A peptide-linkage deletion procedure for estimate of energetic contributions of individual peptide groups in a complex environment: Application to parallel beta-sheets.
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.
Guo
Haobo
H
Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA. hguo1@utk.edu
Gorin
Andrey
A
Guo
Hong
H
D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D010455:Peptides