A FAST ESTIMATE OF ELECTROSTATIC GROUP CONTRIBUTIONS TO THE FREE-ENERGY OF PROTEIN-INHIBITOR BINDING

Dissecting ligand-protein binding free energies in individual contribu tions of protein residues (which are referred to here as 'group contri butions') is of significant importance. For example, such contribution s could help in estimating the corresponding mutational effects and in studies of drug resistance problems, However, the meaning of group co ntributions is not always uniquely defined and the approximations for rapid estimates of such contributions are not well developed, In this paper, the nature of group contributions to binding free energy is exa mined, focusing particularly on electrostatic contributions which are expected to be well behaved. This analysis examines different definiti ons of group contributions; the 'relaxed' group contributions that rep resent the change in binding energy upon mutation of the given residue to glycine, and the 'non-relaxed' group contributions that represent the scaled Coulomb interaction between the given residue and the ligan d. Both contributions are defined and evaluated by the linear response approximation (LRA) of the PDLD/S method. The present analysis consid ers the binding of pepstatin to endothiapepsin and 23 of its mutants a s a test case for a neutral ligand. The 'non-relaxed' group contributi ons of 15 endothiapepsin residues show significant peaks in the 'elect rostatic fingerprint'. The residues that contribute to the electrostat ic fingerprint are located in the binding site of endothiapepsin. They include the aspartic dyad (Asp32, Asp215) with adjacent residues and the flap region. Twelve of these 15 residues have a heavy atom distanc e of <3.75 Angstrom to pepstatin, The contributions of 8 (10) of these 12 residues can be reconciled with the calculated 'relaxed' group con tributions where one allows the protein and solvent (solvent only) to relax upon mutation of the given residue to glycine. On the other hand , it was found that residues at the second 'solvation shell' can have relaxed contributions that are not captured by the non-relaxed approac h. Hence, whereas residues with significant non-relaxed electrostatic contributions are likely to contribute to binding, residues with small non-relaxed contributions may still affect the binding energy, At any rate, it is established here that even in the case of uncharged inhib itors it is possible to use the non-relaxed electrostatic fingerprint to detect 'hot' residues that are responsible for binding, This is sig nificant since some versions of the non-relaxed approximation are fast er by several orders of magnitude than more rigorous approaches, The g eneral applicability of this approach is outlined, emphasizing its pot ential in studies of drug resistance where it is crucial have a rapid way of anticipating the effect of mutation on both drug binding and ca talysis.