PDF(Pubmed)
Abstract：
After ATP-actin monomers assemble filaments, the ATP\'s [Formula: see text]-phosphate is hydrolyzedwithin seconds and dissociates over minutes. We used all-atom molecular dynamics simulations to sample the release of phosphate from filaments and study residues that gate release. Dissociation of phosphate from Mg2+ is rate limiting and associated with an energy barrier of 20 kcal/mol, consistent with experimental rates of phosphate release. Phosphate then diffuses within an internal cavity toward a gate formed by R177, as suggested in prior computational studies and cryo-EM structures. The gate is closed when R177 hydrogen bonds with N111 and is open when R177 forms a salt bridge with D179. Most of the time, interactions of R177 with other residues occlude the phosphate release pathway. Machine learning analysis reveals that the occluding interactions fluctuate rapidly, underscoring the secondary role of backdoor gate opening in Pi release, in contrast with the previous hypothesis that gate opening is the primary event.
摘要：
ATP-肌动蛋白单体组装细丝后，ATP的[配方:见正文]-磷酸盐在数秒内水解并在数分钟内解离。我们使用全原子分子动力学模拟对细丝中磷酸盐的释放进行采样，并研究了释放的残留物。磷酸盐从Mg2中的解离是限速的，并且与20kcal/mol的能垒有关，与磷酸盐释放的实验速率一致。磷酸盐然后在内部空腔内朝向由R177形成的栅极扩散,如在先前的计算研究和低温EM结构中所建议的。当R177与N111氢键结合时,门关闭,当R177与D179形成盐桥时,门打开。大多数时候,R177与其他残基的相互作用会阻碍磷酸盐释放途径。机器学习分析表明，闭塞的相互作用波动迅速，强调背门开启在Pi释放中的次要作用，与之前的假设相反，闸门打开是主要事件。
