Study on conformational homology of the HIV-1 gp120 protein V3 loop. Structural analysis of the HIV-RF and HIV-thailand viral strains

Abstract

A conformation of the H-IV-RF gp120 V3 loop giving rise to the virus principal neutralizing determinant as well as determinants of cell tropism and syncytium formation was built by computer modeling methods using NMR spectroscopy data. The elements of the HIV-RF V3 loop secondary structure and conformational states of its irregular stretches were determined. The structural elements preserved in two viral strains, were identified using the comparative analysis of simulated structure with that of homologous site for the HIV-Thailand gp120 V3 loop. Conservative structure elements of the HIV-1 V3 loop are considered to be promising targets for deriving its chemically modified forms characterized by the enhanced immunogenicity and cross-reactivity of neutralizing antibodies, as well as for the antiviral drug design resulting from these researches.