title: Energetic Mechanism of Cytochrome c-Cytochrome c Oxidase Electron Transfer Complex Formation under Turnover Conditions Revealed by Mutational Effects and Docking Simulation.
abstract: Based on the mutational effects on the steady-state kinetics of the electron transfer reaction and our NMR analysis of the interaction site (Sakamoto, K., Kamiya, M., Imai, M., Shinzawa-Itoh, K., Uchida, T., Kawano, K., Yoshikawa, S., and Ishimori, K. (2011) Proc. Natl. Acad. Sci. U.S.A. 108, 12271-12276), we determined the structure of the electron transfer complex between cytochrome c (Cyt c) and cytochrome c oxidase (CcO) under turnover conditions and energetically characterized the interactions essential for complex formation. The complex structures predicted by the protein docking simulation were computationally selected and validated by the experimental kinetic data for mutant Cyt c in the electron transfer reaction to CcO. The interaction analysis using the selected Cyt c-CcO complex structure revealed the electrostatic and hydrophobic contributions of each amino acid residue to the free energy required for complex formation. Several charged residues showed large unfavorable (desolvation) electrostatic interactions that were almost cancelled out by large favorable (Columbic) electrostatic interactions but resulted in the destabilization of the complex. The residual destabilizing free energy is compensated by the van der Waals interactions mediated by hydrophobic amino acid residues to give the stabilized complex. Thus, hydrophobic interactions are the primary factors that promote complex formation between Cyt c and CcO under turnover conditions, whereas the change in the electrostatic destabilization free energy provides the variance of the binding free energy in the mutants. The distribution of favorable and unfavorable electrostatic interactions in the interaction site determines the orientation of the binding of Cyt c on CcO.
authors.affiliation: From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628.
authors.forename: Wataru
authors.initials: W
authors.lastname: Sato
authors.affiliation: the Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0315.
authors.forename: Seiji
authors.initials: S
authors.lastname: Hitaoka
authors.affiliation: the Division of Chemistry, Graduate School of Science, and.
authors.forename: Kaoru
authors.initials: K
authors.lastname: Inoue
authors.affiliation: From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628.
authors.forename: Mizue
authors.initials: M
authors.lastname: Imai
authors.affiliation: From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, and.
authors.forename: Tomohide
authors.initials: T
authors.lastname: Saio
authors.affiliation: From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, and.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Uchida
authors.affiliation: the Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan.
authors.forename: Kyoko
authors.initials: K
authors.lastname: Shinzawa-Itoh
authors.affiliation: the Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan.
authors.forename: Shinya
authors.initials: S
authors.lastname: Yoshikawa
authors.affiliation: the Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0315.
authors.forename: Kazunari
authors.initials: K
authors.lastname: Yoshizawa
authors.affiliation: From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, and koichiro@sci.hokudai.ac.jp.
authors.forename: Koichiro
authors.initials: K
authors.lastname: Ishimori
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D002417:Cattle; D045304:Cytochromes c / Q000737:chemistry* / Q000235:genetics; D003576:Electron Transport Complex IV / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D062105:Molecular Docking Simulation; D020125:Mutation, Missense
chemical_list: D045304:Cytochromes c; D003576:Electron Transport Complex IV
keywords: bioenergetics; cytochrome c; cytochrome c oxidase (complex IV); electron transfer complex; molecular docking