Bioinformatics-based Prediction of Character of Envelope Glycoprotein and Analysis of Epitopes of B- and T-cell of gp120

Abstract

1Objectives: To analyze the characteristics of gp120 gene sequence and protein structure of HIV-1 CRF01_AE and to predict B- and T-cell epitopes and to forecast binding sites between gp120 and mD1.22 by using bioinformatics in order to lay a foundation for the research and development of AIDS vaccines and peptide-based drugs. Methods: The gene sequences and the amino acid sequences of gp120 were obtained from NCBI GeneBank database. Physicochemical property, membrane-panning region, PTMs sites of gp120 and secondary structure were analyzed by Expasy ProtParam, TMpred, NetPhos and GlycoMine and SOPMA, respectively. Epitopes of B-cell were predicted by VaxiJen v2.0, AllerTOP v2.0 and IEDB while epitopes of T-cell were predicted by IEDB. Protein-protein docking were forecast by Z-dock, pymol and so on. Results: The calculation formula of gp120 is C1033H1633N299O319S9. The number of amino acids is 211, and the molecular weight is 23633.68. The theoretical isoelectric point (pI) is 7.76. It is estimated that 17 residues are phosphorylation sites, while gp120 has more than 5 glycosylation sites. The protein contains alpha helix (blue mark), beta turn (green mark), random coil (purple mark) and thin slice (red mark), which are 26.54%, 6.16%, 40.28% and 27.01% respectively. We selected the top 10 possible epitopes of B cells, but only the top 5 epitopes of MHC-I. The most possible binding site between gp120 and mD1.22 was showed. Conclusion: With the potential humoral immunity and cellular immunity, gp120 of HIV-1 is a promising target for HIV-1 treating. The interaction of gp120 with CD4 is the first step of HIV cycle which allows the entry of HIV into CD4+ T-cells. This study has analyzed and predicted the binding sites between gp120 and mD1.22 and the character and B-cell and T-cell epitopes of gp120, could be a foundation for subsequent study of developing vaccine and polypeptide drugs.

Multi-epitopes vaccine design for surface glycoprotein against SARS-CoV-2 using immunoinformatic approach

“…ExPASy Protparam ( https://web.expasy.org/protparam-doc.html ) was used to analyze the vaccine's physiochemical features [ 33 ]. Analysis of solubility was used to identify the purity of a chemical quantitatively.…”

“…Analysis of solubility was used to identify the purity of a chemical quantitatively. SOLpro ( http://scratch.proteomics.ics.uci.edu/ ) was used to analyze the solubility of the multi-epitope vaccine construct [ 33 ].…”