A peptide-linkage deletion procedure for estimate of energetic contributions of individual peptide groups in a complex environment: Application to parallel beta-sheets

Interdisciplinary Sciences, Computational Life Sciences
Haobo GuoHong Guo

Abstract

A peptide-linkage deletion procedure is introduced for extracting the quantum mechanical (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 beta-sheets. For the beta-sheets studied here, the results show that the contributions from the H-bond acceptors (C=O) can be significantly greater than the contributions from the donors (N-H). It is suggested that this imbalance may be induced, at least in part, by the inter-strand C(alpha)-Hcdots, three dots, centeredO=C interactions which may play an important role in stabilizing beta-sheets. The results demonstrate the usefulness of the approach proposed in this paper to study interactions in complex protein environments.

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Citations

Nov 2, 2016·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Steve Scheiner
Sep 14, 2013·The Journal of Physical Chemistry. B·Upendra Adhikari, Steve Scheiner

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