Simulations of the Alternating Access Mechanism of the Sodium Symporter Mhp1
Simulations of the Alternating Access Mechanism of the Sodium Symporter Mhp1
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DOI：
10.1016/j.bpj.2011.09.061
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发表时间：
2011-11-16
影响因子：
3.4
通讯作者：
Grabe, Michael
中科院分区：
文献类型：
--
作者：
Adelman, Joshua L.;Dale, Amy L.;Grabe, Michael
五螺旋反向重复序列（5HIR）超家族的钠偶联共转运蛋白使用交替进入机制将无数小分子转运穿过细胞膜。该机制中的主要步骤之一是从准备结合细胞外底物的状态到能够将底物递送至细胞质的状态的构象转变。在这里，我们构建了一个粗粒度模型的5HIR苯甲基海因转运蛋白Mhpl，它结合了实验结构的外向和内向开放的状态，调查这种构象变化的机制。使用加权系综路径采样方法，我们严格采样的向外面向内的过渡路径系综。过渡路径合奏揭示了一个异构的一组连接两个国家的途径，并确定了两种模式的运输：一个符合严格的交替访问机制和另一个内部和外部的门去耦导致瞬态形成一个连续的渗透途径，通过运输。我们还表明，向外和向内开放状态之间的构象转换的结果从刚性体运动的哈希基序相对于基板束，支持摇摆束假说。最后，我们的方法提供了更详细的化学交替机制的调查基础。
Sodium coupled cotransporters of the five-helix inverted repeat (5HIR) superfamily use an alternating access mechanism to transport a myriad of small molecules across the cell membrane. One of the primary steps in this mechanism is the conformational transition from a state poised to bind extracellular substrates to a state that is competent to deliver substrate to the cytoplasm. Here, we construct a coarse-grained model of the 5HIR benzylhydantoin transporter Mhpl that incorporates experimental structures of the outward- and inward-open states to investigate the mechanism of this conformational change. Using the weighted ensemble path-sampling method, we rigorously sample the outward- to inward-facing transition path ensemble. The transition path ensemble reveals a heterogeneous set of pathways connecting the two states and identifies two modes of transport: one consistent with a strict alternating access mechanism and another where decoupling of the inner and outer gates causes the transient formation of a continuous permeation pathway through the transporter. We also show that the conformational switch between the outward- and inward-open states results from rigid body motions of the hash motif relative to the substrate bundle, supporting the rocking bundle hypothesis. Finally, our methodology provides the groundwork for more chemically detailed investigations of the alternating mechanism.