Water, protons, and ions biomolecular systems

水、质子和离子在生物分子的稳定性、动力学和功能中起着核心作用。通过疏水效应和氢键相互作用，水是蛋白质折叠的主要因素。在许多酶中，它直接参与催化功能。具体地说，蛋白质内部的水经常调节质子在溶剂介质和活性中心之间的转移。这种水通常被限制在相对非极性的纳米尺度的孔和腔中，表现出非常不寻常的性质，如高水流动性、高质子传导性，或者在填充状态和空状态之间的急剧转变。蛋白质在生物功能中利用承压水的这些不同寻常的特性，例如，确保水在水通道中的快速流动，或在生物质子泵和酶中开启质子流动。我们在水、质子和离子与蛋白质功能相关的几个领域取得了进展。 离子通道门控。人类的神经信号和细菌的化学感觉都依赖于五聚体配基门控离子通道中离子传导孔的受控打开和关闭。通过分子动力学模拟，我们可以表征离子通过GLIC离子通道(1-3)传导的能级和动力学。重要的是，我们可以证明GLIC最近的晶体结构对应于功能闭合状态，计算的离子电导与测量的电导(1)一致。我们还可以阐明GLIC和可能的其他通道用来选通离子流的机制。值得注意的是，我们发现，在功能封闭状态下，离子通过GLIC的电导被从15埃疏水收缩(3)中移除水所阻止，这是对收缩孔的构象变化的反应。虽然离子仍然可以相对容易地通过预水化的收缩，但水化的高能量成本有效地阻止了离子的通过。可以说，这是分子干燥的直接功能作用的第一个定量证明。 生物质子泵复合体I和细胞色素C氧化酶。有氧生命是基于一种利用氧气作为终端电子接收器的分子机械。复合体I是线粒体呼吸链的关键入口点，几种细菌本身就是氧化还原驱动的质子泵。在与Wikstrom教授(赫尔辛基大学)的合作下，我们重新检查了质子转移的化学计量学，这是正确理解这一关键酶的关键因素(5)。在最近的结构和我们的化学计量分析的基础上，我们发展了一个粗略的机制模型，涉及跨膜结构域(5)的三个同源和紧密堆积的逆向转运蛋白样亚单位之间的协同质子转运。我们还研究了膜结合的细胞色素c氧化酶(CcO)，它催化线粒体和许多细菌中的氧还原为水。在这个反应中释放的能量是守恒的，通过泵入质子穿过线粒体或细菌膜，产生电化学质子梯度，驱动ATP的产生。与金博士(海军研究实验室，华盛顿特区)合作，我们开发了CCOO中氧化还原耦合质子泵的详细动力学模型。这些模型不仅使我们能够解释如何利用氧化还原化学为线粒体内膜充电来为有氧生命提供动力，而且还解释了机械上的修改如何影响其效率(6)。 蛋白质的内部水合作用。我们研究了水在非极性通道内形成一维导线的能量学(4)，如质子和水传导蛋白质。我们可以证明，与这种水链的形成相关的熵是负的，也就是不利的。因此，预测水链在高温下不稳定。 质子耦合电子直接转移和水介导。质子耦合电子转移(PCET)反应在许多生物过程中都是必不可少的，从光合作用和线粒体中的能量传递(5)到酶催化(7)。我们进行了量子化学计算，研究了两个堆积的酪氨酸之间的直接PCET和水介导的PCET。该系统模拟了Ia类核苷酸还原酶催化反应的关键步骤。我们发现，酪氨酸二聚体的pi堆积导致了强的电子耦合和有效的绝热PCET。我们还表明，水在PCET中的参与可以被微扰识别。 朱飞飞，G.Hummer，五聚体GLIC通道离子传导的理论与模拟，J.化学。《理论计算》，出版社(2012)。Http://dx.doi.org/10.1021/ct2009279 2.朱福华，G.Hummer，GLIC通道疏水门中的干燥转变阻碍了离子传导，生物物理。J.103,219-227(2012)。 3.朱福荣，G.悍马，用加权直方图分析方法计算自由能的收敛和误差估计，J.Comp.化学。33,453-465(2012)。 4.Waghe，J.C.Rasaiah，G.Hummer，(6，6)碳纳米管中单文件水的熵，J.太棒了。137,044709(2012年)。 5.M.Wikstrm，G.Hummer，呼吸复合体质子转运的化学计量学I及其机制含义，Proc.娜塔莉。阿卡德。SCI。美国109,4431-4436(2012)。 6.Y.C.Kim，G.Hummer，细胞色素C氧化酶的质子泵机制：动力学主方程方法，Biochim。生物群落。《生物能量学学报》1817、526-536(2012)。 7.V.R.I.Kaila，G.Hummer，直接和水介导型质子耦合电子转移的能量学，J.化学。SoC。通信133,1904019043(2011年)。

Water, protons, and ions play a central role in the stability, dynamics, and function of biomolecules. Through the hydrophobic effect and hydrogen bond interactions, water is a major factor in the folding of proteins. In many enzymes, it participates directly in the catalytic function. In particular, water in the protein interior often mediates the transfer of protons between the solvent medium and the active site. Such water, often confined into relatively nonpolar pores and cavities of nanoscopic dimensions, exhibits highly unusual properties, such as high water mobility, high proton conductivity, or sharp transitions between filled and empty states. Proteins exploit these unusual properties of confined water in their biological function, e.g., to ensure rapid water flow in aquaporins, or to gate proton flow in biological proton pumps and enzymes. We have made advances in several areas where water, protons, and ions are connected to protein function. Ion channel gating. Nerve signaling in humans and chemical sensing in bacteria both rely on the controlled opening and closing of the ion-conducting pore in pentameric ligand-gated ion channels. By using molecular dynamics simulations we could characterize the energetics and kinetics of ion conduction through the GLIC ion channel (1-3). Importantly, we could demonstrate that a recent crystal structure of GLIC corresponds to a functionally closed state, with the calculated ion conductance in agreement with the measured conductance (1). We could also shed light on the mechanism employed by GLIC and possibly other channels to gate the ion flow. Remarkably, we found that conductance of ions through GLIC in its functionally closed state is blocked by removal of water from a 15 Angstrom hydrophobic constriction (3), in response to a conformational change that tightens the pore. Whereas ions can still pass relatively easily through a