Locked on One Side Only: Ground State Dynamics of the Outer Membrane Efflux Duct ToIC
Locked on One Side Only: Ground State Dynamics of the Outer Membrane Efflux Duct ToIC
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DOI：
10.1021/bi201814s
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发表时间：
2012-02-28
期刊：
影响因子：
2.9
通讯作者：
Kandt, Christian
中科院分区：
文献类型：
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作者：
Raunest, Martin;Kandt, Christian
外膜通道ToIC与三种蛋白超家族的内膜转运蛋白一起在抗生素的排出和细胞毒素的分泌中起主要作用，外膜通道ToIC以至少两种状态发生，阻止或允许底物通过。潜在的门控机制的细节尚未完全理解。为了解决细胞外通路控制和周质门控机制的问题，我们在磷脂膜/150 mM NaCl水环境中对野生型ToIC进行了一系列独立的、无偏的150-300 ns分子动力学模拟。我们发现ToIC在细胞外侧自由地打开和关闭，这表明在分离的蛋白质中在这一侧不存在门控机制。在周质方面，我们观察到外周质瓶颈区域在所有模拟中采用比ToIC野生型晶体结构更开放的构象，直到在一次运行中，两个钠离子的连续结合诱导过渡到比任何可用的ToIC X射线结构更封闭的构象。与Asp 374附近的钠驻留概率增加同时，Asp 374处的内周质瓶颈区域在整个模拟过程中保持关闭，除非从系统中去除所有NaCl，从而诱导外瓶颈和内瓶颈重新打开。我们的研究结果表明，ToIC仅以钠依赖性方式锁定在周质侧。
Playing a major role in the expulsion of antibiotics and the secretion of cell toxins in conjunction with inner membrane transporters of three protein superfamilies, the outer membrane channel ToIC occurs in at least two states blocking or permitting the passage of substrates. The details of the underlying gating mechanism are not fully understood. Addressing the questions of extracellular access control and periplasmic gating mechanism, we conducted a series of independent, unbiased 150-300 ns molecular dynamics simulations of wild-type ToIC in a phospholipid membrane/150 mM NaCl water environment. We find that ToIC opens and closes freely on the extracellular side, suggesting the absence of a gating mechanism on this side in the isolated protein. On the periplasmic side, we observe the outer periplasmic bottleneck region adopting in all simulations a conformation more open than the ToIC wild-type crystal structures until in one run the successive binding of two sodium ions induces the transition to a conformation more closed than any of the available ToIC X-ray structures. Concurrent with a heightened sodium residence probability near Asp374, the inner periplasmic bottleneck region at Asp374 remains closed throughout the simulations unless all NaCl is removed from the system, inducing a reopening of the outer and inner bottleneck. Our findings suggest that ToIC is locked only on the periplasmic side in a sodium-dependent manner.