INTRODUCTION - Canadian Journal of BioInformatics & Biosciences

Canadian Journal of Bioinformatics & Biosciences 1(15):5-10, 2015
Submitted: February 3, 2015
Accepted: March 27, 2015
Published: April 5, 2015
Research Article:
MOLECULAR MODELING OF LIPOID PROTEINOSIS (ECM1) PROTEIN AND ITS DOMAINS
Iram Ghafoor, Javed Iqbal, Zubair Anwar, Uzma Soukat, Mohammad Ismail and Jabar Zaman Khan Khattak*
1.
2.
International Islamic University, Islamabad
IBGE, Islamabad Pakistan
Abstract: Lipoid proteinosis (LP) is rare autosomal recessive skin disorder, with varying severity of clinical
manifestations. Common clinical appearances of LP are weak cry and early infancy with hoarseness, widespread
scarring and infiltrated plaques on mucosal surfaces and skin, especially at the sites of minor trauma and on sunexposed areas. Lipoid proteinosis is the consequences from pathogenetic loss-of-function mutations in the gene
encoding extracellular matrix protein1 (ECM1), mapped to a locus on chromosome 1q21. Forty six ECM1 gene
mutations have been described to date in discrete patients affected with lipoid proteinosis. The mutations in LP include
predominantly 19 insertions/deletions, 8 missense, 15 nonsense, and 4 splice site mutations and mostly are present on
exon 6 and 7. The present study was undertaken with a view to model ECM1 of full-length and its domains. Therefore,
increased quality model of the ECM1 protein through threading modeling approach and its domains through
comparative modeling has been generated. The structural prediction of the ECM1 would likely help in attempts to
accurately predict the effect of mutations on the overall structure of the protein.
Key words: Lipoid proteinosis, extracellular matrix protein1, dimethyl sulfoxide
INTRODUCTION
Lipoid proteinosis (LP) is also known as Urbach–
Wiethe disease or hyalinosis cutis et mucosae. Its
consequences are from mutations in the extracellular
matrix protein1 (ECM1) present on the chromosome
band 1q21. It is a rare, autosomal recessive disorder
worldwide, was detailed review for the first time by a
Viennesedermatologist and otorhinolaryngologist,
Urbach and Wiethe, in 1929 (OMIM 247100) (Urbach
et al., 1929). The mutations in ECM1 are due to the
loss-of-function (Hamda et al., 2002). Human ECM1
encodes glycoprotein known as secretary protein (85
kDa); function of this protein is unknown. It was the
protein recognized in a murine osteogenic stromal cell
line MN7 first time, by using techniques twodimensional polyacrylamide gel electrophoresis,
Western blotting and micro sequencing and protein
was drived from bone marrow stroma of the adult
mouse (Mathieu et al., 1994; Bhalerao et al., 1995;
Smits et al., 1997; Johnson et al., 1997).
Main symptoms of lipoid proteinosis are the
hoarseness of the voice, widespread warty
hyperkeratosis and marking of the skin (Gordon et al.,
1971). During infancy, disorder hoarseness of voice is
usually observed; it is most dazzling clinical features
in LP (Nanda et al., 2001) such as vocal cord that
contained the hyaline-like material deposited in the
mucous membranes of the or faint or weak cry. In
some cases, symptoms were developed at early age
after first or few years of life and soon after birth. The
typical and most common symptom is the “beaded”
papules on the eyelid (Balck et al., 1998; Bozdag et al.,
200; Dinakaran et al., 2001) at the site of cilia skin
openings (Scott and Findlay, 1960; Ozbek et al., 1994;
Bozdag et al., 2000). Other cutaneous changes include
diffuse skin infiltration and a thickness of general skin
having waxy and yellow manifestation, and in one
region warty hyperkeratosis was emphasized.
Mechanical friction is the region where
Hyperkeratosis is also, such as the elbows, axillae,
buttocks, hands, knees and, also often occurrence of
flexural lichenification (Pariak et al., 2005). During
childhood, friction or minor trauma damaged the skin,
which cause blisters and scar formation (Hu et al.,
2005). The mucosae of the tonsils, soft palate,
pharynx, tongue, and lips are also accessed and also
cause the respiratory difficulty, especially in
affilication with an upper respiratory tract infection,
which sometimes require tracheostomy (Ramsey et al.,
1985).
