Unveiling allosteric pathways in ion channels

离子通道是普遍存在的蛋白质--大自然的一种--S精致的纳米级分子机器--驻留在可兴奋的细胞膜上。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(转换器域)的构象变化触发了门(效应域)，门可以打开和关闭，从而控制离子通过细胞膜的流量。这种所谓的变构通讯的细节与生理学具有广泛的相关性：几种药物分子以离子通道为靶点，包括神经毒素和麻醉药，并通过干扰转导和效应域之间的耦合来发挥作用。因此，在分子水平上描述变构信号在这种电压门控类离子通道中的传播可能会为选择性变构药物的设计提供信息。重要的是，定量变构模型对于阐明神经元电活动的调制机制至关重要，最近独立的大规模科学计划(如美国大脑和欧盟人脑项目)的资助使这一努力尤其及时，这些计划旨在实现对神经元回路的前所未有的了解。尽管变构的宏观热力学概念具有广泛的关联性，但仅用实验很难描述它的特征。该项目旨在使用基于分子动力学(MD)的完全原子模拟来弥合热力学观测数据和离子通道功能所涉及的潜在微观动力学之间的差距。最终目标是解开一个功能通道--S组成的氨基酸之间能量和统计耦合的复杂电路，以突出支持不同蛋白质结构域之间机械耦合的残基-残基相互作用网络。为此，将利用Blue Waters的千万亿级能力来生成长时间尺度的MD轨迹。所产生的数据将涉及规范集合，或者通过使用增强的抽样技术，例如元动态抽样技术，适当地偏向概率分布。关键的里程碑是描述通道激活/开放的自由能格局及其在调节药物结合时的重塑。对自由能情况的了解将为该项目的最后一个里程碑提供信息，该项目利用对产生的MD轨迹进行的新的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。本研究主要研究了三类电压门控离子通道：瞬时受体电位通道、电压门控阳离子通道和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.