连续恒 pH 分子动力学模拟跨膜蛋白。
Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins.
机构信息
College of Computer Engineering, Jimei University, Xiamen, Fujian, China.
University of Maryland School of Pharmacy, Baltimore, MD, USA.
出版信息
Methods Mol Biol. 2021;2302:275-287. doi: 10.1007/978-1-0716-1394-8_15.
Abstract
Many membrane channels, transporters, and receptors utilize a pH gradient or proton coupling to drive functionally relevant conformational transitions. Conventional molecular dynamics simulations employ fixed protonation states, thus neglecting the coupling between protonation and conformational equilibria. Here we describe the membrane-enabled hybrid-solvent continuous constant pH molecular dynamics method for capturing atomic details of proton-coupled conformational dynamics of transmembrane proteins. Example protocols from our recent application studies of proton channels and ion/substrate transporters are discussed.
摘要
许多膜通道、转运体和受体利用 pH 梯度或质子偶联来驱动功能相关的构象转变。传统的分子动力学模拟采用固定的质子化状态，因此忽略了质子化和构象平衡之间的耦合。在这里，我们描述了一种用于捕获跨膜蛋白质子偶联构象动力学原子细节的膜允许混合溶剂连续恒 pH 分子动力学方法。我们最近在质子通道和离子/底物转运体应用研究中的实例方案进行了讨论。
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