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。我们在水、质子和离子与蛋白质功能相关的领域取得了一些进展。 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。我们与芬兰赫尔辛基大学的Wikstrom博士和华盛顿特区海军研究实验室的Kim博士合作，使用分子模拟和CCOO中氧化还原耦合质子泵的详细动力学模型。在2009/2010年，我们可以展示如何使用依赖于时间的外部电场来探测这种分子机器的功能(Kim等人，Phys.莱特牧师。2009年)。我们证明了质子泵浦效率和稳态电子电流敏感地依赖于外加电场的频率和幅度，这使得我们能够区分机器的不同微观机制。从光谱分析中，我们可以确定与CcO的电子门控质子泵浦机制相一致的主要反应步骤。这项研究为深入了解CCOO的作用机理提供了依据，并为新的实验表征开辟了道路。 离子通道门控。我们研究了五聚体配体门控离子通道(朱，悍马，生物物理)的门控跃迁。J.，2009)。这些通道形成了一个重要的膜蛋白家族，在包括神经信号在内的许多生理过程中发挥关键作用。它们功能的一个关键要素是控制孔的打开和关闭，以选通穿过膜的离子电流。基于该家族两个原核生物在开放和关闭状态下的最新晶体结构，我们构建了混合弹性网络模型来研究跨膜结构域在通道开放和关闭过程中的运动。为了探索门控跃迁中的构象变化，计算了一条粗粒度的跃迁路径，该路径平滑地连接了通道的闭合和开放构象。我们发现构象转变不涉及跨膜螺旋的主要旋转，而是以M2和M3螺旋的协调虹膜样倾斜为特征。此外，螺旋M2改变了它的弯曲状态，这导致在从打开到关闭的转变过程中气孔提前关闭。

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. We have made a number of advances in areas where water, protons, and ions are connected to protein function. 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 the production of ATP. In collaboration with Dr. Wikstrom (University of Helsinki, Finland) and Dr. Kim (Naval Research Lab, Washington, DC), we use molecular simulations and detailed kinetic models of the redox-coupled proton pump in CcO. In 2009/2010, we could show how time-dependent external electric fields can be used to probe the function of this molecular machine (Kim et al, Phys. Rev. Lett. 2009). We showed that the proton pumping efficiency and the electronic currents in steady state depend sensitively on the frequency and amplitude of the applied field, allowing us to distinguish between different microscopic mechanisms of the machine. From a spectral analysis we could identify dominant reaction steps that were consistent with an electron-gated proton pumping mechanism of CcO. This study provides insights into the mechanism of CcO function, and opens the way for novel experimental characterizations. Ion channel gating. We have studied the gating transition of pentameric ligand-gated ion channels (Zhu, Hummer, Biophys. J., 2009). These channels form an important family of membrane proteins that play key roles in many physiological processes, including nerve signaling. A key element of their function is the controlled opening and closing of a pore to gate the ionic current across the membrane. Based on recent crystal structures of two prokaryotic members of the family in open and closed states, we constructed mixed elastic network models to study the motions of the transmembrane domain during channel opening and closing. To explore the conformational changes in the gating transition, a coarse-grained transition path is computed that smoothly connects the closed and open conformations of the channel. We find that the conformational transition involves no major rotations of the transmembrane helices, and is instead characterized by a concerted iris-like tilting of helices M2 and M3. In addition, helix M2 changes its bending state, which results in an early closure of the pore during the open-to-closed transition.