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。 通过疏水作用和氢键相互作用，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。 特别地，蛋白质内部的水通常介导质子在溶剂介质和活性位点之间的转移。 这种水，通常被限制在相对非极性的孔隙和纳米尺度的空腔中，表现出非常不寻常的性质，如高水流动性，高质子传导性，或填充和空状态之间的急剧转变。蛋白质在其生物功能中利用了承压水的这些不寻常的特性，例如，以确保水通道蛋白中的快速水流，或控制质子泵和酶中的质子流。 细胞色素c氧化酶的功能。有氧生活是基于一种分子机制，利用氧气作为终端电子汇。膜结合细胞色素c氧化酶（CcO）催化线粒体和许多细菌中的氧还原为水。这里面释放的能量 通过泵送质子穿过线粒体或细菌膜，产生驱动ATP产生的电化学质子梯度，反应得以保存。 与Wikstrom博士（芬兰赫尔辛基大学）合作，我们开发了CcO中氧化还原偶联质子泵的详细动力学模型（Kim等人，Proc. Natl. Acad. sci. USA 2009）。 该模型是一致的热力学原理，CcO的结构，实验已知的质子亲和力，和中间反应的平衡常数。 CcO的高泵效率需要质子负载（泵）站点和电子站点（血红素a）之间的强静电耦合，以及内部质子转移的动力学门控。门控是通过提高质子转移率从保守的Glu-242的泵网站减少血红素，符合我们的水门控模型的质子泵的预测。 与Kaila和Wikstrom博士（芬兰赫尔辛基大学）合作，我们通过分子动力学模拟探索了如何防止CcO泵送的质子在该过程中向后流动（Kaila等人，生物化学生物Biophys.生物能源学报2009年）的报告。 我们已经研究了Glu242（牛编号）作为质子阀的功能，通过探索周围金属中心的氧化还原状态，介电效应和膜电位，影响电荷运动的能量学。 核糖核酸酶H功能。我们已经研究了耐盐芽孢杆菌的RNase H酶对RNA/DNA杂交双链体的RNA骨架的催化切割（罗斯塔等人，J. Comput. 2009）。这种蛋白质是HIV病毒RNaseH的近亲。 我们发现，在水对磷酸二酯的初始攻击中，单独的氧-磷距离不足以作为反应坐标。 当接近屏障时，攻击的水分子将其一个质子转移到磷酸基团的O1P氧。在屏障顶部，产生的氢氧根离子形成五配位磷酸盐中间体。在这项工作中使用的方法，以确定重要的自由度，并优化反应坐标的程序是通用的，应该是有用的，在经典的和QM/MM自由能计算。 1D水管：我们与奥地利维也纳大学的Dellago和Kofinger博士合作，对一维水线进行了研究。 这种导线是生物水通道和蛋白质中质子传导导线的重要元素。 我们开发了一个详细的偶极晶格模型，并表明，它准确地恢复了一维承压水的关键属性相比，原子详细的模拟（Kofinger等人，J.化学物理2009）。 水在纳米限制和接口：在合作与米塔尔博士（LCP，NIDDK），我们已经研究了水的静态和动态特性附近的扩展非极性表面（美国国家科学院院刊。Acad. sci. USA，2008）。借助广泛的分子动力学模拟，我们发现，对于大溶质，界面密度分布由毛细管波加宽。从密度分布的宽度提取的表观界面张力与自由液-气界面的表观界面张力一致。 这些结果揭示了水在分子结合和识别过程中的作用，并为发展精确的理论来描述水介导的相互作用提供了重要的指导。

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 proton pumps and enzymes. Function of cytochrome c oxidase. Aerobic life is based on a molecular machinery that utilizes oxygen as a terminal electron sink. The membrane-bound cytochrome c oxidase (CcO) 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 production of ATP. In collaboration with Dr. Wikstrom (University of Helsinki, Finland) we have developed a detailed kinetic model of the redox-coupled proton pump in CcO (Kim et al., Proc. Natl. Acad. Sci. USA 2009). The model is consistent with thermodynamic principles, the structure of CcO, experimentally known proton affinities, and equilibrium constants of intermediate reactions. The high pumping efficiency of CcO requires strong electrostatic couplings between the proton loading (pump) site and the electron site (heme a), and kinetic gating of the internal proton transfer. Gating is achieved by enhancing the rate of proton transfer from the conserved Glu-242 to the pump site on reduction of heme a, consistent with the predictions of our water-gated model of proton pumping. In collaboration with Drs. Kaila and Wikstrom (University of Helsinki, Finland) we explored by molecular dynamics simulations how the protons pumped by CcO are prevented from flowing backwards during the process (Kaila et al., Biochim. Biophys. Acta Bioenerg. 2009). We have studied the function of Glu242 (bovine numbering) as a proton valve by exploring how the redox state of the surrounding metal centers, dielectric effects, and membrane potential, affect the energetics of charge motion. Ribonuclease H function. We have studied the catalytic cleavage of the RNA backbone of an RNA/DNA hybrid duplex by the RNase H enzyme of Bacillus halodurans (Rosta et al., J. Comput. Chem. 2009). This protein is a close relative of the RNaseH of the HIV virus. We find that in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate. The method used in this work to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free energy calculations. 1D water wires: In collaboration with Drs. Dellago and Kofinger from the University of Vienna, Austria, we performed studies of one-dimensional water wires. Such wires are important elements of biological water channels and proton conduction wires in proteins. We developed a detailed dipole lattice model and showed that it accurately recovers key properties of 1D confined water when compared to atomically detailed simulations (Kofinger et al, J. Chem. Phys. 2009). Water in nanoconfinement and at interfaces: In collaboration with Dr. Mittal (LCP, NIDDK) we have studied the static and dynamic properties of water near extended nonpolar surfaces (Proc. Natl. Acad. Sci. USA, 2008). With the help of extensive molecular dynamics simulations, we showed that for large solutes, the interfacial density profile is broadened by capillary waves. The apparent interfacial tension extracted from the width of the density profiles agrees with that of a free liquid-vapor interface. These results shed new light on the role of water in molecular binding and recognition processes, and provide important guidance for the development of accurate theories to describe water-mediated interactions.