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Structural fluctuation and concerted motions in F 1 ‐ATPase: A molecular dynamics study
Author(s) -
Ito Yuko,
Ikeguchi Mitsunori
Publication year - 2010
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21508
Subject(s) - protein subunit , beta (programming language) , gamma subunit , biophysics , g alpha subunit , molecular dynamics , atpase , chemistry , crystallography , physics , biology , enzyme , biochemistry , computational chemistry , gene , computer science , programming language
F 1 ‐ATPase is an adenosine tri‐phosphate (ATP)‐driven rotary motor enzyme. We investigated the structural fluctuations and concerted motions of subunits in F 1 ‐ATPase using molecular dynamics (MD) simulations. An MD simulation for the α 3 β 3 γ complex was carried out for 30 ns. Although large fluctuations of the N‐terminal domain observed in simulations of the isolated β E subunit were suppressed in the complex simulation, the magnitude of fluctuations in the C‐terminal domain was clearly different among the three β subunits (β E , β TP , and β DP ). Despite fairly similar conformations of the β TP and β DP subunits, the β DP subunit exhibits smaller fluctuations in the C‐terminal domain than the β TP subunit due to their dissimilar interface configurations. Compared with the β TP subunit, the β DP subunit stably interacts with both the adjacent α DP and α E subunits. This sandwiched configuration in the β DP subunit leads to strongly correlated motions between the β DP and adjacent α subunits. The β DP 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 β DP subunit can effectively induce movements of the γ subunit. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010