Modeling SNARE-Mediated Membrane Fusion

SNARE 介导的膜融合建模

• 批准号: 10445738
• 负责人: Ben O'Shaughnessy
• 金额: $ 33.89万
• 依托单位: COLUMBIA UNIV NEW YORK MORNINGSIDE
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10445738
• 关键词: Action Potentials; Beta Cell; Biochemical; Catalogs; Cell fusion; Cell membrane; Cells; Chromaffin Cells; Closure by clamp; Communities; Complex; Computer Models; Core Protein; Coupled; Data; Dense Core Vesicle; Docking; Dynamin; Entropy; Event; Evoked Potentials; Evolution; Exocytosis; Family; Functional disorder; Funding; Goals; Grain; Growth; Hormones; Hot Spot; Impairment; Informal Social Control; Kinetics; Laboratories; Machine Learning; Measurement; Mechanics; Mediating; Membrane; Membrane Fusion; Membrane Lipids; Modeling; Molecular; Mutate; Mutation; Neuraxis; Neurodegenerative Disorders; Neurodevelopmental Disorder; Neuroendocrine Cell; Neurons; Neurotransmitters; Pathway interactions; Physiological; Probability; Process; Property; Proteins; Regulation of Exocytosis; Reproducibility; Research; Respiratory Diaphragm; Rest; Running; S-nitro-N-acetylpenicillamine; SNAP receptor; Scheme; Secretory Vesicles; Shapes; Signal Transduction; Site; Stimulus; Structure; Study models; Synapses; Synaptic Cleft; Synaptic Vesicles; Testing; Thinness; Type 2 diabetic; Vesicle; experimental study; foot; hydrophilicity; in silico; insulin secretion; mathematical model; membrane model; millisecond; molecular dynamics; multi-scale modeling; nanodisk; neurotransmission; neurotransmitter release; novel; predictive modeling; reconstitution; response; sensor; simulation; synaptotagmin; synaptotagmin I; synaptotagmin II; syntaxin; target SNARE proteins; vesicular SNARE proteins; vesicular release

PROJECT SUMMARY Many basic processes rely on secretion of bioactive molecules by exocytosis, when membrane-enclosed vesicles containing neurotransmitters (NTs), hormones or other molecules fuse with the plasma membrane (PM) and release their contents through fusion pores. Neurotransmission relies on NT release at neuronal synapses, when a multicomponent machinery senses Ca!"influx triggered by an action potential and fuses small synaptic vesicles with the plasma membrane on sub-millisecond timescales, releasing NTs into the synaptic cleft to elicit a post-synaptic response. Other regulated exocytosis is slower, such as hormone release from neuroendocrine cells when a stimulus provokes large dense core vesicles to release contents after seconds or longer. In all cases, the membrane fusion step is accomplished by the SNARE proteins, when vesicle-associated VAMP (the v-SNARE) and two PM-associated t-SNAREs syntaxin and SNAP 25 zipper into a ternary complex, pulling the membranes together and fusing them. However, the mechanism of membrane fusion remains unclear. Other components in the machinery block (“clamp”) SNARE-mediated fusion, until the Ca!"signal releases the clamp. Synaptotagmin (Syt) is the Ca!"sensor for synchronous release, but the molecular identity of the clamp and the Ca!"-triggered unclamping mechanism are not established. Mutations in SNARE proteins and other NT release machinery components are associated with neurodevelopmental and neurodegenerative disorders, and impaired fusion pore dilation is associated with reduced insulin secretion by β-cells of type-2 diabetics. The proposed research aims to use mathematical modeling to establish the mechanisms of regulated membrane fusion and the mechanisms that regulate the vesicle and its pore for controlled contents release following fusion. From the previous funding period, we have working molecular dynamics (MD) simulations of SNARE-mediated membrane fusion and of the NT release machinery incorporating the core SNARE and Syt components. The simulations used sufficiently coarse-grained (CG) representations to achieve the computationally demanding millisecond physiological timescales of fusion and release. Aim 1 is to advance the SNARE-mediated fusion simulations with more realistic SNAREs, and to use machine learning to catalogue the pathways to membrane fusion as a function of the size of the fusing vesicles and other key variables. Mutated SNAREs will be simulated and compared to experiments by collaborators. Aim 2 is to use continuum mathematical modeling to establish the structure, energetics and evolution of the fused vesicle-PM complex and its fusion pore, and the mechanisms of SNARE- and Syt-mediated pore dilation. Aim 3 is to advance the MD simulations of the NT release machinery by introducing molecularly explicit representation of the membranes, and by incorporating additional components as their interactions become experimentally characterized, toward a long-term goal of “reconstituting” the machinery in silico. Simulations will test hypothesized Ca!"-triggered unclamping schemes, and will be run with mutations in the SNARE and Syt components that will be implemented experimentally by our collaborators.

项目摘要 当膜封闭时，许多基本过程依赖于胞吐作用的生物活性分子的分泌 含有神经递质（NTS），激素或其他分子与质膜（PM）融合的蔬菜 并通过融合孔释放其内容物。神经传递依赖于NT释放在神经元突触中的释放， 当多组分机械感觉Ca！ 在亚毫秒尺度上具有质膜的囊泡，将NTS释放到突​​触裂缝中以引起 突触后反应。其他受调节的胞吐作用较慢，例如从神经内分泌中释放马龙 当刺激会引起大型密集的核心蔬菜时，细胞在几秒钟或更长时间后释放含量。 在所有情况下，膜融合步骤都是通过囊泡相关的鞋面完成的。 （V-SNARE）和两个与PM相关的T-SNARES语法素，然后将25拉链捕入三元络合物，拉动 膜融合的机制尚不清楚。其他 机械块中的组件（“夹具”）圈养介导的融合，直到CA！”信号释放夹具。 Synaptotagmin（SYT）是同步释放的传感器，但是夹具的分子身份和 Ca！” - 未建立触发的解开机制。军团蛋白和其他NT释放中的突变 机械组件与神经发育和神经退行性疾病有关，以及 受损的融合孔字典与2型糖尿病患者的β细胞减少胰岛素分泌有关。 拟议的研究旨在使用数学建模来建立受调节膜的机制 融合及其调节囊泡及其孔的机制在融合后释放后释放。 从上一个融资期开始，我们进行了SNARE介导的分子动力学（MD）模拟 膜融合以及编码Core SNARE和SYT组件的NT释放机械。这 模拟使用正确粗粒（CG）表示来实现计算要求 融合和释放的毫秒物理时间尺度。 AIM 1是推进媒介介导的融合 模拟使用更逼真的弹头，并使用机器学习来对通往膜的途径进行分类 融合是融合蔬菜和其他关键变量的大小的函数。将模拟突变的网罗 并与合作者的实验相比。目标2是使用连续数学建模来建立 融合囊泡-PM复合物及其融合孔的结构，能量和演变以及机制 编式和syt介导的孔字典。 AIM 3是推进NT释放机械的MD模拟 通过引入膜的分子显式表示，并导入其他组件 随着它们的互动变得实验表征，朝着“重新建立”的长期目标 硅的机械。模拟将测试假设的CA！ 我们的合作者将通过实验实施的工资和SYT组件中的突变。