Biopolym. Cell. 2005; 21(2):165-173.
Bioorganic Chemistry
Computer modelling of the immunoreactive conformation of the HIV-RF immunodominant epitope
1Andrianov A. M., 1Sokolov Yu. A.
  1. Institute of Bioorganic Chemistry, NAS of Belarus
    5/2, Kuprevich Str., Minsk, Republic of Belarus, 220141


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 γ-turn at the stretch Gly-Pro-Gly is transformed into the non-standard β-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.
Keywords: human immunodeficiency virus, protein gp120, immunodominant epitope, conformational analysis, NMR spectroscopy, three-dimensional structure


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