The Conformational Transition Pathway of ATP Binding Cassette Transporter MsbA Revealed by Atomistic Simulations*
The Conformational Transition Pathway of ATP Binding Cassette Transporter MsbA Revealed by Atomistic Simulations*
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DOI：
10.1074/jbc.m109.056432
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发表时间：
2009-12
期刊：
影响因子：
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通讯作者：
J. Weng;Kangnian Fan;Wenning Wang
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文献类型：
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作者：
J. Weng;Kangnian Fan;Wenning Wang
ATP结合盒转运蛋白是整合的膜蛋白，其利用两个核苷酸结合结构域（NBD）处ATP水解释放的能量通过两个跨膜结构域（TMD）处的通道跨细胞膜转运多种底物。来自革兰氏阴性菌的MsbA是一种脂质和多药耐药性ATP结合盒输出体，其可以在不同状态下的晶体结构所揭示的外向和内向构象之间发生大规模构象变化。在这里，我们使用有针对性的分子动力学模拟方法来探索的原子细节的构象转变，从外向内面向状态的MsbA。分子动力学轨迹揭示了一个明确的时空顺序的构象运动。在NBD二聚体界面的核苷酸结合位点的破坏是引发以下构象变化的第一个事件，验证了构象转换是由ATP水解触发的假设。NBD的保守X环被鉴定为参与稳定TMD的细胞质四螺旋束的相互作用网络，并在介导NBD和TMD之间的串扰中发挥重要作用。NBD二聚体的运动通过X环传递以破坏四螺旋束，依次诱导细胞质侧和周质侧的跨膜螺旋的包装重排。TMD的每个周质翼内的包装重排导致底物结合位点的暴露发生在轨迹的末端阶段，防止结合位点可及性的错误定时。
ATP binding cassette transporters are integral membrane proteins that use the energy released from ATP hydrolysis at the two nucleotide binding domains (NBDs) to translocate a wide variety of substrates through a channel at the two transmembrane domains (TMDs) across the cell membranes. MsbA from Gram-negative bacteria is a lipid and multidrug resistance ATP binding cassette exporter that can undergo large scale conformational changes between the outward-facing and the inward-facing conformations revealed by crystal structures in different states. Here, we use targeted molecular dynamics simulation methods to explore the atomic details of the conformational transition from the outward-facing to the inward-facing states of MsbA. The molecular dynamics trajectories revealed a clear spatiotemporal order of the conformational movements. The disruption of the nucleotide binding sites at the NBD dimer interface is the very first event that initiates the following conformational changes, verifying the assumption that the conformational conversion is triggered by ATP hydrolysis. The conserved x-loops of the NBDs were identified to participate in the interaction network that stabilizes the cytoplasmic tetrahelix bundle of the TMDs and play an important role in mediating the cross-talk between the NBD and TMD. The movement of the NBD dimer is transmitted through x-loops to break the tetrahelix bundle, inducing the packing rearrangements of the transmembrane helices at the cytoplasmic side and the periplasmic side sequentially. The packing rearrangement within each periplasmic wing of TMD that results in exposure of the substrate binding sites occurred at the end stage of the trajectory, preventing the wrong timing of the binding site accessibility.