权益分类	功能权益	普通用户	{{item.name}}会员
{{category.name}}	{{benefitItem.name}}

OPENING ION CHANNELS WITH A TRANS-CIS PROLINE SWITCH: A COMPUTATIONAL METADYNAMICS STUDY

用反式-顺式脯氨酸开关打开离子通道：计算元动力学研究

基本信息

批准号：
EP/E014585/1
负责人：
Carla Molteni
金额：
$ 18.78万
依托单位：
King's College London
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2007
资助国家：
英国
起止时间：
2007 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=EP%2FE014585%2F1
关键词：
OPENING ION CHANNELS TRANS CIS

项目摘要

Ligand-Gated ion Channels (LGICs) are important mediators in neuronal transmission and are involved in many neurological disorders, such as Alzheimer's and Parkinson's diseases. These receptors, located in the membrane of nerve cells, are large proteins, consisting of different subunits arranged around an ion-conducting central pore; each subunit is composed by an extracellular domain, a transmembrane domain and an intracellular domain. The activation of LGICs is initiated by the binding of a small neurotransmitter to the extracellular domain: this triggers a series of chemical events and conformational changes in the protein culminating with the opening (gating) of the channel: ions can then flood across the cell membrane modifying the cell activity. The most intriguing question concerning LGICs is how the binding of a small neurotransmitter in the extracellular domain translates into the opening of the channel in the transmembrane domain more than 50 + away. Recent experiments on the 5-hydroxytryptamine type 3 receptor (5-HT3R) led to the proposal that a specific proline amino-acid (Pro 8*), located at the apex of a loop between two transmembrane helices (M2-M3 loop), can act as a switch for ion channel gating by means of a trans-cis isomerisation and of its structural effects on the protein backbone. Since structural information on LGICs is limited, atomistic simulations can play a crucial role in verifying the gating mechanism supported by the experiments, providing additional insights. In particular, the goal of this exploratory computational project is to demonstrate whether the use of metadynamics (a novel simulation technique to explore the free energy surfaces of complex polyatomic systems) can provide an atomistic picture of the proposed gating mechanism. Using a combination of classical and quantum mechanical methods, we will start investigating the proline switch in a 20 amino-acid model peptide mimicking the 5-HT3R relevant (M2-M3) loop. We will assess the effects of proline mutations with proline analogues, preferring either the cis or the trans conformations, which in experiments produced functional or non-functional receptors, and evaluate the influence of the environment on the isomerisation mechanism. We will then increase the complexity of the model system, e.g. including the channel lining (M2) helix which is thought to be repositioned by the proline switch. Finally, we will extend the analysis to receptors of the same superfamily as 5-HT3R, searching for similar or alternative switches. The proposed research will lead to the development of protocols for the use of the metadynamics technique to study switching mechanisms in biomolecules.

配体门控离子通道（lgic）是神经元传递的重要介质，参与许多神经系统疾病，如阿尔茨海默病和帕金森病。这些受体位于神经细胞的膜上，是由排列在离子传导中心孔周围的不同亚基组成的大蛋白质；每个亚基由胞外结构域、跨膜结构域和胞内结构域组成。lgic的激活是由一种小的神经递质与细胞外结构域结合而启动的：这触发了蛋白质的一系列化学事件和构象变化，最终导致通道的打开（门控）：离子可以在细胞膜上泛滥，改变细胞活性。关于LGICs最有趣的问题是，细胞外区域的小神经递质结合如何转化为超过50英里的跨膜区域通道的开放。最近对5-羟色胺3型受体（5-HT3R）的实验表明，位于两个跨膜螺旋（M2-M3环）之间的环顶端的特定脯氨酸氨基酸（Pro 8*）可以通过反式顺式异构化及其对蛋白质主链的结构影响作为离子通道门控的开关。由于lgic的结构信息有限，原子模拟可以在验证实验支持的门控机制方面发挥关键作用，提供额外的见解。特别是，这个探索性计算项目的目标是证明是否使用元动力学（一种探索复杂多原子系统自由能表面的新型模拟技术）可以提供所提出的门控机制的原子图像。利用经典和量子力学方法的结合，我们将开始研究模拟5-HT3R相关（M2-M3）环的20个氨基酸模型肽中的脯氨酸开关。我们将评估脯氨酸突变对脯氨酸类似物的影响，倾向于顺式或反式构象，在实验中产生功能性或非功能性受体，并评估环境对异构化机制的影响。然后，我们将增加模型系统的复杂性，例如，包括通道内衬（M2）螺旋，它被认为是由脯氨酸开关重新定位的。最后，我们将把分析扩展到与5-HT3R相同的超家族受体，寻找类似或替代开关。提出的研究将导致使用元动力学技术来研究生物分子中的开关机制的协议的发展。