Formate/nitrite transporters (FNTs) selectively transport monovalent anions and are found in prokaryotes and lower eukaryotes. They play a significant role in bacterial growth and act against the defense mechanism of infected hosts. Because FNTs do not occur in higher animals, they are attractive drug targets for many bacterial diseases. Phylogenetic analysis revealed that they can be classified into eight subgroups, two of which belong to the uncharacterized YfdC-α and YfdC-β groups. Experimentally determined structures of FNTs belonging to different phylogenetic groups adopt the unique aquaporin-like hourglass helical fold. We considered the formate channel from Vibrio cholerae, the hydrosulphide channel from Clostridium difficile, and the uncharacterized channel from Escherichia coli (EcYfdC) to investigate the mechanism of transport and selectivity. Using equilibrium molecular dynamics and umbrella sampling studies, we determined temporal channel radius profiles, permeation events, and potential of mean force profiles of different substrates with the conserved central histidine residue in protonated or neutral form. Unlike the formate channel from V. cholerae and the hydrosulphide channel from C. difficile, molecular dynamics studies showed that the formate substrate was unable to enter the vestibule region of EcYfdC. Absence of a conserved basic residue and presence of acidic residues in the vestibule regions, conserved only in YfdC-α, were found to be responsible for high energy barriers for the anions to enter EcYfdC. Potential of mean force profiles generated for ammonia and ammonium ion revealed that EcYfdC can transport neutral solutes and could possibly be involved in the transport of cations analogous to the mechanism proposed for ammonium transporters. Although YfdC members belong to the FNT family, our studies strongly suggest that EcYfdC is not an anion channel. Absence or presence of specific charged residues at particular positions makes EcYfdC selective for neutral or possibly cationic substrates. Further experimental studies are needed to get a definitive answer to the question of the substrate selectivity of EcYfdC. This provides an example of membrane proteins from the same family transporting substrates of different chemical nature.

中文翻译：

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甲酸盐/亚硝酸盐转运蛋白家族的大肠杆菌同系物是阴离子通道吗？计算研究

甲酸盐/亚硝酸盐转运蛋白 (FNT) 选择性转运单价阴离子，存在于原核生物和低等真核生物中。它们在细菌生长中起重要作用，并对抗受感染宿主的防御机制。由于 FNT 不会出现在高等动物中，因此它们是许多细菌性疾病的有吸引力的药物靶标。系统发育分析表明，它们可分为八个亚组，其中两个属于未表征的 YfdC-α 和 YfdC-β 组。属于不同系统发育组的 FNT 的实验确定结构采用独特的水通道蛋白样沙漏螺旋折叠。我们考虑了来自霍乱弧菌的甲酸盐通道，来自艰难梭菌的氢硫化物通道，以及来自大肠杆菌（EcYfdC）的未表征通道，以研究运输和选择性的机制。使用平衡分子动力学和伞形采样研究，我们确定了不同底物的时间通道半径分布、渗透事件和平均力分布的潜力，其中保守的中心组氨酸残基为质子化或中性形式。与来自霍乱弧菌的甲酸盐通道和来自艰难梭菌的氢硫化物通道不同，分子动力学研究表明甲酸盐底物无法进入 EcYfdC 的前庭区域。发现仅在 YfdC-α 中保守的前庭区域中不存在保守的碱性残基和存在酸性残基是阴离子进入 EcYfdC 的高能垒的原因。氨和铵离子产生的平均力分布的潜力表明，EcYfdC 可以运输中性溶质，并且可能参与阳离子的运输，类似于为铵转运蛋白提出的机制。虽然 YfdC 成员属于 FNT 家族，但我们的研究强烈表明 EcYfdC 不是阴离子通道。在特定位置不存在或存在特定带电残基使 EcYfdC 对中性或可能的阳离子底物具有选择性。需要进一步的实验研究才能对 EcYfdC 的底物选择性问题给出明确的答案。这提供了来自同一家族的膜蛋白转运不同化学性质的底物的例子。