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Water, protons, and ions biomolecular systems

水、质子和离子生物分子系统

基本信息

批准号：
8553413
负责人：
Gerhard Hummer
金额：
$ 45.84万
依托单位：
NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
依托单位国家：
美国
项目类别：
财政年份：
资助国家：
美国
起止时间：
至
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/8553413
关键词：
Active Sites Aerobic Affect Agreement Area Bacteria Binding Bioenergetics Biological Biological Process Biology Carbon Nanotubes Catalysis Charge Chemicals Chemistry Collaborations Communication Complex Coupled Coupling Dimensions District of Columbia Electron Transport Electronics Electrons Ensure Entropy Enzymes Equation Excision Exhibits Free Energy Gated Ion Channel Goals Human Hydration status Hydrogen Bonding Inner mitochondrial membrane Investigation Ion Channel Ion Channel Gating Ions Kinetics Life Ligands Light Measures Mediating Mediation Membrane Methods Mitochondria Modeling Modification Molecular NADH dehydrogenase (ubiquinone)Nerve Oxidation-Reduction Oxygen Photosynthesis Play Production Property Proteins Proton Pump Protons Reaction Research Respiratory Chain Ribonucleotide Reductase Role Signal Transduction Solvents Structure System Temperature Tyrosine Universities Water Weight antiporter base constriction cost cytochrome c oxidase dimer molecular dynamics protein folding protein function quantum response simulation stoichiometry theories water channel water flow

项目摘要

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).

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。特别是，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，或门控生物质子泵和酶中的质子流。我们在水、质子和离子与蛋白质功能相关的多个领域取得了进展。离子通道门控。人类的神经信号和细菌的化学传感都依赖于五聚体配体门控离子通道中离子传导孔的受控打开和关闭。通过使用分子动力学模拟，我们可以表征通过GLIC离子通道的离子传导的能量学和动力学（1-3）。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一致（1）。我们还可以阐明GLIC和可能的其他通道门控离子流的机制。值得注意的是，我们发现，响应于收紧孔的构象变化，从15埃疏水收缩中除去水（3），可以阻断离子通过功能闭合状态的GLIC的电导。尽管离子仍然可以相对容易地通过预水合收缩部，但水合的高能量成本有效地阻止了离子通过。可以说，这相当于第一次定量地证明了分子干燥的直接功能作用。生物质子泵复合物I和细胞色素c氧化酶。有氧生活是基于一种分子机制，利用氧气作为终端电子汇。复合物I是进入线粒体和几种细菌功能的呼吸链的关键入口点，其本身作为氧化还原驱动的质子泵发挥作用。与Wikstrom教授（赫尔辛基大学）合作，我们重新研究了质子易位的化学计量学，作为正确理解这种关键酶的一个重要因素（5）。在最近的结构和我们的化学计量分析的基础上，我们开发了一个粗略的机制模型，涉及跨膜结构域的三个同源和紧密堆积的反转运蛋白样亚基中的协同质子转运（5）。我们还研究了膜结合细胞色素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。与Kim博士（海军研究实验室，华盛顿，DC）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。这些模型不仅使我们能够解释如何利用氧化还原化学来为线粒体内膜充电，为有氧生活提供动力，而且还解释了机器的修改如何影响其效率（6）。蛋白质的内部水合作用。我们已经研究了水在非极性通道内形成一维线的能量学（4），如质子和水传导蛋白质所见。我们可以证明，与这种水链的形成相关的熵是负的，即，不利的。因此，预测水链在高温下是不稳定的。质子耦合电子转移直接和水介导。质子耦合电子转移（PCET）反应对许多生物过程至关重要，从线粒体中的光合作用和能量转导（5）到酶催化（7）。我们进行了量子化学计算，研究直接和水介导的两个堆叠酪氨酸之间的PCET。该系统模拟了Ia类核糖核苷酸还原酶催化反应中的关键步骤。我们发现，酪氨酸二聚体的π堆叠的结果在强的电子耦合和有效的绝热PCET。我们还表明，水参与的PCET可以确定扰动。 1. F. Zhu，G.胡明，五聚体GLIC通道中离子传导的理论和模拟，化学理论计算，出版（2012年）。http://dx.doi.org/10.1021/ct2009279 2. F. Zhu，G. Hummer，GLIC通道疏水门中的干燥转变阻断离子传导，Biophys。J. 103，219-227（2012）中所述。 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湾Hummer，Entropy of single-file water in（6，6）carbon nanotubes，J.Chem.Phys.137，044709（2012）. 5. M. Wikstrm，G. Hummer，呼吸复合物I的质子转运化学计量学及其机制影响，Proc. Natl。Acad. Sci. USA 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。Biophys. Acta-Bioenergetics 1817，526-536（2012）. 7. 诉R. I.凯拉湾Hummer，直接和水介导的质子耦合电子转移的能量学，J. Am. Chem. Soc. Communication 133，1904019043（2011）。

项目成果

期刊论文数量（12）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Kinetic gating of the proton pump in cytochrome c oxidase.

细胞色素 c 氧化酶中质子泵的动力学门控。

DOI：
10.1073/pnas.0903938106
发表时间：
2009
期刊：
Proceedings of the National Academy of Sciences of the United States of America
影响因子：
11.1
作者：
Kim,YoungC;Wikstrom,Marten;Hummer,Gerhard
通讯作者：
Hummer,Gerhard

Energetics and dynamics of proton transfer reactions along short water wires.