A Peptide-Linkage Deletion Procedure for Estimate of Energetic Contributions of Individual Peptide Groups in a Complex Environment: Application to Parallel β-Sheets

A peptide-linkage deletion procedure is introduced for extracting the quantum merchanical (QM) interaction energies of individual groups in a complex environment and applied for the determination of the energetic contributions of the individual hydrogen bond acceptors (C=O's) and donors (N-H's) in parallel β-sheets. For the β-sheets studied here, the results show that the contributions from the H-bond acceptors (C=O) can be significantly greater than the contribution from the donors (N-H). It is suggested that this imbalance may be induced, at least in part, by the inter-strand C-H...O=C interactions which may play an important role in stabilizing β-sheets. The results demonstrate the usefulness of the approach proposed in this paper to study interactions in complex protein environments.