Böckmann Rainer A, Grubmüller Helmut
Theoretical Molecular Biophysics Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Biophys J. 2003 Sep;85(3):1482-91. doi: 10.1016/S0006-3495(03)74581-0.
According to the different nucleotide occupancies of the F(1)-ATPase beta-subunits and due to the asymmetry imposed through the central gamma-subunit, the beta-subunit adopts different conformations in the crystal structures. Recently, a spontaneous and nucleotide-independent closure of the open beta-subunit upon rotation of the gamma-subunit has been proposed. To address the question whether this closure is dictated by interactions to neighbored subunits or whether the open beta-subunit behaves like a prestressed "spring," we report multinanosecond molecular dynamics simulations of the isolated beta-subunit with different start conformations and different nucleotide occupancies. We have observed a fast, spontaneous closure motion of the open beta(E)-subunit, consistent with the available x-ray structures. The motions and kinetics are similar to those observed in simulations of the full (alpha beta)(3)gamma-complex, which support the view of a prestressed "spring," i.e., that forces internal to the beta(E)-subunit dominate possible interactions from adjacent alpha-subunits. Additionally, nucleotide removal is found to trigger conformational transitions of the closed beta(TP)-subunit; this provides evidence that the recently resolved half-closed beta-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 gamma-depleted (alpha beta)(3) has a drastically reduced hydrolysis rate.
根据F(1)-ATP酶β亚基的不同核苷酸占据情况，以及由于中心γ亚基所施加的不对称性，β亚基在晶体结构中呈现出不同的构象。最近，有人提出在γ亚基旋转时，开放的β亚基会发生自发且不依赖核苷酸的闭合。为了解决这种闭合是由与相邻亚基的相互作用所决定，还是开放的β亚基表现得像一个预应力“弹簧”这一问题，我们报告了对具有不同起始构象和不同核苷酸占据情况的分离β亚基进行的多纳秒分子动力学模拟。我们观察到开放的β(E)亚基有快速、自发的闭合运动，这与现有的x射线结构一致。其运动和动力学与在完整的(αβ)3γ复合体模拟中观察到的相似，这支持了预应力“弹簧”的观点，即β(E)亚基内部的力主导了来自相邻α亚基的可能相互作用。此外，发现去除核苷酸会触发闭合的β(TP)亚基的构象转变；这提供了证据表明最近解析出的半闭合β亚基构象是产物释放前的中间状态。观察到的运动为为什么释放结合的ATP需要ADP和Pi，以及为什么γ缺失的(αβ)3水解速率大幅降低提供了合理的解释。
