Conformational flexibility of the catalytic Asp dyad in HIV-1 protease: anab initio study on the free enzyme

The enzyme protease from the human immunodeficiency virus type 1 (HIV-1 PR) is one of the main targets for therapeutic intervention in AIDS. Computer modeling is useful for probing the binding of novel ligands, yet empirical force field-based methods have encountered problems in adequately describin g interactions of the catalytic aspartyl pair. In this work we use ab initi o dynamic methods to study the molecular interactions and the conformationa l flexibility of the Asp dyad in the free enzyme. Calculations are performe d on model complexes that include, besides the Asp dyad, the conserved Thr2 6 and Gly27 residues and water molecules present in the active site channel , Our calculations provide proton location and binding mode of the active-s ite water molecule, which turn out to be different from those of the eukari otic isoenzyme. Furthermore, the calculations reproduce well the structural features of the aspartyl dyad in the protein. Finally, they allow the iden tification of both dipole/charge interactions and a low-barrier hydrogen bo nd as important stabilizing factors for the peculiar conformation of the ac tive site. These findings are consistent with site-directed mutagenesis exp eriments on the 27, 27' positions (Bagossi et al., Protein Eng 1996;9:997-1 003). The electric held of the protein frame (included in some of the calcu lations) does not affect significantly the chemical bonding at the cleavage site. (C) 2000 Wiley-Liss, Inc.