2. In- silico prediction of vp40 matrix protein of Ebola
virus through homology modelling
Abstract
Ebola virus (EBOV), formerly designated Zaire Ebola virus is one of five known viruses
within the genus Ebolavirus. Four of the five known Ebola viruses, including EBOV, cause a
severe and often fatal hemorrhagic fever in humans and other mammals , known as Ebola
virus disease.Ebola virus has caused the majority of human deaths from EVD, and is the cause
of the 2013–2015.The negative-sense RNA that encodes seven viral proteins out of which
Matrix protein Vp40 of Ebola virus plays a vital role in virus assembly and budding. The 3D
structure of this protein is not available yet. So, I have done homology modeling which was
performed to generate good quality models. The assessment of generated three dimensional
structure against structure verification tools PHYRE, PSIPRED, PROCHECK, showed that
model generated by Swiss Model was more acceptable to that by GENO 3D. The predicted
model can be used in structure based drug designing and vaccine development.
Keywords: Vp40 matrix protein , PHYRE ,PROCHECK, GENO -3D , PSIPRED
3. Introduction :-
Ebola is xoonotic virus.
It is negatively charge single stranded RNA
It causes the hazardous fatal effect like hemorrhagic fever
It originates from bats and fruit bats .
Group Negative strand ss RNA
Family Filoviridae
Oder Mononegavirale
genus Ebola virus
5. Material and methods:-
1) Retrieval of target sequence:-
The amino acid sequence of the matrix protein of Ebola virus was obtained from the
sequence database of NCBI (http://www.ncbi.nlm.nih.gov/protein/Vp40s protein)
>gi|465460|sp|Q05128.1|VP40_EBOZM RecName: Full=Matrix protein VP40; Alt Name:
Full=Membrane-associated
proteinVP40MRRVILPTAPPEYMEAIYPVRSNSTIARGGNSNTGFLTPESVNGDTPSNPLRPIA
DDTIDHASHTPGSVSSAFILEAMVNVISGPKVLMKQIPIWLPLGVADQKTYSFDSTTAAIMLA
SYTITHFGKATNPLVRVNRLGPGIPDHPLRLLRIGNQAFLQEFVLPPVQLPQYFTFDLTALKLI
TQPLPAATWTDDTPTGSNGALRPGISFHPKLRPILLPNKSGKKGNSADLTSPEKIQAIMTSLQ
DFKIVPIDPTKNIMGIEVPETLVHKLTGKKVTSKNGQPIIPVLLPKYIGLDPVAPGDLTMVITQ
DCDTCHSPASLPAVIEK.
6. Conti…….
2) Physico-chemical characterization:-
The values of theoretical isoelectric point (pI), molecular weight, total number
of positive and negative, using the Expasy’s ProtParam server
(http://us.expasy.org/tools/protparam.html). residues, extinction coefficient ,
instability index, aliphatic index and grand average hydropathy (GRAVY) were
computed. For Physico-chemical characterization The results were shown in
Table 1.
7. Continue…………..
Sr.
no
Property Value
1 No. of amino acid 288
2 Molecular weight 32520.8
3 Theoritical PI 8.40
4 Total no. of negative charge
residues (asp+glu)
37
5 Total no. of positively charge
residues (arg+lys)
40
6 Extinction coefficient 28460
7 Extinction coefficient 27960
8 Instability index 52.08
9 Aliphatic index 78.26
10 Grand average of hydropathicity -0.607
Table 1-Parameters computed using Expasy’s ProtParam tool
8. 3) Secondary structure prediction:-
I have predicted secondary structure of Ebola virus by using Pspired software
(http://www.sbg.bio.ic.ac.uk/pspired) software where the FASTA format of the sequence
was given as input.
Figure -2 secondary structure of Ebola virus
9. 4. Model building and quality assessment:-
The modeling of the three dimensional structure of the protein was done using
homology modelling programs Geno 3D.
The overall stereochemical property of the protein was assessed by
Ramchandran plot analysis.
The evaluation of structure models obtained from the software tools was
performed by using PROCHECK.
14. Residue in most
favored region
163 72.1%
Residue in additional
allowed region
57 25.2%
Residue in generously
allowed region
5 2.2%
Residue in disallowed
region
1 0.4%
Total no of residue is 272
15. Conclusion:-
On the basis of various structural and physiochemical parameters assessment, it
can be concluded that the predicted three dimensional structure of matrix
protein of Ebola virus is stable.
Since no effective therapeutic or vaccine is available for Ebola virus structure
information of this model can be effectively used and can be further
implemented in future drug designing.
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