Song Jianing, Ji Changge, Zhang John Z H
State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China.
Proteins. 2014 Feb;82(2):240-9. doi: 10.1002/prot.24368. Epub 2013 Sep 17.
MATE (multidrug and toxic compound extrusion) transporter proteins mediate metabolite transport in plants and multidrug resistance in bacteria and mammals. MATE transporter NorM from Vibrio cholerae is an antiporter that is driven by Na+ gradient to extrude the substrates. To understand the molecular mechanism of Na+-substrate exchange, molecular dynamics simulation was performed to study conformational changes of both wild-type and mutant NorM with and without cation bindings. Our results show that NorM is able to bind two Na(+) ions simultaneously, one to each of the carboxylic groups of E255 and D371 in the binding pocket. Furthermore, this di-Na(+) binding state is likely more efficient for conformational changes of NorM_VC toward the inward-facing conformation than single-Na(+) binding state. The observation of two Na(+) binding sites of NorM_VC is consistent with the previous study that two sites for ion binding (denoted as Na1/Na2 sites) are found in the transporter LeuT and BetP, another two secondary transporters. Taken together, our findings shed light on the structure rearrangements of NorM on Na(+) binding and enrich our knowledge of the transport mechanism of secondary transporters.
多药及毒性化合物外排（MATE）转运蛋白在植物中介导代谢物运输，在细菌和哺乳动物中介导多药耐药性。霍乱弧菌的MATE转运蛋白NorM是一种反向转运蛋白，由钠离子梯度驱动以排出底物。为了解钠离子-底物交换的分子机制，我们进行了分子动力学模拟，以研究野生型和突变型NorM在有或没有阳离子结合情况下的构象变化。我们的结果表明，NorM能够同时结合两个钠离子，一个与结合口袋中E255和D371的羧基各结合一个。此外，这种双钠离子结合状态对于NorM_VC向向内构象的构象变化可能比单钠离子结合状态更有效。观察到NorM_VC的两个钠离子结合位点与之前的研究一致，即在转运蛋白LeuT和另一种二级转运蛋白BetP中发现了两个离子结合位点（称为Na1/Na2位点）。综上所述，我们的研究结果揭示了NorM在钠离子结合时的结构重排，并丰富了我们对二级转运蛋白运输机制的认识。
