Project 1: Molecular Dynamics Simulations of Channels and Voltage Sensors

可兴奋细胞中的电信号是由离子流过膜上的蛋白质通道而产生的。 在电压门控离子通道的情况下，离子的流动由离子的开启和关闭控制 传导孔对跨膜电势的变化作出反应。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 肌肉紊乱。电压门控钾(Kv)通道，超家族中研究最广泛的通道 电压门控离子通道，是拟议研究的主题。尽管有水晶可用， 结构和各种光谱和功能数据，电压门控的机制仍然是 不是很清楚。尚待敲定的细节包括确定 通道闭合状态下的电压传感器域(VSD)，即VSD所经过的路径 去极化过程中的膜，以及通过其进行机电耦合的性质 室间隔缺损的运动可以打开和关闭毛孔。质子传输被用来维持膜的极化 在免疫防御过程中产生活性氧物种。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还完全不清楚。本计划 项目#年将采用X射线和中子散射测量相结合的方法(项目2和3)。 结合分子动力学模拟(项目1)阐明VSD的结构和运动 液体类脂膜。项目1还将设法确定通过Hv和Hv的离子传输机制。 KV VSD。具体目标是：(1)使用MD模拟生成Kv通道VSD的原子模型 以及基于当前可用的结构和功能数据在打开和关闭状态下的整个Kv通道； 使用这些模型来帮助优化要在项目2和3中执行的实验，并尝试 协调文献中的数据，这些数据导致VSD位置和运动的图片截然不同。(2)发展 约束潜力将迫使MD模拟生成与以下各项一致的配置 实验散射数据。当项目2和3中的数据可用时，我们将使用 MD模拟，从一维数据生成动态的三维结构模型 VSD、通道和VSTxl毒素在多层和单层系留脂双层中。(3)模型质子 Hv蛋白模型中的转移(PT)和Kv电压传感域中的omega孔。我们将建造 基于Kv VSD和量子力学/分子力学相结合的高压通道模型 通过VSD调查PT的模拟。这将建立用于附加模拟的协议 质子和其他阳离子通过Kv通道VSD突变体中发现的“omega孔”进行的运输。

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.