Structural fluctuation and concerted motions in F1-ATPase: A molecular dynamics study

Authors

  • Yuko Ito,

    1. Graduate School of Nanobioscience, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
    Search for more papers by this author
  • Mitsunori Ikeguchi

    Corresponding author
    1. Graduate School of Nanobioscience, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
    • Graduate School of Nanobioscience, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
    Search for more papers by this author

Abstract

F1-ATPase is an adenosine tri-phosphate (ATP)-driven rotary motor enzyme. We investigated the structural fluctuations and concerted motions of subunits in F1-ATPase using molecular dynamics (MD) simulations. An MD simulation for the α3β3γ complex was carried out for 30 ns. Although large fluctuations of the N-terminal domain observed in simulations of the isolated βE subunit were suppressed in the complex simulation, the magnitude of fluctuations in the C-terminal domain was clearly different among the three β subunits (βE, βTP, and βDP). Despite fairly similar conformations of the βTP and βDP subunits, the βDP subunit exhibits smaller fluctuations in the C-terminal domain than the βTP subunit due to their dissimilar interface configurations. Compared with the βTP subunit, the βDP subunit stably interacts with both the adjacent αDP and αE subunits. This sandwiched configuration in the βDP subunit leads to strongly correlated motions between the βDP and adjacent α subunits. The βDP subunit exhibits an extensive network of highly correlated motions with bound ATP and the γ subunit, as well as with the adjacent α subunits, suggesting that the structural changes occurring in the catalytically active βDP subunit can effectively induce movements of the γ subunit. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010

Ancillary