Unveiling allosteric pathways in ion channels

离子通道是无处不在的蛋白质——自然的一种？精细的纳米级分子机器——驻留在可兴奋细胞的细胞膜上。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（换能器结构域）的蛋白质部分的构象变化触发门（效应结构域），它可以打开和关闭，从而控制离子穿过细胞膜的通量。这种所谓的变构通讯的细节与生理学有着广泛的相关性：一些药物分子靶向离子通道，包括神经毒素和麻醉剂，并通过干扰传感器和效应域之间的耦合来起作用。因此，在这种电压门状离子通道中对变构信号传播的分子水平描述可能会为选择性变构药物的设计提供信息。重要的是，定量变弹性模型对于阐明神经元电活动的调节机制至关重要，这是最近独立的大规模科学计划（例如，美国大脑和欧盟人类大脑项目）的资助特别及时的一项努力，旨在实现对神经元回路的前所未有的理解。尽管它具有广泛的相关性，但变构的宏观热力学概念很难仅用实验来表征。该项目旨在利用基于全原子模拟的分子动力学（MD）来弥合离子通道功能中涉及的热力学可观测值和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中能量和统计耦合的复杂电路。S组成氨基酸，以突出残基-残基相互作用的网络，维持不同蛋白质结构域之间的机械偶联。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。生成的数据要么涉及规范集合，要么通过使用增强的抽样技术，如元组学，适当地偏倚概率分布。关键的里程碑是表征通道激活/打开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为项目的最终里程碑提供信息，该项目利用对生成的MD轨迹进行新颖的粗粒度分析，以突出对变弹性信号传播至关重要的残留物-残留物相互作用。该研究重点研究了三种被不同刺激激活的电压门控离子通道：瞬态受体电位通道、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.