MONTE CARLO SIMULATION OF PRESYNAPTIC CALCIUM DYNAMICS AND NEUROTRANSMITTER REL

突触前钙动力学和神经递质相关性的蒙特卡罗模拟

• 批准号: 8171830
• 负责人: JOEL R. STILES
• 金额: $ 14.76万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8171830
• 关键词: Action Potentials; Algorithms; Architecture; Binding; Binding Sites; Calcium; Calcium Binding; Calcium Channel; Calcium Signaling; Calcium ion; Computer Retrieval of Information on Scientific Projects Database; Coupled; Data; Diffusion; Dimensions; Funding; Generations; Grant; Institution; Ions; Kinetics; Knowledge; Length; Lipid Binding; Manuscripts; Membrane Lipids; Memory; Modeling; Nerve; Neurotransmitters; Operating System; Output; Pattern; Physiological; Postdoctoral Fellow; Preparation; Probability; Process; Proteins; Publications; Publishing; Rana; Research; Research Personnel; Resources; Running; SNAP receptor; Simulate; Site; Source; Speed; Synaptic Vesicles; System; Time; United States National Institutes of Health; Vesicle; Work; abstracting; base; complement C2a; design; extracellular; mathematical model; nanosecond; neuromuscular; neurotransmitter release; presynaptic; sensor; shared memory; simulation; stoichiometry; synaptotagmin I; three dimensional structure; voltage

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Monte Carlo simulation of presynaptic calcium dynamics and neurotransmitter release. This computational project is directed by J. Stiles and is being carried out by John Pattillo, a post-doc in his lab. Using realistic nerve terminal ultrastructure and data such as that described in II.A.1.c, MCell simulations of active zone calcium dynamics encompass action potential-activation of voltage-gated calcium channels, stochastic calcium ion entry and diffusion, calcium binding to sensor sites on arrays of synaptic vesicles, and prediction of vesicle fusion and resulting transmitter release. To our knowledge, this is the only study to date that has included the 3-D structure of an entire presynaptic active zone, and that has used multiple experimental constraints to enable quantitative predictions, e.g., the number of calcium-binding sites on synaptic vesicles, and the relationship between number of binding sites, number of sites that must be bound to initiate neurotransmitter release, and the importance of active zone spatial organization. In brief, a supralinear (~4th order)1 relationship (CRR) between extracellular Ca2+ ([Ca2+]o) and transmitter release indicates that multiple Ca2+ ions are required for fusion of a synaptic vesicle (SV), but how this empirical observation relates to the stoichiometry and architecture of voltage-gated Ca2+ channels (VGCCs), Ca2+ binding sites, and SVs is unclear. We created a spatially realistic model of a frog neuromuscular active zone (AZ), and used MCell to simulate action potential (AP)-induced Ca2+ influx through VGCCs, Ca2+ binding to SVs, and several models of Ca2+-dependent SV fusion. We varied spatial parameters to simultaneously reproduce 3 experimental observations: 1.) average release probability (pr) per trial per AZ at physiological [Ca2+]o; 2.) the distribution of release latencies (Ldis); and 3.) the 