Computational Biochemistry, Interdisciplinary Center for Scientific Computing, University of Heidelberg, D-69120 Heidelberg, Germany.
Computational Biochemistry, Interdisciplinary Center for Scientific Computing, University of Heidelberg, D-69120 Heidelberg, Germany
Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):E2947-56. doi: 10.1073/pnas.1401862111. Epub 2014 Jul 8.
Myosin is a molecular motor responsible for biological motions such as muscle contraction and intracellular cargo transport, for which it hydrolyzes adenosine 5'-triphosphate (ATP). Early steps of the mechanism by which myosin catalyzes ATP hydrolysis have been investigated, but still missing are the structure of the final ADP·inorganic phosphate (Pi) product and the complete pathway leading to it. Here, a comprehensive description of the catalytic strategy of myosin is formulated, based on combined quantum-classical molecular mechanics calculations. A full exploration of catalytic pathways was performed and a final product structure was found that is consistent with all experiments. Molecular movies of the relevant pathways show the different reorganizations of the H-bond network that lead to the final product, whose γ-phosphate is not in the previously reported HPγO4(2-) state, but in the H2PγO4(-) state. The simulations reveal that the catalytic strategy of myosin employs a three-pronged tactic: (i) Stabilization of the γ-phosphate of ATP in a dissociated metaphosphate (PγO3(-)) state. (ii) Polarization of the attacking water molecule, to abstract a proton from that water. (iii) Formation of multiple proton wires in the active site, for efficient transfer of the abstracted proton to various product precursors. The specific role played in this strategy by each of the three loops enclosing ATP is identified unambiguously. It explains how the precise timing of the ATPase activation during the force generating cycle is achieved in myosin. The catalytic strategy described here for myosin is likely to be very similar in most nucleotide hydrolyzing enzymes.
肌球蛋白是一种分子马达，负责生物运动，如肌肉收缩和细胞内货物运输，为此它水解腺苷 5'-三磷酸 (ATP)。肌球蛋白催化 ATP 水解的机制的早期步骤已经被研究过，但仍然缺少最终 ADP·无机磷酸盐 (Pi) 产物的结构和通向它的完整途径。在这里，根据结合量子经典分子力学计算，制定了肌球蛋白催化策略的综合描述。对催化途径进行了全面探索，并找到了最终产物结构，该结构与所有实验都一致。相关途径的分子电影显示了导致最终产物的氢键网络的不同重排，其 γ-磷酸盐不在先前报道的 HPγO4(2-) 状态，而是在 H2PγO4(-) 状态。模拟表明，肌球蛋白的催化策略采用了三管齐下的策略：(i) 将 ATP 的 γ-磷酸盐稳定在游离的焦磷酸盐 (PγO3(-)) 状态。(ii) 极化攻击水分子，从该水分子中提取质子。(iii) 在活性位点中形成多个质子线，以有效地将提取的质子转移到各种产物前体。明确识别了包围 ATP 的三个环在该策略中各自发挥的特定作用。它解释了肌球蛋白在产生力的循环中如何精确地实现 ATP 酶的激活时机。这里为肌球蛋白描述的催化策略在大多数核苷酸水解酶中可能非常相似。
