Immunoinformatics Study of gp120 of Human Immunodeficiency Virus Type 1 Subtype CRF35_AD Isolated from Iranian Patients

Human Immunodeficiency Virus (HIV)-1 infection is one of the most important infectious diseases in Iran, and common isolates belong to the new CRF35_AD subtypes. The Gp120 protein, which is located on the surface of the HIV envelope, plays a role in entrance into host cells and immune responses. As there isn’t any clear analysis of the envelope protein of Iranian isolates regarding potential variations, structural and immunological properties, in the current study we attempted to research in this area. The present study was designed to demonstrate the immunoinformatics of gp120 of human immunodeficiency virus Type 1 subtype CRF35_AD, isolated from Iranian patients. In this analytical perspective bioinformatics study, the steps were as follows; data collection and sequence classification (303 sequences), finding the mutational/conserved regions, evaluation of N-linked glycosylation sites, prediction of tertiary structures, model validation, and prediction of conformational and linear B-cell epitopes. High degrees of sequence variation in the CRF35_AD subtype and also more than 10 variation sites in gp120 protein segments were identified. The total N-linked glycosylation sites for selected complete env sequences in NX [ST] pattern and the NXS and NXT combination count revealed that most of the glycosylation sites were conserved. Tertiary structure was obtained by homology modeling, and the Ramachandran plot assessment showed model validity. Finally, mapped consensus discontinuous immunogenic regions (epitopes) were AA25-65, AA337-365 and AA443-505. The obtained results provide a background for understanding CRF35_AD molecular characteristics, as well as design and development of effective HIV-1 vaccines and immunotherapeutic regimens against CRF35_AD subtype.