PMID- 27226541
OWN - NLM
STAT- MEDLINE
DCOM- 20170505
LR  - 20210205
IS  - 1083-351X (Electronic)
IS  - 0021-9258 (Print)
IS  - 0021-9258 (Linking)
VI  - 291
IP  - 29
DP  - 2016 Jul 15
TI  - Energetic Mechanism of Cytochrome c-Cytochrome c Oxidase Electron Transfer 
      Complex Formation under Turnover Conditions Revealed by Mutational Effects and 
      Docking Simulation.
PG  - 15320-31
LID - 10.1074/jbc.M115.708065 [doi]
AB  - 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.
CI  - (c) 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
FAU - Sato, Wataru
AU  - Sato W
AD  - From the Graduate School of Chemical Sciences and Engineering, Hokkaido 
      University, Sapporo 060-8628.
FAU - Hitaoka, Seiji
AU  - Hitaoka S
AD  - the Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 
      819-0315.
FAU - Inoue, Kaoru
AU  - Inoue K
AD  - the Division of Chemistry, Graduate School of Science, and.
FAU - Imai, Mizue
AU  - Imai M
AD  - From the Graduate School of Chemical Sciences and Engineering, Hokkaido 
      University, Sapporo 060-8628.
FAU - Saio, Tomohide
AU  - Saio T
AD  - 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.
FAU - Uchida, Takeshi
AU  - Uchida T
AD  - 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.
FAU - Shinzawa-Itoh, Kyoko
AU  - Shinzawa-Itoh K
AD  - the Department of Life Science, Graduate School of Life Science, University of 
      Hyogo, Hyogo 678-1297, Japan.
FAU - Yoshikawa, Shinya
AU  - Yoshikawa S
AD  - the Department of Life Science, Graduate School of Life Science, University of 
      Hyogo, Hyogo 678-1297, Japan.
FAU - Yoshizawa, Kazunari
AU  - Yoshizawa K
AD  - the Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 
      819-0315.
FAU - Ishimori, Koichiro
AU  - Ishimori K
AD  - 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.
LA  - eng
SI  - PDB/2PQR
SI  - PDB/3ZCF
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20160513
PL  - United States
TA  - J Biol Chem
JT  - The Journal of biological chemistry
JID - 2985121R
RN  - 9007-43-6 (Cytochromes c)
RN  - EC 1.9.3.1 (Electron Transport Complex IV)
SB  - IM
MH  - Amino Acid Substitution
MH  - Animals
MH  - Cattle
MH  - Cytochromes c/*chemistry/genetics
MH  - Electron Transport Complex IV/*chemistry/genetics
MH  - Humans
MH  - *Molecular Docking Simulation
MH  - *Mutation, Missense
PMC - PMC4946943
OTO - NOTNLM
OT  - bioenergetics
OT  - cytochrome c
OT  - cytochrome c oxidase (complex IV)
OT  - electron transfer complex
OT  - molecular docking
EDAT- 2016/05/27 06:00
MHDA- 2017/05/06 06:00
PMCR- 2017/07/15
CRDT- 2016/05/27 06:00
PHST- 2015/12/03 00:00 [received]
PHST- 2016/05/27 06:00 [entrez]
PHST- 2016/05/27 06:00 [pubmed]
PHST- 2017/05/06 06:00 [medline]
PHST- 2017/07/15 00:00 [pmc-release]
AID - S0021-9258(20)41273-6 [pii]
AID - M115.708065 [pii]
AID - 10.1074/jbc.M115.708065 [doi]
PST - ppublish
SO  - J Biol Chem. 2016 Jul 15;291(29):15320-31. doi: 10.1074/jbc.M115.708065. Epub 
      2016 May 13.