Density functional study of molecular interactions in secondary structures of proteins

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Author(s)

    • Takano Yu
    • Institute for Protein Research, Osaka University|Graduate School of Information Sciences, Hiroshima City University|JST, CREST

Abstract

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using <i>ab initio</i> wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

Journal

  • Biophysics and Physicobiology

    Biophysics and Physicobiology 13(0), 27-35, 2016

    The Biophysical Society of Japan

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