HIV Protein Sequence/Structure Analysis in Support of Vaccine Development.
Abstract
The CD4 molecules on the target macrophage and T cell are the primary receptors for the HIV-1 surface glycoprotein, gp120. In addition, chemokine receptors on the macrophage and T cell serve as co-receptors in the virus-cell interactions. An understanding of the mechanism of virus-cell interactions requires quantitative analyses of the structure-function correlations of the surface epitopes on gp120 which contains several constant (C) and variable (V) subdomains linked as C1-V1-V2-C2-V3-C3-V4-C4-V5-C5. The surface epitope inside the C4 loop is critical for CD4 binding. The epitopes inside the V1-V2 and V3 loops elicit HIV-1 neutralizing response as well as determine tropism, fusion, and infectivity of the virus. In absence of a high resolution structure of the entire gp120, we have adopted an alternative approach to analyzing the structural properties of these surface epitopes. For this purpose, we have combined theoretical and experimental techniques including sequence analysis, molecular modeling, polypeptide engineering, NMR spectroscopy, antibody binding, and neutralization assay 5. First, we have analyzed the sequence-structure-antigenicity correlations of the third variable (V3) loop of gp120 both as a cyclic 35 amino acid long peptide and in the context of the native gp120. Second, we have obtained average low-energy structures of various other subdomains of gp120 including the V1-V2 and V4-C4 loops. Finally, we have constructed a working model of gp120 based upon the knowledge of (1) the structures of the gp120 subdomains obtained by molecular modeling in conjunction with NMR and other spectroscopic data, (2) the surface exposure data of various contiguous regions in gp120, and (3) the data on subdomain-subdomain interactions obtained from replication competency, monoclonal antibody binding, fusion, and infectivity assays.
Document Details
- Document Type
- Technical Report
- Publication Date
- Jan 01, 1994
- Accession Number
- ADA322181
Entities
People
- Goutam Gupta
Organizations
- United States Department of Energy