Biopolymers and cell. 2005; 21 (6): 536 - 547

Local structure for the HIV-1 gp120 V3 loop. Comparative analysis of the fragment conformations in HIV-MN and HIV-Thailand isolates

A. M. Andrianov

Secondary structure elements and conformations of irregular stretches for the HIV-MN gp120 V3 loop, comprising the virus immunogenic crown as well as the sites liable for cell tropism and cell fusion, were defined using the theoretical method developed previously. Computations based on the published data of NMR spectroscopy in water point out that the V3 loop N-terminal segment exhibits the extended site 1─4 separated by a double (b-turn 15─20 from its unordered C-terminal region 21─35. Collating the conformation obtained with the one derived earlier for the Thailand HIV-1 gp120 V3 loop indicates that the differences in their local structures are statistically significant. Despite the essential structures divergence, fourteen amino acids of the stretch under consideration, seven of which reside in its functionally active sites, were shown to preserve their conformational states in the MN and Thailand HIV-1 isolates. The residues keeping their conformations can be considered as the potential targets for the protein engineering methods used in the studies on developing the antiviral agents.