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Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model.

Dimerization of HIV-I protease (HIV PR) monomers is an essential prerequisite for viral proteolytic activity and the subsequent generation of infectious virus particles. Disrupting dimerization of the enzyme can inhibit its activity. We have calculated the relative binding free energies between different dimers of the HIV protease using molecular dynamics and a continuum model, which we call MM/PBSA. We examined the dominant negative inhibition of the HIV PR by a mutated form of the protease and found relative dimerization free energies of homo- and hetero-dimerization consistent with experimental data. We also developed a rapid screening method, which was called the virtual mutagenesis method to consider other mutations which might stabilize non-wild-type heterodimers. Using this approach, we considered the mutations near the dimer interface which might cause dominant negative inhibition of the HIV PR. The rapid method we developed can be used in studying any ligand-protein and protein-protein interaction, in order to identify mutations that can enhance the binding affinities of the complex.