Project 1: Molecular Dynamics Simulations of Channels and Voltage Sensors

项目1：通道和电压传感器的分子动力学模拟

• 批准号: 8374889
• 负责人: Douglas J Tobias
• 金额: $ 24.41万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 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/8374889
• 关键词: Arginine; Arrhythmia; Biotin; Cations; Cells; Charge; Coupling; Cysteine; Data; Disease; Environment; Epilepsy; Gated Ion Channel; Gene Mutation; Immune; Ion Channel; Ion Transport; Ions; Knowledge; Lead; Link; Lipid Bilayers; Liquid substance; Literature; Location; Measurement; Mechanics; Membrane; Membrane Lipids; Membrane Potentials; Modeling; Molecular; Motion; Mutate; Myopathy; Nature; Neurodegenerative Disorders; Neutrons; Potassium; Process; Production; Proteins; Protocols documentation; Protons; Reactive Oxygen Species; Reagent; Research; Roentgen Rays; Signal Transduction; Structural Models; Structure; Toxin; Work; base; chromophore; density; electrical potential; molecular dynamics; monomer; mutant; programs; quantum; research study; response; restraint; sensor; simulation; voltage; voltage gated channel

Electrical signals in excitable cells are generated by the flow of ions through protein channels in membranes. In the case of voltage-gated ion channels, the flow of ions is controlled by the opening and closing of the ion conducting pores in response to changes in the transmembrane electrical potential. Mutations of genes encoding these channels are linked to neurodegenerative disease, epilepsy, cardiac arrhythmias, and muscle disorders. Voltage-gated potassium (Kv) channels, the most extensively studied of the superfamily of voltage-gated ion channels, are the subject of the proposed research. In spite of the availability of crystal structures and a wide variety of spectroscopic and functional data, the mechanism of voltage gating is still not well understood. The details that remain to be worked out include the establishment of the location of the voltage sensor domain (VSD) in the closed state of the channel, the path that the VSD takes to traverse the membrane during depolarization, and the nature of the electromechanical coupling through which the motion of the VSD opens and closes the pore. Proton transport is used to maintain membrane polarization during the production of reactive oxygen species in immune defense processes. The putative voltage-gated proton conducting (Hv) channel is a protein that consists only of a VSD homologous to Kv channel VSDs. The proton-conduction mechanism of the Hv proteins is presently completely unknown. This Program Project will employ a combination of X-ray and neutron scattering measurements (Projects 2 and 3) in concert with molecular dynamics simulations (Project 1) to elucidate the structure and motion of VSDs in fluid lipid membranes. Project 1 will also seek to determine the mechanism of ion transport through Hv and Kv VSDs. The specific aims are: (1) Use MD simulations to generate atomistic models of Kv channel VSDs and whole Kv channels in open and closed states based on currently available structural and functional data; use these models to help optimize the experiments to be performed in Projects 2 and 3, and to attempt to reconcile data in the literature that lead to vastly different pictures of VSD location and motion. (2) Develop restraint potentials that will force MD simulations to generate configurations that are consistent with experimental scattering data. As the data from Projects 2 and 3 becomes available, we will use restrained MD simulations to produce dynamic, three-dimensional structural models from one-dimensional data for VSDs, channels, and the VSTxl toxin in multilamellar and single, tethered lipid bilayers. (3) Model proton transfer (PT) in models for Hv proteins and the omega pores in Kv voltage sensor domains. We will build model Hv channels based on Kv VSDs and use combined quantum mechanical/molecular mechanical simulations to investigate PT through the VSDs. This will establish the protocols for additional simulations of the transport of protons and other cations through the "omega pores" found in mutants of Kv channel VSDs.

可兴奋细胞中的电信号是由离子流过膜中蛋白质通道产生的。 在电压门控离子通道的情况下，离子的流动由离子的打开和关闭控制 响应跨膜电位的变化的传导孔。基因突变 编码这些通道与神经退行性疾病、癫痫、心律失常和 肌肉疾病。电压门控钾 (Kv) 通道，是超家族中研究最广泛的通道 电压门控离子通道的研究是拟议研究的主题。尽管有水晶 结构以及各种光谱和功能数据，电压门控的机制仍然是 不太理解。仍有待制定的细节包括确定地点 通道关闭状态下的电压传感器域 (VSD)，VSD 遍历的路径 去极化过程中的膜，以及机电耦合的性质 VSD 的运动打开和关闭毛孔。质子传输用于维持膜极化 在免疫防御过程中产生活性氧的过程中。假定的电压门控 质子传导 (Hv) 通道是一种仅由与 Kv 通道 VSD 同源的 VSD 组成的蛋白质。 Hv 蛋白的质子传导机制目前完全未知。本计划 项目将结合使用 X 射线和中子散射测量（项目 2 和 3） 与分子动力学模拟（项目 1）相结合，阐明 VSD 的结构和运动 液体脂质膜。项目 1 还将寻求确定 Hv 和离子传输的机制 Kv VSD。具体目标是：（1）使用MD模拟生成Kv通道VSD的原子模型 基于当前可用的结构和功能数据，处于打开和关闭状态的整个 Kv 通道； 使用这些模型来帮助优化项目 2 和 3 中要执行的实验，并尝试 协调文献中的数据，这些数据导致 VSD 位置和运动的图像截然不同。 (2) 开发 约束势将迫使 MD 模拟生成与 实验散射数据。当项目 2 和 3 的数据可用时，我们将使用受限的 MD 模拟可从一维数据生成动态三维结构模型 多层和单一束缚脂质双层中的 VSD、通道和 VSTxl 毒素。 (3) 模型质子 Hv 蛋白模型中的转移 (PT) 和 Kv 电压传感器域中的 omega 孔。我们将建设 基于 Kv VSD 建模 Hv 通道并使用组合的量子力学/分子力学 通过 VSD 进行模拟研究 PT。这将建立额外模拟的协议 质子和其他阳离子通过 Kv 通道 VSD 突变体中发现的“欧米茄孔”的传输。