Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates.
Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates.
复制标题
p97 复合物的模拟表明水解中间体的新构象状态。
DOI：
10.1002/pro.2024
复制
发表时间：
2012
期刊：
影响因子：
--
通讯作者：
McCammon,JAndrew
中科院分区：
文献类型：
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作者：
Wereszczynski,Jeff;McCammon,JAndrew
非常重要的AAA(与各种细胞活动相关的ATPase)蛋白p97参与细胞功能，从复制到错误折叠蛋白的降解，最近被认为是一个新的化疗靶点。P97是一种大分子机器，已被证明在体外可以六角化，每个单体由一个负责与效应蛋白结合的N结构域和两个AAA重复序列(D1和D2)组成。然而，结构研究在几个重要的特征上没有定论或相互不一致，如N结构域的位置，D_1和D_2环的相对取向，以及中心孔的尺寸。在这里，我们提供了p97六聚体在预水解、过渡和后水解状态下的原子尺度模拟。为了提高低分辨率和高分辨率实验研究之间的一致性，我们首先使用了一种有偏的模拟技术，分子动力学柔性拟合(MDFF)，来提高这些实验中描述的结构之间的相关性。在此之后，我们进行了扩展的经典分子动力学模拟，这些模拟不仅表明在MDFF阶段产生的结构是稳定的，而且揭示了对每个状态重要的动力学。模拟结果提出了一种混合模型，其中N和D2结构域是动态的，而D_1结构域是相对静态的，盐桥在预水解状态下稳定了N结构域的位置，由D_1和D_2形成的环相对彼此旋转。
The vitally important AAA (ATPases associated with various cellular activities) protein p97 is involved in cellular functions ranging from replication to degradation of misfolded proteins and has recently been proposed as a novel chemotherapeutic target. p97 is a large molecular machine that has been shown to hexamerizein vitro, with each monomer consisting of an N domain responsible for binding to effector proteins and two AAA repeats (D1 and D2). However, structural studies are inconclusive or in disagreement with one another on several important features such as the locations of the N domains, the relative orientations of the D1 and D2 rings, and the dimensions of the central pore. Here, we present atomic‐scale simulations of the p97 hexamer in the prehydrolysis, transition, and post‐hydrolysis states. To improve the agreement between low‐ and high‐resolution experimental studies, we first use a biased simulation technique, molecular dynamics flexible fitting (MDFF), to improve the correlation between the structures described in these experiments. We follow this with extended, classical molecular dynamics simulations, which not only show that structures generated in the MDFF phase are stable, but reveal insights into the dynamics important to each state. Simulation results suggest a hybrid model for hydrolysis, in which the N and D2 domains are dynamic while the D1 domains are relatively static, salt bridges stabilize the position of the N domains in the pre‐hydrolysis state, and the rings formed by D1 and D2 rotate relative to one another.