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

• 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

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，与许多神经系统疾病有关，例如阿尔茨海默病和帕金森病。这些受体位于神经细胞膜上，是大蛋白质，由排列在离子传导中心孔周围的不同亚基组成；每个亚基由胞外结构域、跨膜结构域和胞内结构域组成。 LGIC 的激活是由一种小型神经递质与细胞外结构域的结合引发的：这会引发一系列化学事件和蛋白质的构象变化，最终导致通道的打开（门控）：然后离子可以涌过细胞膜改变细胞活性。关于 LGIC 最有趣的问题是，细胞外域中的小神经递质的结合如何转化为超过 50+ 距离的跨膜域中通道的打开。最近对 5-羟色胺 3 型受体 (5-HT3R) 的实验得出这样的结论：位于两个跨膜螺旋（M2-M3 环）之间环的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充当离子通道门控的开关。由于 LGIC 的结构信息有限，原子模拟在验证实验支持的门控机制方面可以发挥至关重要的作用，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元动力学（一种探索复杂多原子系统自由能表面的新颖模拟技术）的使用是否可以提供所提出的门控机制的原子图。我们将结合经典方法和量子力学方法，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。我们将评估脯氨酸类似物的脯氨酸突变的影响，优选顺式或反式构象，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，例如包括通道内壁 (M2) 螺旋，其被认为是通过脯氨酸开关重新定位的。最后，我们将分析扩展到与 5-HT3R 相同的超家族的受体，寻找类似或替代的开关。拟议的研究将导致使用元动力学技术研究生物分子转换机制的协议的开发。

项目成果

Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations.

通过原子模拟阐明五聚体配体门控离子通道中的配体结合和通道门控机制。

• DOI: http://dx.10.1042/bst20140259
• 发表时间: 2015
• 期刊: Biochemical Society transactions
• 影响因子: 3.9
• 作者: Comitani F

Mechanism of action of cyclophilin A explored by metadynamics simulations

通过元动力学模拟探索亲环蛋白 A 的作用机制

• DOI: http://dx.10.1016/j.bpj.2008.12.2266
• 发表时间: 2009
• 期刊: Biophysical Journal
• 影响因子: 3.4
• 作者: Leone V

Mechanism of action of cyclophilin a explored by metadynamics simulations.

通过元动力学模拟探索亲环蛋白的作用机制。

• DOI: http://dx.10.1371/journal.pcbi.1000309
• 发表时间: 2009
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Leone V

Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor.

脯氨酸类似物的反顺式转换机制及其与 5-HT3 受体门控的相关性。

• DOI: http://dx.10.1021/jp9046962
• 发表时间: 2009
• 期刊: The journal of physical chemistry. B
• 作者: Melis C

Chemical and protein shifts in the spectrum of the photoactive yellow protein: a time-dependent density functional theory/molecular mechanics study.

光敏黄色蛋白光谱中的化学和蛋白质变化：时间依赖性密度泛函理论/分子力学研究。

• DOI: 10.1039/b902615k
• 发表时间: 2009-05-27
• 期刊: Physical chemistry chemical physics : PCCP
• 作者: Eneritz Muguruza González;L. Guidoni;C. Molteni
• 通讯作者: C. Molteni