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Abstract
A model of the spatial structure of the immunodominant epitope of human immunodeficiency virus type 1 (HIV-Haiti virion) consistent with the NMR data was constructed using an earlier proposed method based on theoretical calculations. It was found that, in aqueous solution, the main immunogenic region of the virus protein gp120 took the prevalent conformation of a double β-turn IV-IV. It is shown that two structures of this fragment found in the crystal were present in the set of preferable conformations of the HIV-Haiti immunodominant epitope. On the basis of comparative analysis of the 3D structures of the immunodominant epitopes of type 1 human immunodeficiency virus (HIV-Haiti, HIV-Thailand, and HIV-MN virions), it was concluded that the studied gp120 fragment forms similar spatial backbone structures in these three virus subtypes; however, these structures are formed from different local minimums of the constituent amino acids. It was assumed that the detected distinctions between the local structures of this fragment determine the specificity of HIV-1 binding to virus-neutralizing antibodies.[PUBLICATION ABSTRACT]