Structural characteristics of yeast F 1-ATPase before and after 16-degree rotation of the γ subunit: Theoretical analysis focused on the water-entropy effect

Takashi Yoshidome, Yuko Ito, Nobuyuki Matubayasi, Mitunori Ikeguchi, Masahiro Kinoshita

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)

Abstract

We have recently proposed a novel picture of the rotation mechanism for F 1-ATPase [T. Yoshidome, Y. Ito, M. Ikeguchi, and M. Kinoshita, J. Am. Chem. Soc. 133, 4030 (2011)]10.1021/ja109594y. In the picture, the asymmetric packing in F 1-ATPase, originating from the water-entropy effect, plays the key role in the rotation. Here, we analyze the differences between the experimentally determined structures of yeast F 1-ATPase before and after 16° rotation of the γ subunit with the emphasis on the water-entropy effect. For each of these structures, we calculate the hydration entropies of three sub-complexes comprising the γ subunit, one of the β subunits, and two α subunits adjacent to them. The β E, β TP, and β DP subunits are involved in sub-complexes I, II, and III, respectively. The calculation is performed using a hybrid of the angle-dependent integral equation theory combined with the molecular model for water and the morphometric approach. The absolute value of the hydration entropy is in the following order: sub-complex I > sub-complex II > sub-complex III. The packing efficiency of the sub-complex follows the opposite order. The rotation gives rise to less efficient packing in sub-complex III and a corresponding water-entropy loss. However, the other two sub-complexes, accompanying water-entropy gains, become more efficiently packed. These results are consistent with our picture of the rotation mechanism, supporting its validity. The water-entropy analysis shows that the interfaces of α DPDP and α EE become more open after the rotation, which is in accord with the experimental observation.

Original languageEnglish
Article number035102
JournalJournal of Chemical Physics
Volume137
Issue number3
DOIs
Publication statusPublished - 2012 Jul 21
Externally publishedYes

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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