Unveiling allosteric pathways in ion channels

离子通道是普遍存在的蛋白质--自然界的一种？这种精巧的纳米级分子机器存在于可兴奋细胞的膜中。它们的作用是将化学和电刺激转化为离子电流。负责感知刺激的蛋白质部分（换能器结构域）的构象变化触发门（效应器结构域），门可以打开和关闭，从而控制离子穿过细胞膜的通量。这种所谓的变构通信的细节与生理学有着广泛的相关性：几种药物分子靶向离子通道，包括神经毒素和麻醉剂，并通过干扰换能器和效应器结构域之间的耦合来发挥作用。因此，在这种电压门控样离子通道中的变构信号传播的分子水平描述将可能告知选择性变构药物的设计。重要的是，定量变构模型对于阐明神经元电活动的调节机制至关重要，最近对独立的大规模科学计划（例如，美国大脑和欧盟人脑项目），旨在实现对神经元回路的前所未有的理解。尽管其广泛的相关性，宏观热力学概念的变构是很难表征使用唯一的实验。本计画的目的是利用分子动力学（MD）为基础的完全原子模拟，以弥合热力学观测值与离子通道运作中所涉及的微观动力学之间的差距。最终的目标是解开一个功能通道之间的能量和统计耦合的复杂电路？的组成氨基酸，以突出网络的残基相互作用维持不同的蛋白质结构域之间的机械耦合。为此，Blue沃茨的千万亿次能力将被用来生成长时间尺度的MD轨迹。生成的数据将涉及规范集合，或者通过使用增强的采样技术，如元数据，适当偏置的概率分布。关键的里程碑是表征通道激活/开放的自由能景观及其在调节药物结合后的重塑。自由能景观的知识将告知该项目的最后里程碑，该项目利用对生成的MD轨迹的新粗粒度分析来突出对变构信号传播至关重要的残基-残基相互作用。该研究集中在三个家庭的电压门控样离子通道，激活不同的刺激：瞬时受体电位通道，电压门控阳离子通道，超极化激活的环核苷酸结合通道。

Ion channels are ubiquitous proteins--one of Nature?s exquisite nano-scale molecular machines--that reside in membranes of excitable cells. Their role is to convert chemical and electrical stimuli into ionic currents. Conformational changes in the part of the protein responsible for sensing a stimulus (transducer domain) trigger the gate (effector domain), which can open and close, thereby controlling the flux of ions across the cell membrane. Details of this so-called allosteric communication are of broad relevance to physiology: several drug molecules target ion channels, including neurotoxins and anesthetics, and work by interfering with the coupling between the transducer and effector domains. Thus, a molecular-level description of allosteric signal propagation in such voltage-gated-like ion channels will likely inform the design of selective allosteric drugs. Importantly, quantitative allosteric models can be crucial to shed light on the mechanisms of modulation of electrical activity in neurons, an endeavor that is made particularly timely by the recent funding of independent large-scale scientific initiatives (e.g., the US Brain and the EU Human Brain projects), which are aimed at achieving unprecedented understanding of neuronal circuits. Despite its broad relevance, the macroscopic thermodynamic concept of allostery is difficult to characterize using only experiment. This project aims to use molecular dynamics (MD) based fully atomistic simulations to bridge the gap between thermodynamic observables and the underlying microscopic dynamics involved in the functioning of ion channels. The ultimate goal is to disentangle the intricate circuitry of energetic and statistical coupling among a functioning channel?s constituent amino acids in order to highlight the network of residue-residue interactions sustaining the mechanical coupling between distinct protein domains. To this end, the petascale capabilities of Blue Waters will be harnessed to generate long time-scales MD trajectories. Data generated will involve either the canonical ensemble or, by using enhanced sampling techniques such as metadyamics, appropriately biased probability distributions. Crucial milestones are the characterization of the free-energy landscape for channel activation/opening and its reshaping upon binding of modulating drugs. Knowledge of the free-energy landscape will inform the final milestone of the project, which takes advantage of a novel coarse-grained analysis of the generated MD trajectories to highlight residue-residue interactions crucial for allosteric signal propagation. The study focuses on three families of voltage-gated-like ion channels that are activated by different stimuli: transient receptor potential channels, voltage gated cation channels, and hyperpolarization-activated cyclic nucleotide-binding channels.