Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
J Phys Chem B. 2010 Nov 25;114(46):15172-9. doi: 10.1021/jp104508k. Epub 2010 Oct 26.
AmtB is one of the ammonium transporter proteins facilitating the ammonium transport across the cellular membranes. Experimentally, the substrate used in in vitro studies is the radio labeled [(14)C]methylammonium, rather than ammonium itself. To explore the similarity and difference of the conduction mechanism of methylamine and ammonia molecules through AmtB, molecular dynamics simulations on 22 carefully designed systems were performed, which demonstrated that methylamine could be automatically transported in a very similar way to ammonia. The driving force for the conduction is mainly the hydrogen bond network comprising His168, His318, and Tyr32, working in coordination with NH-π interaction with residue Trp212. Then, Ser263 translocated the substrates from the exit gate into the cytoplasm by hydrogen bond interaction. The aromatic ring of Trp212 acted like a springboard to facilitate the translocation of the substrates from site Am2 to Am4 via NH-π interaction. Without the mediation of Trp212, further movement of substrate in the channel would be hampered by the strong hydrogen bonding from His168. In agreement with experimental results, the substrates could be transported by W212F mutant but not by W212A within the simulation time as long as 20 ns. In addition, we predicted that the mutants S263D and S263C remain the function of the transporter but S263A does not. The difference of transporting the two substrates is that methylamine involves more hydrophobic interactions than ammonia. In conclusion, methylamine molecule is a good mimic for investigating the translocation mechanism of ammonium transporter AmtB.
AmtB 是一种铵转运蛋白，可促进细胞内外的铵转运。在实验中，体外研究中使用的底物是放射性标记的 [(14)C]甲铵，而不是铵本身。为了探索甲胺和氨分子通过 AmtB 传导机制的相似性和差异性，对 22 个精心设计的系统进行了分子动力学模拟，结果表明甲胺可以以非常相似的方式自动转运，类似于氨。传导的驱动力主要是由 His168、His318 和 Tyr32 组成的氢键网络，与残基 Trp212 上的 NH-π 相互作用协同作用。然后，Ser263 通过氢键相互作用将底物从出口门转移到细胞质中。Trp212 的芳环起到跳板的作用，通过 NH-π 相互作用促进底物从 Am2 位到 Am4 位的转运。没有 Trp212 的介导，由于 His168 形成的强氢键，底物在通道中的进一步移动将受到阻碍。与实验结果一致，在长达 20ns 的模拟时间内，突变体 W212F 可以转运底物，但突变体 W212A 则不能。此外，我们预测 S263D 和 S263C 突变体仍保持转运蛋白的功能，但 S263A 则没有。两种底物转运的差异在于，甲胺比氨涉及更多的疏水相互作用。总之，甲胺分子是研究铵转运蛋白 AmtB 转运机制的良好模拟物。
