Understanding gating kinetics in Cys-loop receptors

了解 Cys 环受体的门控动力学

• 批准号: BB/S001247/1
• 负责人: Philip Biggin
• 金额: $ 46.77万
• 依托单位: University of Oxford
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FS001247%2F1
• 关键词: Understanding; gating; kinetics; Cys; loop

Ligand-gated ion channels are proteins that are present throughout the body and mediate the fast cell-to-cell communication that occurs at the synapses. They are necessary for controlling many important processes including those fundamental to memory and learning as well as muscle control. It is therefore perhaps unsurprising that these receptors have been implicated in a range of neurological conditions including epilepsy and spasticity. In order to perform their function, these proteins must, upon binding a neurotransmitter, change conformation (shape) in order to allow ions to pass into or out of the cell. This process is a very dynamic one and the speeds of movement between the channel being in closed or open states directly underpins the behaviour of the central nervous system.Despite huge progress, exactly how these receptors change conformation (shape) and what factors control the overall dynamic response remain very poorly understood at the molecular level. In this proposal, we will try and address this most fundamental of questions, via examination of the glycine receptor as a key example channel protein. The structure is usually obtained by crystallography and the functional behavior of the channel is usually monitored by recoding the channel's electrical activity via electrophysiological experiments. To make the link between structure and function and to elucidate key information about the underling dynamics, the most appropriate and useful tool is molecular simulation and computational modelling.One of the key questions we wish to try and understand is exactly why do very similar agonists (compounds that open the channel) give very different functional responses? For example, the response of the glycine receptor to glycine is significantly stronger (larger overall current) compared to alanine, a molecule that differs only by the presence of a methyl group (compared to a single hydrogen atom in glycine). In order to answer this kind of question, we could wait for more structural information (via crystallography), but there is no guarantee that a high-resolution structure will be solved in the near future and regardless, we would like to understand the behaviour of several different agonists. Furthermore, our previous data suggests that even when bound to the receptor, agonists may be quite mobile and exhibit multiple binding modes (perhaps contributing to their functional complexity). Thus, in order to address these kinds of questions we are proposing to using various molecular dynamics methodologies. These simulations can provide working hypotheses which can be tested via our on-going collaboration with colleagues at UCL. In turn, the functional experiments performed at UCL can be explored with molecular simulation in order to provide insight into results that might otherwise be difficult to rationalize. Our proposal utilizes the power of molecular simulations to provide atomic-level detail of what controls the way the binding site behaves in response to different compounds. A full understanding of this is necessary if we are to not only extend our fundamental knowledge of ion channel behavior but also to have any chance of developing compounds that target these kinds of proteins in the future as treatments for various neurological conditions.

配体门控离子通道是存在于全身并介导发生在突触处的快速细胞间通讯的蛋白质。它们是控制许多重要过程所必需的，包括记忆和学习以及肌肉控制的基础。因此，这些受体与包括癫痫和痉挛状态在内的一系列神经疾病有关可能并不令人惊讶。为了执行它们的功能，这些蛋白质必须在结合神经递质时改变构象（形状），以允许离子进入或离开细胞。这个过程是一个非常动态的过程，通道在关闭或打开状态之间的运动速度直接支撑着中枢神经系统的行为。尽管取得了巨大的进展，但这些受体究竟如何改变构象（形状）以及哪些因素控制着整体的动态反应在分子水平上仍然知之甚少。在这个建议中，我们将尝试解决这个最基本的问题，通过检查甘氨酸受体作为一个关键的例子通道蛋白。结构通常通过晶体学获得，并且通道的功能行为通常通过经由电生理学实验记录通道的电活性来监测。为了建立结构与功能之间的联系并阐明有关基础动力学的关键信息，最合适和有用的工具是分子模拟和计算建模。我们希望尝试和理解的关键问题之一到底是为什么非常相似的激动剂（打开通道的化合物）会产生非常不同的功能反应？例如，与丙氨酸相比，甘氨酸受体对甘氨酸的反应明显更强（更大的总电流），丙氨酸是一种仅因甲基的存在而不同的分子（与甘氨酸中的单个氢原子相比）。为了回答这类问题，我们可以等待更多的结构信息（通过晶体学），但不能保证在不久的将来解决高分辨率结构，无论如何，我们希望了解几种不同激动剂的行为。此外，我们以前的数据表明，即使与受体结合，激动剂也可能是相当移动的，并表现出多种结合模式（可能有助于其功能的复杂性）。因此，为了解决这些问题，我们建议使用各种分子动力学方法。这些模拟可以提供工作假设，这些假设可以通过我们与UCL同事的持续合作进行测试。反过来，在UCL进行的功能实验可以用分子模拟来探索，以提供对结果的洞察，否则可能难以合理化。我们的建议利用分子模拟的力量来提供控制结合位点对不同化合物的反应方式的原子级细节。如果我们不仅要扩展我们对离子通道行为的基础知识，而且要有机会开发出靶向这些蛋白质的化合物，作为未来治疗各种神经系统疾病的药物，那么对这一点的充分理解是必要的。

项目成果

Atomistic mechanisms of human TRPA1 activation by electrophile irritants through molecular dynamics simulation and mutual information analysis.

• DOI: 10.1038/s41598-022-08824-7
• 发表时间: 2022-03-23
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Habgood M;Seiferth D;Zaki AM;Alibay I;Biggin PC
• 通讯作者: Biggin PC

Structural correlates of human muscle nicotinic acetylcholine receptor subunit assembly mediated by d(+) interface residues

d()界面残基介导的人肌肉烟碱乙酰胆碱受体亚基组装的结构相关性

• DOI: 10.1101/2020.06.11.145466
• 发表时间: 2020
• 作者: Epstein M

A Refined Open State of the Glycine Receptor Obtained Via Molecular Dynamics Simulations

通过分子动力学模拟获得的甘氨酸受体的精细开放状态

• DOI: 10.1101/668830
• 发表时间: 2019
• 作者: Dämgen M

Conformational transitions and allosteric modulation in a heteromeric glycine receptor.

• DOI: 10.1038/s41467-023-37106-7
• 发表时间: 2023-03-13
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Gibbs, Eric;Klemm, Emily;Seiferth, David;Kumar, Arvind;Ilca, Serban L.;Biggin, Philip C.;Chakrapani, Sudha
• 通讯作者: Chakrapani, Sudha

Molecular determinants of binding of non-oxime bispyridinium nerve agent antidote compounds to the adult muscle nAChR

• DOI: 10.1016/j.toxlet.2021.01.013
• 发表时间: 2021-01-25
• 期刊: TOXICOLOGY LETTERS
• 影响因子: 3.5
• 作者: Epstein, Max;Bali, Karan;Biggin, Philip C.
• 通讯作者: Biggin, Philip C.