Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
5419399 | Journal of Molecular Structure: THEOCHEM | 2006 | 11 Pages |
Abstract
All-atom molecular dynamics simulations were performed on partially folded states (with different secondary structure content) of the dimeric enzyme HIV-1 protease in aqueous solution. The calculations were based on previous simulations of the folding process of the protein based on a Go-model. The structures turn out to be stable, and the subunit-subunit contact surface is smaller than that of the native state. Interestingly, the flexibility of the partially folded states is similar to that observed for the monomer in the native state. The intersubunit contacts are formed by conserved residues, suggesting that these residues may play a role for the folding process. Docking a large set of molecules suggests that several ligands not yet associated to HIV-1 protease may bind to these partially unfolded structures.
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Authors
Manuela Cavallari, Caterina Ghio, Susanna Monti, Mauro Ferrario, Amos Maritan, Paolo Carloni,