liberski Paweł P.
47. Lisowiec Jolanta
48. Magner Dorota
49. Małecka Ewelina
50. Małgowska Magdalena
51. Manszewski Tomasz
52. Marcinkowska-Swojak Małgorzata
53. Materna Magda
54. Mazur Joanna
55. Milewski Marek Cezary
56. Nawrot Barbara
57. Nowak Karolina
58. Pasternak Anna
59. Pawela Aleksandra
60. Philips Anna
61. Pokornowska Maria
62. Rypniewski Wojciech
63. Sierocka Izabela
64. Sikorski Michał M.
65. Sobańska Daria
66. Stefaniak Agnieszka Katarzyna
67. Stelmaszczuk Michał
68. Stróżycki Paweł
69. Strugała Aleksander
70. Stuart David
71. Szabat Marta
72. Szpotkowski Kamil
73. Szymanska-Michalak Agnieszka
74. Śliwiak Joanna
75. Taube Michał
76. Teubert Anna
77. Tworak Aleksander
78. Urbanowicz Anna
79. Wieczorek Przemysław
80. Woźniak Krzysztof
81. Wyszko Eliza
82. Zarębski Mirosław
szymon@amu.edu.pl
tadkul@ibch.poznan.pl
dominikl@ibch.poznan.pl
ppliber@csk.am.lodz.pl
lisowiec@ibch.poznan.pl
dorotaw@ibch.poznan.pl
emalecka@amu.edu.pl
magdalena.malgowska@gmail.com
tomasz@manszewski.pl
m-marcinkowska@o2.pl
materna.magda@gmail.com
joanna.mazur.jm@gmail.com
marmil@man.poznan.pl
bnawrot@cbmm.lodz.pl
karolinan@ibch.poznan.pl
apa@ibch.poznan.pl
apawela@man.poznan.pl
aphilips@ibch.poznan.pl
chwalisz@ibch.poznan.pl
wojtekr@ibch.poznan.pl
izapaste@amu.edu.pl
mmsik@ibch.poznan.pl
daria.grygiel@amu.edu.pl
astef@ibch.poznan.pl
michal.stelmaszczuk@ibch.poznan.pl
spprom@ibch.poznan.pl
bernardzkniei7@gmail.com
stuart-pa@strubi.ox.ac.uk
martaociepa87@o2.pl
kamilsz@amu.edu.pl
agaszyma@ibch.poznan.pl
joanna.sliwiak@gmail.com
mtaube@amu.edu.pl
ateubert@ibch.poznan.pl
tworak@ibch.poznan.pl
aniau@ibch.poznan.pl
wieczerz@wp.pl
kwozniak@chem.uw.edu.pl
wyszkoe@ibch.poznan.pl
miroslaw.zarebski@uj.edu.pl
The Conference accompanying event
„Microscape”
Joanna Hoffmann-Dietrich
Sound composition: Andre Bartetzki
Joanna Hoffmann, a renowned Polish artist sharing her life between Poznan & Berlin. She is
Professor (Dr.hab) of the University of Arts in Poznan and leader of the Studio for
Transdisciplinary Projects and Research. She is also the Chair of Art & Science Node in Berlin.
Joanna Hoffmann's transdisciplinary works combine art, science and technology. Her use of
multimedia installations, 3d stereoscopy, experimental video animation and other media explore
the visualization of molecular as well as cosmic space. Her work relates to advanced scientific
research on the phenomenon of life and to the interplay between scientific and cultural, sensual
and illusive, digital and biological, natural and synthetic. www.johoffmann.com
“Microscape” brings together a few threads of artistic research being developed within the frame
of the long-term project „Hidden Topologies of Being” inspired by the origin and complex
geometry of protein molecules, named "basic bricks of life". “Proteins are associated mostly with
cellular robots. For me however, as an ‘assembly of proteins’ a protein molecule became a key to
explore relations between micro and macro scales of my existence, a unique unite of my “spacetime”[…]
The artistic presentation „Microscape” accompanying the Conference "Multidisciplinary Approach
to Structural Biology. From Macromolecules to Cells" embraces:
πρωτεο/ Proteo hologram-like animation
The work’s title refers to the Greek root of the word protein (Gr. πρωτεῖος the first, in the lead) as
well as to the philosophical tradition of searching for arche – the essence of the physical world.
Πρωτεο / Proteo is an animation portraying a cloud of particles creating a mini-universe folded in
the form of Calabi-Yau space, in which, according to superstring theory, successive dimensions
of our world are “curled up” at the subatomic level. Giving birth to a convoluted protein molecule
and its dynamic molecular 'dance of life', it brings to mind a question about the relations between
the energy, matter and form.
“If the scientific hypothesis about multi-dimensional nature of the world is true, then these hidden
spaces are everywhere, in each ‘point’ of the space outside as well as inside us. (…) One day,
maybe, our brain will be able to perceive how we exist in the multidimensional universe. For the
time being, we have only our imagination in command and enormous diversity of protein globules,
each of them suggesting, in other scale, a blister of some world."
“Microscape” 3D multimedia installation
The 3D multimedia installation is based on scientific data of molecular structures and transcribed
by the artist into a computer animation. The work, in tandem with Andre Bartetzki’s sound
composition, relates specifically to the viewer’s body and present itself as an artistic study on
space and existence.
By using technologies as diverse as Pepper's ghost (a forerunner of holography) and 3D video,
Hoffmann's work merges interpretations of scientific data, image, sound and poetry.
“Microscape” poses questions about the challenges and boundaries of our cognition creating an
emotional bridge between our sensual experiences and abstractness of contemporary science.
Conference room nr 312, Science Center, Wieniawskiego 17/19, Poznań
March 6, 2015 at 9:00 – 20:00h