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。 我们已经在水、质子和离子与蛋白质功能相关的领域取得了许多进展。 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。在这个反应中释放的能量是通过泵送质子穿过线粒体或细菌膜来保存的，从而产生驱动ATP产生的电化学质子梯度。 Wikstrom博士（芬兰赫尔辛基大学）和Kim博士（海军研究实验室，华盛顿，DC）合作，我们使用CcO中氧化还原偶联质子泵的分子模拟和详细的动力学模型。 在2009/2010年，我们可以展示如何使用时间依赖性外部电场来探测该分子机器的功能（Kim等人，Phys.Rev.Lett. 2009年）。我们表明，质子泵效率和稳态的电子电流敏感地依赖于所施加的场的频率和幅度，使我们能够区分不同的微观机制的机器。从光谱分析，我们可以确定占主导地位的反应步骤，是一致的电子门控质子泵机制的CCO。这项研究提供了深入了解CcO功能的机制，并开辟了新的实验表征的方式。 离子通道门控。我们已经研究了五聚体配体门控离子通道的门控转变（Zhu，Hummer，Biophys. J.，2009年）。这些通道形成了一个重要的膜蛋白家族，在许多生理过程中发挥关键作用，包括神经信号传导。其功能的一个关键要素是控制孔的打开和关闭，以控制跨膜的离子电流。 基于最近的晶体结构的两个原核成员的家庭在开放和关闭状态下，我们构建了混合弹性网络模型来研究跨膜结构域在通道打开和关闭过程中的运动。为了探索门控转变中的构象变化，计算平滑地连接通道的闭合和开放构象的粗粒度转变路径。我们发现，构象转变不涉及跨膜螺旋的主要旋转，而是其特征在于由一致的虹膜状倾斜的螺旋M2和M3。此外，螺旋M2改变其弯曲状态，这导致在开放到闭合转变期间孔的早期闭合。

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.