title: Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method.
abstract: A visualization method for inter-fragment interaction energies (IFIEs) of biopolymers is presented on the basis of the fragment molecular orbital (FMO) method. The IFIEs appropriately illustrate the information about the interaction energies between the fragments consisting of amino acids, nucleotides and other molecules. The IFIEs are usually analyzed in a matrix form called an IFIE matrix. Analyzing the IFIE matrix, we detect important fragments for the function of biomolecular systems and quantify the strength of interaction energies based on quantum chemistry, including the effects of charge transfer, electronic polarization and dispersion force. In this study, by analyzing a protein-DNA complex, we report a visual representation of the IFIE matrix, a so-called IFIE map. We comprehensively examine what information the IFIE map contains concerning structures and stabilities of the protein-DNA complex.
authors.affiliation: Graduate School of Science and Technology, Kobe University, 1-1, Rokkodai, Nada, Kobe 657-8501, Japan. kurisaki@insilico.h.kobe-u.ac.jp
authors.forename: Ikuo
authors.initials: I
authors.lastname: Kurisaki
authors.forename: Kaori
authors.initials: K
authors.lastname: Fukuzawa
authors.forename: Yuto
authors.initials: Y
authors.lastname: Komeiji
authors.forename: Yuji
authors.initials: Y
authors.lastname: Mochizuki
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Nakano
authors.forename: Janine
authors.initials: J
authors.lastname: Imada
authors.forename: Aneta
authors.initials: A
authors.lastname: Chmielewski
authors.forename: Stuart M
authors.initials: SM
authors.lastname: Rothstein
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Watanabe
authors.forename: Shigenori
authors.initials: S
authors.lastname: Tanaka
mesh_terms: D000595:Amino Acid Sequence; D002627:Chemistry, Physical / Q000379:methods*; D000242:Cyclic AMP / Q000737:chemistry*; D002373:Cyclic AMP Receptor Protein / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011789:Quantum Theory
chemical_list: D002373:Cyclic AMP Receptor Protein; D004247:DNA; D000242:Cyclic AMP