4th order CRR. Also, a 4-state VGCC model reproduced macroscopic Ca2+ current kinetics, and the on and off rates for Ca2+ binding were based on the synaptotagmin-1 C2A domain. Given all these constraints, we obtained a surprisingly unique set of model parameters and several counter-intuitive predictions. With a VGCC:SV stoichiometry of 1:1 (supported by the experimental and mathematical modeling data outlined above), each SV contains ~20 Ca2+ binding sites, and 6 sites must be bound simultaneously to induce fusion. Alternative models were either much too Ca2+-insensitive to reproduce pr or could not simultaneously reproduce Ldis and CRR. These results demonstrate the dramatic sensitivity of CRR, pr, and Ldis to presynaptic architecture, and suggest that vesicle fusion may require a variety of SNARE protein and membrane lipid binding sites for Ca2+. This work has been published in abstract form (Pattillo et al., 2004), and several full length manuscripts are in preparation. This project has required something on the scale of 105 simulations to date, primarily run on the PSC HP GS1280 machine(s), for which we are one of the preferred user groups. This machine is based on latest-generation Alpha EV7 processors, large shared memory, and outstanding memory bandwidth, and is optimally suited to our Monte Carlo algorithms and run-time optimizations within MCell. Specifically, MCell simulations require larges amounts of memory with random access patterns. In addition, this project admirably demonstrates the advantages to MCell's unique Monte Carlo algorithms for bimolecular interactions. The spatial dimensions of the active zone are tightly confined, and our simulations show that the average calcium concentration in the vicinity of vesicular binding sites corresponds to less than a single ion at any instant in time. Despite these conditions, MCell is able to accurately simulate these calcium dynamics with a time step on the sub-microsecond scale, rather than the sub-nanosecond scale (as would be required with less sophisticated algorithms for bimolecular interactions). Thus, this project has been possible only through a combination of optimized algorithms coupled with outstandingly designed and supported hardware. Computational Challenges These simulation have been performed using PSC's Marvel systems. Within this study, we are usually running one "project" at any given time. Each "project" includes 24 "sets" of simulations, and each "set" requires 500-1000 separate (embarrassingly parallel) simulations, each of which runs in 3 GBytes of RAM. Because of the Marvel's outstanding memory bandwidth and MCell's frequent random memory accesses, our simulations run very efficiently even compared to other more recent processors running at higher clock speeds. Perhaps even more important, we have never had any problems related to compilers or operating system issues. This is especially impressive given that each "project" generates up to 48 million output files that would consume up to 2.4 TBytes of disk space, except that we post-process the results on-the-fly, obtaining a reduction of ~1000-fold before transfer