Biopolymers and cell. 2005; 21 (2): 165 - 173

Computer modelling of the immunoreactive conformation of the HIV-RF immunodominant epitope

A. M. Andrianov, Yu. A. Sokolov

3D structure for the HIV-RF immunodominant epitope was computed in terms of NMR spectroscopy data using the theoretical procedure including a probabilistic approach in conjunction with the molecular mechanics algorithms and quantum chemical methods. The immunogenic crown of the virus protein gp120 was shown to form in water solution the prevalent conformation in which the inverse g-turn at the stretch Gly-Pro-Gly is transformed into the non-standard g-turn IV (Gly-Arg-Val-Ile). The best energy conformation of the HIV-RF immunogenic tip was found to be similar to that revealed in crystal for peptide antigen complex with the Fab fragment of antibody 58.2. The following conclusion was drawn from the comparative analysis of simulated structures with the ones computed previously for the HIV-Thailand and HIV-MN isolates: the immunogenic tip of gp120 gives rise to the similar spatial backbone forms in different HIV-1 strains but has some inherent conformational flexibility of its individual amino acid residues.

Key words: human immunodeficiency virus, protein gp120, immunodominant epitope, conformational analysis, NMR spectroscopy, three-dimensional structure.