pre-hydrated constriction, the high energetic cost of hydration effectively blocks ion passage. This amounts, arguably, to the first quantitative demonstration of a direct functional role of molecular drying. Biological proton pumps Complex I and cytochrome c oxidase. Aerobic life is based on a molecular machinery that utilizes oxygen as a terminal electron sink. Complex I is a key entry point into the respiratory chain of mitochondria and several bacteria functions that itself functions as a redox-driven proton pump. In collaboration with Prof. Wikstrom (University of Helsinki) we re-examined the stoichiometry of proton translocation, as a factor essential for a proper understanding of this key enzyme (5). On the basis of the recent structure and our stoichiometric analysis, we developed a rough mechanistic model involving concerted proton translocation in the three homologous and tightly packed antiporter-like subunits of the trans-membrane domain (5). We also studied the membrane-bound cytochrome c oxidase (CcO), which catalyzes the reduction of oxygen to water in mitochondria and many bacteria. The energy released in this reaction is conserved by pumping protons across the mitochondrial or bacterial membrane, creating an electrochemical proton gradient that drives the production of ATP. In collaboration with Dr. Kim (Naval Research Lab, Washington, DC), we developed detailed kinetic models of the redox-coupled proton pump in CcO. These models have allowed us not only to explain how redox chemistry can be harnessed to charge up the inner mitochondrial membrane to power aerobic life, but also how modifications in the machinery affect its efficiency (6). Interior hydration of proteins. We have studied the energetics of water forming one-dimensional wires inside a nonpolar channel (4), as seen proton and water conducting proteins. We could show that the entropy associated with the formation of such water chains is negative, i.e., unfavorable. As a result the water chains are predicted to be unstable at elevated temperatures. Proton-coupled electron transfer direct and water mediated. Proton-coupled electron transfer (PCET) reactions are essential to many biological processes, ranging from photosynthesis and energy transduction in mitochondria (5) to enzymatic catalysis (7). We performed quantum chemical calculations to study the direct and water-mediated PCET between two stacked tyrosines. This system mimics a key step in the catalytic reaction of class Ia ribonucleotide reductases. We found that the pi-stacking of the tyrosine dimer results in strong electronic coupling and effective adiabatic PCET. We also showed that water participation in the PCET can be identified perturbatively. 1. F. Zhu, G. Hummer, Theory and simulation of ion conduction in the pentameric GLIC channel, J. Chem. Theory Comput., in press (2012). http://dx.doi.org/10.1021/ct2009279 2. F. Zhu, G. Hummer, Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction, Biophys. J. 103, 219-227 (2012). 3. F. Zhu, G. Hummer, Convergence and error estimation in free energy calculations using the weighted histogram analysis method, J. Comp. Chem. 33, 453-465 (2012). 4. Waghe, J. C. Rasaiah, G. Hummer, Entropy of single-file water in (6, 6) carbon nanotubes, J. Chem. Phys. 137, 044709 (2012). 5. M. Wikstrm, G. Hummer, Stoichiometry of proton translocation by respiratory Complex I and its mechanistic implications, Proc. Natl. Acad. Sci. USA 109, 4431-4436 (2012). 6. Y. C. Kim, G. Hummer, Proton-pumping mechanism of cytochrome c oxidase: A kinetic master-equation approach, Biochim. Biophys. Acta-Bioenergetics 1817, 526-536 (2012). 7. V. R. I. Kaila, G. Hummer, Energetics of direct and water-mediated proton-coupled electron transfer, J. Am. Chem. Soc. Communication 133, 1904019043 (2011).