The most important LP changes are present in the
dermis and subcutis of the skin, at the dermal–
epidermal intersection basement membrane was
thickened, also present at approximately adnexal
epithelia and around blood vessels and in the dermis
the evidence of deposition of hyaline material (Muda
Corresponding Author: Jabar Zaman Khan Khattak jabar.khattak@iiu.edu.pk
Canadian Journal of Bioinformatics & Biosciences 1(15):5-10, 2015
et al., 1995). The gene ECM1 has four known splice
variants ECM1a, ECM1b, ECM1c and ECM1d have
been reported, but fourth splice variant of ECM1 has
been reported recently. The most broadly expressed
splice variant is ECM1a(1.8 kb), and originate in a
variety of tissues including skin, lung, prostate, ovary,
skeletal muscle, pancreas, kidney and liver, testis,
small intestines, but expressed predominantly in heart
tissues and placenta tissues. On the other hand, limited
expression pattern is present in ECM1b (1.4 kb)
expressed only in skin, keratinocytes and tonsils. The
ECM1c expression pattern is not resolute yet,
expressed in two cancer cell lines, but it reports that in
skin for 15% approximately of total ECM1 mRNA
expression. The fourth splice variant’s expression
pattern is not identified yet.
process comprises fold assignment, alignment
between target and template, building model and
model evaluation. The 3D structure of ECM1 was
predicted
through
the
I-TASSER
(http://zhanglab.ccmb.med.umich.edu/I-TASSER/).
The structure of the domains of ECM1 was predicted
through the MODELLER 9v11 ().
Evaluation of structures
The evaluation of models is a compulsory phase in
almost all projects. The modeling of various ECM1 is
basic step of project, so the evaluation is important for
verifying the energy values of predicted models. Also
determined the stereochemical properties and all the
possible errors present in the generated structures are
explored. Each structure contains the favored and nonfavored regions that are determined through
evaluation. 3D structure was evaluated through
PROCHECK (Laskowski et al., 2001) and Rampage
(http://mordred.bioc.cam.ac.uk/~rapper
/rampage.php).
There are 300 mutations of LP have been described
into the literature so forth (Hofer, 1973). The disease
LP appears throughout the world but more frequent in
geographical areas where the common effects of
consanguinity, an initiator cause from Northern Cape
Province of South Africa (Heyl, 1971; Gordon et al.,
1971; Stine and Smith, 1990; Hamda et al., 2002).No
effective treatment of Lipoid proteinosis is available
so forth. The therapy dimethyl sulfoxide (DMSO)
gives the expressive response to LP disease (Wrong
and Lin, 1988). Another useful therapy is Dpenicillamine, but its experience is limited (Kaya et
al., 2002). On this ground, I have generated a reliable
model of full-leng ECM1 protein by threading
approach and the model of domains of ECM1 protein
by homology modelling. For the prediction of ECM1
model the I-TASSER and MODELLER software were
used.
RESULTS & DISCUSSION
The three Dimensional structure is important for
providing valuable insight into molecular functions of
the protein. Other computational methods for structure
prediction X-ray and NMR are time consuming and
expensive. 3D structure of target protein ECM1 based
on the known protein structures. The 3D structure of
ECM1 was predicted by I-TASSER in Fig. 1 and
Phyre2. On the high confidence and converge basis the
best model was selected. I-TASSER covered all the
540 residues for structure prediction. The selection of
model is on the basis of high C-score and higher
Cluster density. Phyre2 covered only 265 residues
(195-471) for 3D structure prediction. 49% of
sequence has been modeled with 99.2% confidence by
meaningfully predicted. The 3D structures of four
domains of ECM1 were also predicted Fig.2.
The 3D structure of N-terminal cysteine-free domain
of ECM1 protein was predicted by I-TASSER and
other 3 domains ECM1 repeat 1, ECM1 repeat 2 and
C-terminal region were predicted by modeler (9.11)
the single highest scoring template. 54% of sequence
is predicted disordered. Disordered regions cannot be
software. The template of these domains was obtained
from
the
BLAST
(http://blast.ncbi.nlm.nih.gov/Blast.cgi) shown in
Table 1. The maximum identity of template with query
sequence is best for good quality of 3D model. More
than 30% identity is required for the homology
modeling.
