In- Silico prediction of Vp40 matrix protein of Ebola virus through

homology modelling

By Komal Vavadiya TY BIOTECHNOLOGY

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

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

Figure 1 structure of Ebola virus

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 proteinVP40MRRVILPTAPPEYMEAIYPVRSNSTIARGGNSNTGFLTPESVNGDTPSNPLRPIADDTIDHASHTPGSVSSAFILEAMVNVISGPKVLMKQIPIWLPLGVADQKTYSFDSTTAAIMLASYTITHFGKATNPLVRVNRLGPGIPDHPLRLLRIGNQAFLQEFVLPPVQLPQYFTFDLTALKLITQPLPAATWTDDTPTGSNGALRPGISFHPKLRPILLPNKSGKKGNSADLTSPEKIQAIMTSLQDFKIVPIDPTKNIMGIEVPETLVHKLTGKKVTSKNGQPIIPVLLPKYIGLDPVAPGDLTMVITQDCDTCHSPASLPAVIEK.

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.

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

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

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.

3D structure of Ebola virus by using Geno-3D

Figure 3 results of PROCHECK of Vp40 protein

Figure:-5 Ramachandran plot of Matrix protein of Ebola virus generated using Procheck software

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

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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