to mass storage. Without a stable system combining large memory, outstanding memory bandwidth, fast I/O, and reliable transfer to mass storage, our projects probably could not have been done. Publications: Pattillo, JM, Meriney, SD, and Stiles, JR., 2004, in press, Spatially realistic Monte Carlo simulations predict calcium dynamics underlying transmitter release at a neuromuscular active zone. Soc. Neurosci. Abst. Footnotes: 1. The calcium source is generally more than one channel, each of which is at a different distance from the vesicle that happens to fuse. The calcium sensing (binding) sites are arrayed around the base of each vesicle. The calcium gradient is very steep and different (in space and time) from each channel to each sensor. Thus it is very different from a situation in which multiple binding sites are each responding to the same calcium signal. The apparent cooperativity also depends on how we define the fusion model, e.g., the results are different depending on whether or not we require ~6 sites to be bound simultaneously or just to have been bound at some point in time.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 突触前钙动力学和神经递质的蒙特卡洛模拟 发布。 这个计算项目由J. Stiles执导，正在 由约翰·帕蒂洛（John Pattillo）在他的实验室中的大多数人约翰·帕蒂洛（John Pattillo）执行。 使用逼真的神经 终端超微结构和诸如II.A.1.C中描述的数据，McEll 活动区钙动力学的模拟包含动作 电压门控钙通道的潜在激活，随机钙离子 进入和扩散，钙结合在突触阵列上的传感器位点 囊泡，以及囊泡融合的预测和产生的发射器释放。 据我们所知，这是迄今为止唯一包括3-D的研究 整个突触前活动区的结构，并且使用了多个 实验性约束以实现定量预测，例如 突触囊泡上的钙结合位点以及 绑定站点的数量，必须绑定才能启动的站点数量 神经递质的释放和活动区空间的重要性 组织。 简而 Ca2+（[Ca2+] O）和发射器释放表明多个Ca2+离子是 融合突触囊泡（SV）所必需的，但是这种经验是如何 观察与电压门控Ca2+的化学计量和结构有关 通道（VGCC），Ca2+结合位点和SV尚不清楚。 我们创建了一个 青蛙神经肌肉活性区（AZ）的空间现实模型，并使用 MCELL模拟动作电位（AP）诱导的Ca2+通过VGCC，CA2+涌入 与SV的结合以及Ca2+依赖性SV融合的几种模型。 我们变化了 同时再现3个实验观察的空间参数： 1.）每个AZ在生理学上每次试验的平均释放概率（PR） [Ca2+] o; 2.）释放潜伏期的分布（LDIS）；和 3.）第四阶CRR。 此外，一个4状态的VGCC模型再现了宏观CA2+当前动力学，并且 Ca2+结合的开关速率基于突触触及量-1 C2A 领域。 鉴于所有这些约束，我们获得了一套令人惊讶的独特集 模型参数和几个违反直觉预测。 使用VGCC：SV 1：1的化学计量法（由实验和数学建模支持 上面概述的数据），每个SV包含约20个Ca2+绑定位点，必须6个站点必须 同时绑定以诱导融合。 替代模型要么多 Ca2+不敏感无法再现PR或不能同时再现LDI 和Crr。 这些结果表明CRR，PR和 LDI到突触前结构，并建议囊泡融合可能需要 Ca2+的多种核心蛋白和膜脂质结合位点。 这项工作 已经以抽象形式出版（Pattillo等，2004），几个完整 长度手稿正在准备。 迄今为止，该项目需要105个模拟的规模， 主要在PSC HP GS1280机器上运行，我们是其中之一 首选的用户组。 该机器基于最新一代Alpha EV7 处理器，大共享内存和出色的内存带宽，并且是 最适合我们的蒙特卡洛算法和运行时间优化 在麦克尔内。具体而言，McEll模拟需要大量的内存 随机访问模式。此外，这个项目令人钦佩地证明 麦克尔独特的蒙特卡洛算法的优势用于双分子 互动。 活动区的空间尺寸紧密限制， 我们的模拟表明，附近的平均钙浓度 在任何瞬间，囊泡结合位点的对应于小于单个离子 及时。 尽管有这些条件，McEll仍然能够准确模拟这些 钙动力学在子微秒刻度上具有时间步长，而不是 子纳秒量表（如算法较少所必需的 用于双分子相互作用）。 因此，这个项目只有可能 通过优化算法结合结合的结合与脱颖而出的算法 设计和支持的硬件。 计算挑战 这些模拟已使用PSC的Marvel Systems进行。在此 研究，我们通常在任何给定时间运行一个“项目”。 每个“项目” 包括24个模拟的“集合”，每个“集合”需要500-1000个单独 （令人尴尬的平行）模拟，每个模拟都在3 gbytes中运行。 因为漫威的出色记忆带宽和麦克尔的频繁 随机内存访问，我们的模拟即使与 其他最新的处理器以更高的时钟速度运行。 也许更多 重要的是，我们从来没有与编译器或操作有关的任何问题 系统问题。 考虑到每个“项目”，这尤其令人印象深刻 生成多达4800万个输出文件，最多可消耗2.4 tbytes 磁盘空间，除了我们在即时进行后处理结果，获得了 在转移到质量存储之前，还原约1000倍。 没有稳定 系统结合了大型内存，出色的内存带宽，快速I/O和 可靠地转移到大众存储，我们的项目可能不可能 完毕。 出版物： Pattillo，JM，Meriney，SD和Stiles，Jr。，2004年，印刷中，在空间上现实 蒙特卡洛模拟预测发射器释放的钙动力学 在神经肌肉活性区。 Soc。 Neurosci。弃权。 脚注： 1。钙源通常不止一个通道，每个通道是 与恰好融合的囊泡不同的距离。 钙 感应（结合）位点在每个囊泡的底部周围阵列。 这 钙梯度非常陡峭，并且（在空间和时间上）与每个钙梯度不同 通道到每个传感器。 因此与 多个结合位点每个都响应相同的钙信号。 这 明显的合作性也取决于我们如何定义融合模型，例如 结果是不同的，具体取决于我们是否需要6个站点 同时或只是在某个时间点被绑定。