MATERIALS & METHODS
Target Sequence
The amino acid sequence of Extracellular Matrix
Protein 1 (ECM1) was obtained from NCBI database
(http://www.ncbi.nlm.nih.gov/) (Q16610). There are
540 amino acid residues present in the sequence. The
3D structure of ECM1 is not present in the database.
So it is predicted through the threading approach. The
3D structure of the domains of ECM1 is also predicted.
3D Structure Prediction
Modeling approach predicts the 3-D structure of a
target protein sequence based on its alignment with a
known protein structure called as template. The
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Canadian Journal of Bioinformatics & Biosciences 1(15):5-10, 2015
Fig. 2 – Cartoon structure of domains of
ECM1 protein a) N-terminal cysteine-free
domain, b) ECM1 repeat 1, c) ECM1 repeat 2, d)
C-terminal region.
Fig. 2- Cartoon structure of ECM1 protein,
coloured by domain (red = Signal peptide, blue
= N-terminal cysteine-free domain, yellow =
ECM1 repeat 1, magenta = ECM1 repeat 2,
green = C-terminal region).
Table 1- Max. Identity between ECM1 sequence and template.
Models
Model 1
Model 2
Domain 1
Domain 2
Domain 3
Domain 4
Template
1n5uA
c1e7bA_
1mv3A
1AF2_A
1YVU_A
3V08_A
Tool used
I-TASSER
Phyre 2
I-TASSER
Modeller
Modeller
Modeller
Max. Identity
37%
41%
41%
No of residues
540 residues
265 residues
158 residues
212 residues
148 residues
108 residues
plot was divided into most favoured regions,
additional allowed, generously allowed and
disallowed regions. This plote shows that the predicted
structures were satisfactory because mostly residues
are laid in the most
3.2.1.3 Evaluation of Structure
The 3D structures of domains of ECM1 were also
evaluated. After 3D structure prediction and
refinement, the model was evaluated using
PROCHECK and RAMPAGE. The evaluation of
structures was shown in Table 2. The ramachandran
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Canadian Journal of Bioinformatics & Biosciences 1(15):5-10, 2015
Fig. 3- Ramachandran plot produced by PROCHECK after modeling of ECM1 protein. [A, B, L] most favored
regions (84.3%); [a, b, l, p] additional allowed regions (11.9%); [~a, ~b, ~l, ~p] generously allowed regions
(1.6%); white areas are disallowed regions (2.2%).
favoured region. This drives Psi and Phi plots, as
denser number of residues are present in the favored
region so it was good quality model. The
Ramachandran Plot statistics determined that Glycine
residues and Proline residues were also present in the
ramachandran plot of the model.
Table 2- Ramachandran plot values of ECM1 protein and its domain by using PROCHEK.
Model
Model 1
Model 2
Domain 1
Domain 2
Domain 3
Domain 4
Favoured
Regions
84.3%
90.5%
54.9%
89.4%
72.2%
68.9%
Allowed Region
11.9%
7.0%
38.9%
8.9%
24.6%
24.4%
8
Generously
Allowed Regions
1.6%
0.8%
3.5%
1.7%
3.2%
6.7%
Disallowed
Regions
2.2%
1.6%
2.7%
0.0%
0.0%
0.0%
Canadian Journal of Bioinformatics & Biosciences 1(15):5-10, 2015
CONCLUSION
Lipoid proteinosis is the deposition of an
amorphous hyaline material in the skin, mucosa, and
viscera. The 3D structure prediction has significant
potential as a tool in rational drug design, in high
throughput in silico screening. This work is a
significant step for bioinformatics analysis of ECM1
protein and supports for further analysis. The
important protein functional features are investigated
by structure and better understanding of its
characteristics. The greater insight of structure is
possible by the detail study of ECM1. 3D structure
provides further computational methods and
understands the binding modes and its antagonists.
The inhibition of ECM1 is understood that is present
in Lipoid proteinosis disease. The development and
computational drug designing is depends upon the
structure. The 3D structure of ECM1 is submitted to
the PMDB (Protein Model DataBase) and the
following ID is assigned PM0078323.
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