Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland.
Biochemistry. 2012 Feb 14;51(6):1281-7. doi: 10.1021/bi2015184. Epub 2012 Feb 3.
Recently, a 3.65 Å resolution structure of the transporter NorM from the multidrug and toxic compound extrusion family has been determined in the outward-facing conformation. This antiporter uses electrochemical gradients to drive substrate export of a large class of antibiotic and toxic compounds in exchange for small monovalent cations (H(+) and Na(+)), but the molecular details of this mechanism are still largely unknown. Here we report all-atom molecular dynamics simulations of NorM, with and without the bound Na(+) cation and at different ion concentrations. Spontaneous binding of Na(+) is observed in several independent simulations with transient ion binding to D36 being necessary to reach the final binding site for which two competitive binding modes occur. Finally, the simulations indicate that the extracellular vestibule of the transporter invariably loses its characteristic V shape indicated by the crystallographic data, and it is reduced to a narrow permeation pathway lined by polar residues that can act as a specific pore for the transport of small cations. This event, together with the available structures of evolutionarily related transporters of the major facilitator superfamily (MFS), suggests that differences in the hydrophobic content of the extracellular vestibule may be characteristic of multidrug resistance transporters in contrast to substrate-selective members of the MFS.
最近，已确定多药和毒性化合物外排家族的转运蛋白 NorM 的 3.65Å 分辨率结构处于向外构象。该反向转运蛋白利用电化学梯度驱动一大类抗生素和毒性化合物的底物输出，以换取小的单价阳离子（H(+)和 Na(+)），但该机制的分子细节仍在很大程度上未知。在这里，我们报告了 NorM 的全原子分子动力学模拟，包括有和没有结合的 Na(+)阳离子以及不同离子浓度的情况。在几个独立的模拟中观察到 Na(+)的自发结合，瞬时结合 D36 对于达到最终结合位点是必要的，对于最终结合位点存在两种竞争结合模式。最后，模拟表明，转运蛋白的细胞外前庭始终失去晶体数据所示的特征 V 形，并且它被简化为一个由极性残基排列的狭窄渗透途径，这些残基可以作为小阳离子运输的特定孔。这一事件，以及主要易化因子超家族（MFS）中进化相关转运蛋白的现有结构，表明细胞外前庭的疏水性含量差异可能是多药耐药转运蛋白的特征，而不是 MFS 中底物选择性成员的特征。
