Department of Physiology, Johns Hopkins University, School of Medicine, Biophysics 206, Baltimore, MD 21205, USA.
J Mol Biol. 2012 Sep 28;422(4):575-93. doi: 10.1016/j.jmb.2012.06.001. Epub 2012 Jun 7.
SERCA is a membrane transport protein that has been extensively studied. There are a large number of highly resolved X-ray structures and several hundred mutations that have been characterized functionally. Despite this, the molecular details of the catalytic cycle, a cycle that includes large conformational changes, is not fully understood. In this computational study, we provide molecular dynamics descriptions of conformational changes during the E2→E1 transitions. The motivating point for these calculations was a series of insertion mutants in the A-M3 linker region that led to significant shifts in measured rates between the E2 and E1 states, as shown by experimental characterization. Using coarse-grained dynamic importance sampling within the context of a population shift framework, we sample on the intermediates along the transition pathway to address the mechanism for the conformational changes and the effects of the insertion mutations on the kinetics of the transition. The calculations define an approximation for the relative changes in entropy and enthalpy along the transition. These are found to be important for understanding the experimentally observed differences in rates. In particular, the interactions between cytoplasmic domains, water interactions, and the shifts in protein degrees of freedom with the insertion mutations show mutual compensation for the E2→E1 transitions in wild-type and mutant systems.
肌浆网钙 ATP 酶（SERCA）是一种膜转运蛋白，其相关研究已经非常深入。目前已有大量高分辨率的 X 射线结构和数百种功能特征明确的突变体。尽管如此，这个包括了巨大构象变化的催化循环的分子细节仍未被完全理解。在这项计算研究中，我们对 E2→E1 转变过程中的构象变化提供了分子动力学描述。这些计算的动机来自 A-M3 连接区的一系列插入突变体，这些突变导致 E2 和 E1 状态之间的测量速率发生显著变化，正如实验特征所表明的那样。我们使用粗粒度动力学重要性抽样，并在种群转变框架内进行采样，以研究构象变化的机制以及插入突变对转变动力学的影响。该计算定义了沿转变途径的熵和焓的相对变化的近似值。这些对于理解实验观察到的速率差异非常重要。特别是，细胞质结构域之间的相互作用、水相互作用以及与插入突变相关的蛋白质自由度的变化，显示了野生型和突变体系统中 E2→E1 转变的相互补偿。
