Energetic mechanism of cytochrome c-cytochrome c oxidase electron transfer complex formation under turnover conditions revealed by mutational effects and docking simulation

Wataru Sato, Seiji Hitaoka, Kaoru Inoue, Mizue Imai, Tomohide Saio, Takeshi Uchida, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Kazunari Yoshizawa, Koichiro Ishimori

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Pages (from-to)15320-15331
Number of pages12
JournalJournal of Biological Chemistry
Volume291
Issue number29
DOIs
Publication statusPublished - Jul 15 2016

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Electron Transport Complex IV
Cytochromes c
Static Electricity
Free energy
Electrons
Coulomb interactions
Hydrophobic and Hydrophilic Interactions
Electrostatics
Amino Acids
Kinetics
Nuclear magnetic resonance
Proteins

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Cell Biology

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Energetic mechanism of cytochrome c-cytochrome c oxidase electron transfer complex formation under turnover conditions revealed by mutational effects and docking simulation. / Sato, Wataru; Hitaoka, Seiji; Inoue, Kaoru; Imai, Mizue; Saio, Tomohide; Uchida, Takeshi; Shinzawa-Itoh, Kyoko; Yoshikawa, Shinya; Yoshizawa, Kazunari; Ishimori, Koichiro.

In: Journal of Biological Chemistry, Vol. 291, No. 29, 15.07.2016, p. 15320-15331.

Research output: Contribution to journalArticle

Sato, Wataru ; Hitaoka, Seiji ; Inoue, Kaoru ; Imai, Mizue ; Saio, Tomohide ; Uchida, Takeshi ; Shinzawa-Itoh, Kyoko ; Yoshikawa, Shinya ; Yoshizawa, Kazunari ; Ishimori, Koichiro. / Energetic mechanism of cytochrome c-cytochrome c oxidase electron transfer complex formation under turnover conditions revealed by mutational effects and docking simulation. In: Journal of Biological Chemistry. 2016 ; Vol. 291, No. 29. pp. 15320-15331.
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AU - Imai, Mizue

AU - Saio, Tomohide

AU - Uchida, Takeshi

AU - Shinzawa-Itoh, Kyoko

AU - Yoshikawa, Shinya

AU - Yoshizawa, Kazunari

AU - Ishimori, Koichiro

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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.

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