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Conformational Dynamics of the F₁-ATPase ß-Subunit: A Molecular Dynamics Study

Theoretical Molecular Biophysics Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany

Correspondence: Address reprint requests to H. Grubmüller, Tel.: 49-551-201-1763; Fax: 49-551-201-1089; E-mail: hgrubmu{at}gwdg.de.

According to the different nucleotide occupancies of the F₁-ATPase ß-subunits and due to the asymmetry imposed through the central -subunit, the ß-subunit adopts different conformations in the crystal structures. Recently, a spontaneous and nucleotide-independent closure of the open ß-subunit upon rotation of the -subunit has been proposed. To address the question whether this closure is dictated by interactions to neighbored subunits or whether the open ß-subunit behaves like a prestressed "spring," we report multinanosecond molecular dynamics simulations of the isolated ß-subunit with different start conformations and different nucleotide occupancies. We have observed a fast, spontaneous closure motion of the open ß_E-subunit, consistent with the available x-ray structures. The motions and kinetics are similar to those observed in simulations of the full (ß)₃-complex, which support the view of a prestressed "spring," i.e., that forces internal to the ß_E-subunit dominate possible interactions from adjacent -subunits. Additionally, nucleotide removal is found to trigger conformational transitions of the closed ß_TP-subunit; this provides evidence that the recently resolved half-closed ß-subunit conformation is an intermediate state before product release. The observed motions provide a plausible explanation why ADP and P_i are required for the release of bound ATP and why -depleted (ß)₃ has a drastically reduced hydrolysis rate.

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