title: Density functional study of molecular interactions in secondary structures of proteins.
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, usingab initiowave 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.
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan; Graduate School of Information Sciences, Hiroshima City University, Hiroshima 731-3194, Japan; JST, CREST, Kawaguchi, Saitama 332-0012, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Takano
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
authors.forename: Ayumi
authors.initials: A
authors.lastname: Kusaka
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura
keywords: density functional theory; force field; hydrogen bond; α-helix; β-sheet