Bond Peter J, Faraldo-Gómez José D, Sansom Mark S P
Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
Biophys J. 2002 Aug;83(2):763-75. doi: 10.1016/S0006-3495(02)75207-7.
The bacterial outer membrane protein OmpA is composed of an N-terminal 171-residue beta-barrel domain (OmpA(171)) that spans the bilayer and a periplasmic, C-terminal domain of unknown structure. OmpA has been suggested to primarily serve a structural role, as no continuous pore through the center of the barrel can be discerned in the crystal structure of OmpA(171). However, several groups have recorded ionic conductances for bilayer-reconstituted OmpA(171). To resolve this apparent paradox we have used molecular dynamics (MD) simulations on OmpA(171) to explore the conformational dynamics of the protein, in particular the possibility of transient formation of a central pore. A total of 19 ns of MD simulations of OmpA(171) have been run, and the results were analyzed in terms of 1) comparative behavior of OmpA(171) in different bilayer and bilayer-mimetic environments, 2) solvation states of OmpA(171), and 3) pore characteristics in different MD simulations. Significant mobility was observed for residues and water molecules within the beta-barrel. A simulation in which putative gate region side chains of the barrel interior were held in a non-native conformation led to an open pore, with a predicted conductance similar to experimental measurements. The OmpA(171) pore has been shown to be somewhat more dynamic than suggested by the crystal structure. A gating mechanism is proposed to explain its documented channel properties, involving a flickering isomerization of Arg138, forming alternate salt bridges with Glu52 (closed state) and Glu128 (open state).
细菌外膜蛋白OmpA由一个跨双层的N端171个残基的β桶结构域（OmpA(171)）和一个结构未知的周质C端结构域组成。有人提出OmpA主要起结构作用，因为在OmpA(171)的晶体结构中未发现贯穿桶中心的连续孔道。然而，有几个研究小组记录了双层重构的OmpA(171)的离子电导。为了解决这一明显的矛盾，我们对OmpA(171)进行了分子动力学（MD）模拟，以探索该蛋白的构象动力学，特别是瞬时形成中心孔道的可能性。我们总共运行了19纳秒的OmpA(171) MD模拟，并从以下几个方面分析了结果：1）OmpA(171)在不同双层和双层模拟环境中的比较行为；2）OmpA(171)的溶剂化状态；3）不同MD模拟中的孔道特征。在β桶内观察到残基和水分子有显著的流动性。在一个模拟中，桶内部假定的门控区域侧链保持在非天然构象，导致形成一个开放孔道，其预测电导与实验测量值相似。已证明OmpA(171)孔道比晶体结构所显示的更具动态性。我们提出了一种门控机制来解释其已记录的通道特性，该机制涉及Arg138的闪烁异构化，与Glu52（关闭状态）和Glu128（开放状态）形成交替盐桥。
