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，或在质子泵和酶中开启质子流动。 细胞色素C氧化酶的功能。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。膜结合的细胞色素c氧化酶(CcO)在线粒体和许多细菌中催化氧还原为水。在这个过程中释放出的能量 反应是保守的，通过将质子泵过线粒体或细菌膜，创建电化学质子梯度，驱动ATP的产生。与Wikstrom博士(芬兰赫尔辛基大学)合作，我们开发了CcO中氧化还原耦合质子泵的详细动力学模型(Kim等人，Proc.娜塔莉。阿卡德。SCI。美国2009)。该模型与热力学原理、CcO的结构、实验上已知的质子亲合势和中间反应的平衡常数是一致的。CcO的高泵浦效率要求质子负载(泵)位和电子位(Heme A)之间有很强的静电耦合，并需要内部质子转移的动能门控。门控是通过提高质子从保守的Glu-242到泵位置的转移速度来减少血红素a来实现的，这与我们的水门控质子泵模型的预测一致。与Kaila博士和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在这个过程中如何防止由CcO泵浦的质子反向流动(Kaila等人，Biochim)。生物群落。生物能源学报。2009年)。我们通过探索周围金属中心的氧化还原状态、介电效应和膜电位如何影响电荷运动的能量，研究了Glu242(牛编号)作为质子阀的功能。 核糖核酸酶H功能。我们研究了嗜盐芽孢杆菌的RNaseH酶对RNA/DNA杂合双链的RNA骨架的催化切割(Rosta等人，J.Comput.化学。2009年)。这种蛋白是HIV病毒的RNAseH的近亲。我们发现，在水对磷酸二酯的初始攻击中，仅有氧-磷距离作为反应坐标是不够的。当接近势垒时，进攻的水分子将它的一个质子转移到磷酸基团的O1P氧上。在势垒顶部，生成的氢氧化物离子形成五配位的磷酸盐中间体。这项工作中用来确定重要自由度的方法和优化反应坐标的步骤是通用的，在经典和QM/MM自由能计算中都是有用的。 一维水线：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。这些线是蛋白质中生物水通道和质子传导线的重要元件。我们开发了一个详细的偶极晶格模型，并表明与原子详细的模拟相比，它准确地恢复了一维承压水的关键性质(Kofinger等人，J.Chem)。太棒了。2009年)。 纳米约束和界面上的水：与Mittal博士(LCP，NIDDK)合作，我们研究了扩展的非极性表面附近水的静态和动态性质(PROC。娜塔莉。阿卡德。SCI。美国，2008)。借助广泛的分子动力学模拟，我们发现对于较大的溶质，界面密度分布被毛细管波加宽。从密度分布的宽度提取的表观界面张力与自由液-汽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，并为发展准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.