Recognition properties of V3-specific antibodies to V3 loop peptides derived from HIV-1 gp120 presented in multiple conformations

TO identify structural constraints and amino acid sequences important for a ntibody recognition of the third variable domain (V3) of HIV-1 gp120, we ha ve studied the solution conformation of three 35-mer circular V3 loop pepti des derived from HIV-1 strains which differ in syncytium- (SI) and nonsyncy tium-inducing (NSI) capacity. In addition to 2D NMR and CD analyses, fluid- and solid-phase immunoassays were performed using V3-specific antibodies t o V3 peptides and gp120 derived from different strains of HIV-1. NMR and CD spectroscopy indicated that circular and linear V3 loops exist in water as a dynamic ensemble of multiple conformations. Amino acid substitutions and biochemical modifications of the V3 loop were found to affect antibody bin ding depending on the presentation of the antigens. From NMR observations a nd immunological experiments, we provide evidence for a V3 loop specific mo noclonal antibody interaction which is directed predominantly against linea r epitopes rather than against discontinuous epitopes. The absence of a sin gle defined solution conformation of 35-mer circular V3 peptides should be taken into account when using VS-related peptides to investigate structural elements in the V3 domain of the gp120 envelope protein of HIV-1 involved in biological processes of the virus.