Voltage-gated proton channels (HV1) are essential for various physiological tasks but are strongly inhibited by Zn2+ cations. Some determinants of Zn2+ binding have been elucidated experimentally and in computational studies. However, the results have always been interpreted under the assumption that Zn2+ binds to monomeric HV1 despite evidence that HV1 expresses as a dimer and that the dimer has a higher affinity for zinc than the monomer and experimental data that suggest coordination in the dimer interface. The results of former studies are also controversial, e.g., supporting either one single or two binding sites. Some structural determinants of the binding are still elusive. We performed a series of molecular dynamics simulations to address different structures of the human proton channel, the monomer and two plausible dimer conformations, to compare their respective potential to interact with and bind Zn2+ via the essential histidines. The series consisted of several copies of the system to generate independent trajectories and increase the significance compared to a single simulation. The amount of time simulated totals 29.9 μs for 126 simulations of systems comprising ∼59,000 to ∼187,000 atoms. Our approach confirms the existence of two binding sites in monomeric and dimeric human HV1. The dimer interface is more efficient for attracting and binding Zn2+ via the essential histidines than the monomer or a dimer with the histidines in the periphery. The higher affinity is due to the residues in the dimer interface that create an attractive electrostatic potential funneling the zinc cations toward the binding sites.

中文翻译：

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通过多重 MD 模拟评估 Zn2+ 与人类 HV1 结合的结构决定因素

电压门控质子通道 (HV1) 对各种生理任务至关重要，但受到 Zn2+ 阳离子的强烈抑制。已通过实验和计算研究阐明了 Zn2+ 结合的一些决定因素。然而，尽管有证据表明 HV1 表达为二聚体并且二聚体对锌的亲和力高于单体和实验数据表明二聚体界面中的配位，但结果总是被解释为 Zn2+ 与单体 HV1 结合。先前研究的结果也存在争议，例如，支持一个或两个结合位点。结合的一些结构决定因素仍然难以捉摸。我们进行了一系列分子动力学模拟，以解决人类质子通道的不同结构、单体和两种可能的二聚体构象，比较它们各自通过基本组氨酸与 Zn2+ 相互作用和结合的潜力。该系列由系统的多个副本组成，以生成独立的轨迹并与单个模拟相比增加显着性。对于包含~59,000 到~187,000 个原子的系统的 126 次模拟，模拟的时间总量为 29.9 μs。我们的方法证实了单体和二聚体人类 HV1 中存在两个结合位点。二聚体界面通过基本组氨酸吸引和结合 Zn2+ 比单体或具有外围组氨酸的二聚体更有效。较高的亲和力是由于二聚体界面中的残基产生有吸引力的静电势，将锌阳离子漏斗到结合位点。