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

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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 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 contributions from the donors (N-H). It is suggested that this imbalance may be induced, at least in part, by the inter-strand Cα-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.

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Author notes

  1. Haobo Guo

    Present address: UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA

Authors and Affiliations

  1. Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA

    Haobo Guo & Hong Guo

  2. Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

    Andrey Gorin

  3. UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA

    Hong Guo

Authors
  1. Haobo Guo
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  2. Andrey Gorin
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  3. Hong Guo
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Correspondence to Hong Guo.

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Guo, H., Gorin, A. & Guo, H. A peptide-linkage deletion procedure for estimate of energetic contributions of individual peptide groups in a complex environment: Application to parallel β-Sheets. Interdiscip Sci Comput Life Sci 1, 12–20 (2009). https://doi.org/10.1007/s12539-008-0011-8

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  • DOI: https://doi.org/10.1007/s12539-008-0011-8

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