Functional and structural characterization of Ebola virus glycoprotein (1976–2015) — Anin silicostudy

Abstract

Ebola virus (EBOV) is the causative agent of a severe hemorrhagic fever disease associated with high mortality rates in humans. This virus has five strains of which Zaire Ebola virus (ZEBOV) is the first and most important strain. It can be transmitted through contact with contaminated surfaces and objects. The genome of EBOV codes one non-structural and seven structural proteins consisting of two forms of glycoprotein (GP): soluble glycoprotein (sGP) and GP (spike). In this paper, we attempted to characterize and predict physicochemical properties, B-cell epitopes, mutation sites, phosphorylation sites, glycosylation sites, and different protein structures of EBOV GP to provide comprehensive data about changes of this GP during a 40-years course (1976–2015). GP sequences were obtained from NCBI gene bank from 1976–2015. Expasy’sProtParam, PROTSCALE, immuneepitope, Bepipred, BcePred, ABCpred, VaxiJen, DISPHOS, NetPhos, and numerous programs were used to predict and analyze all sequences. More variety of mutations were found in 2015 sequences and mutations were related to huge changes in B-cell epitopes, phosphorylation and glycosylation sites. In addition, our results determined different sites of disulfide bonds and an important mutation related to IgE epitope as well as four potent B-cell epitopes (380–387, 318–338, 405–438 and 434–475). In this study, we suggested the effect of mutations on GP properties, six positions for disulfide bonds and four phosphorylation sites for protein kinase C enzyme. Selected sequences were shown different sites for O-link and N-link glycosylation. A mutation that changed GP to an allergen protein and has a significant role in vaccine designing as well as four potent B-cell epitopes in GP protein were found.

The possible regions to design Human Papilloma Viruses vaccine in Iranian L1 protein

“…Bioinformatics has provided a great context to define the structure of virus proteins (Behzad et al 2019;Dehghani et al 2017Dehghani et al , 2019aMoattari et al 2015;Zahra et al 2020). Bioinformatics tools were employed widely in this research to determine the structure of L1 and illustrated that the majority of the secondary structures belonged to the random coil and extended strand.…”

Designing and Modelling of Trivalent Chimeric Vaccine for Capripoxvirus: Lumpy Skin Disease, Sheep Pox and Goat Pox by Immunoinformatics Approach

“…i.e. designing and modeling of epitope vaccine or peptide subunit vaccine for overcoming the di culties of controlling and preventing the infectious diseases (Dehghani et al 2017; Dehghani, Hashempour, and Hasanshahi 2020; Negahdaripour et al 2017). A variety of advanced bioinformatics computational tools have been applied considering various criteria for the construction of peptide vaccine in this study.…”

First report of computational protein–ligand docking to evaluate susceptibility to HIV integrase inhibitors in HIV-infected Iranian patients

“…To determine the tertiary structure, amino acid sequences of the mutated INT proteins were submitted in “I-TASSER” [ 32 , 33 ]. Among the various models suggested by I-TASSER, the highest C-score model was selected as the best one and went through the refinement process in “GalaxyRefine” [ 16 , 34 ].…”