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中的蛋白质通道产生的。 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来控制。 响应于跨膜电势的变化而传导孔。基因突变 编码这些通道与神经退行性疾病，癫痫，心律失常， 肌肉紊乱电压门控钾离子通道是研究最广泛的钾离子通道超家族 的电压门控离子通道，是拟议的研究的主题。尽管晶体的可用性 尽管对结构和各种光谱和功能数据进行了研究，但电压门控的机制仍然是 没有很好地理解。尚待确定的细节包括确定 通道闭合状态下的电压传感器域（VSD），VSD遍历的路径 去极化期间的膜，以及机电耦合的性质， VSD的运动打开和关闭毛孔。质子运输用于维持膜极化 在免疫防御过程中产生活性氧。假定的电压门控 质子传导（Hv）通道是仅由与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未知。这个程序 项目将采用X射线和中子散射测量（项目2和3）的组合， 与分子动力学模拟（项目1），以阐明结构和运动的VSD中 液体脂质膜。项目1还将寻求确定通过Hv的离子运输机制， KV VSD。具体目标是：（1）利用分子动力学模拟方法建立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的开放和闭合状态下的全KV通道; 使用这些模型来帮助优化项目2和项目3中的实验，并尝试 协调文献中的数据，导致室间隔缺损的位置和运动有很大的不同。(2)发展 约束潜力，这将迫使MD模拟生成符合 实验散射数据随着项目2和项目3的数据可用，我们将使用限制 MD模拟从一维数据生成动态三维结构模型， 在多层和单个栓系脂质双层中的VSD、通道和VSTxl毒素。(3)模型质子 在Hv蛋白和Kv电压传感器域中的Ω孔的模型中的PT。我们将建立 基于Kv VSD对Hv通道进行建模，并使用组合的量子力学/分子力学 通过VSD模拟研究PT。这将建立额外模拟的协议， 质子和其它阳离子通过在Kv通道VSD突变体中发现的“Ω孔”的转运。

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.