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: 8364252
• 负责人: JOEL R. STILES
• 金额: $ 8.65万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364252
• 关键词: 3-Dimensional; Action Potentials; Algorithms; Architecture; Binding; Binding Sites; Biomedical Research; Calcium; Calcium Binding; Calcium Channel; Calcium Signaling; Calcium ion; Coupled; Data; Diffusion; Dimensions; Experimental Models; Funding; Generations; Grant; High Performance Computing; Ions; Kinetics; Length; Lipid Binding; Manuscripts; Membrane Lipids; Memory; Modeling; National Center for Research Resources; Nerve; Neurotransmitters; Operating System; Output; Pattern; Physiological; Postdoctoral Fellow; Preparation; Principal Investigator; Probability; Process; Proteins; Publications; Publishing; Rana; Research; Research Infrastructure; Resources; Running; SNAP receptor; Simulate; Site; Source; Speed; Structure; Synaptic Vesicles; System; Time; United States National Institutes of Health; Vesicle; Work; abstracting; base; cost; design; extracellular; mathematical model; nanosecond; neuromuscular; neurotransmitter release; presynaptic; sensor; shared memory; simulation; stoichiometry; synaptotagmin I; voltage

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. 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.

该子项目是利用NIH/NCRR资助的中心赠款提供的资源的许多研究子项目之一。对该子项目的主要支持和子弹的主要研究者可能由其他来源（包括其他NIH来源）提供。 该子项目列出的总成本可能代表了子项目使用的估计中心基础设施的估计数量，而不是NCRR赠款向子项目或副标理人员提供的直接资金。突触前钙动力学和神经递质释放的蒙特卡洛模拟。 该计算项目由J. Stiles执导，由他的实验室后的大多数人约翰·帕蒂洛（John Pattillo）执行。 使用逼真的神经终末超微结构以及II.A.1.C中描述的数据，MCELL对电压门控钙通道的动作电位激活，随机钙离子进入和钙的扩散，钙，钙的扩散，钙结合到接触端的传感器和预测式的trandmition fressition fressition fromitife fromptife from fromsique forsique procestion和transime transmite。 据我们所知，这是迄今为止唯一包括整个突触前活性区的3-D结构，并且使用了多个实验约束来实现定量预测，例如，突触囊泡上的钙结合位点的数量，在结合站点数量之间必须限制的位点之间的关系，启动了神经剂量的释放，并且需要启动神经剂量的释放和该释放。 简而言之，细胞外Ca2+（[Ca2+] O）和递质释放之间的上次（〜4阶）1（CRR）（CRR）表明，融合突触囊泡（SV）需要多个CAC2+离子，但是这种经验观察与该经验观测值与Voltage-ca2+ ca2+ ca2+ capling-ca2+ cansect+ ca2+通道（VGC2+ capling ca2+ canselsement）（ SV不清楚。 我们创建了青蛙神经肌肉活性区（AZ）的空间逼真的模型，并使用McEll模拟了通过VGCC，Ca2+与SVS的CA2+结合以及CA2+依赖性SV融合的几种模型。 我们各种各样的空间参数同时再现了3个实验观察： 1.）每个AZ每个试验的平均释放概率（PR）在生理[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VGCC模型再现了宏观CA2+电流动力学，而Ca2+结合的ON和OFF速率基于Synaptototototagmin-1 C2A结构域。 鉴于所有这些约束，我们获得了一组令人惊讶的独特模型参数和几个违反直觉预测。 使用VGCC：1：1的SV化学计量学（由上面概述的实验和数学建模数据支持），每个SV都包含约20个Ca2+结合位点，并且必须同时绑定6个位点才能诱导融合。 替代模型要么太CA2+不敏感，无法再现PR，要么不能同时再现LDIS和CRR。 这些结果证明了CRR，PR和LDI对突触前结构的敏感性，并表明囊泡融合可能需要各种Ca2+的SNARE蛋白和膜脂质结合位点。 这项工作以抽象的形式出版（Pattillo等，2004），并准备了几个全长手稿。 该项目迄今为止需要105个模拟的规模，主要是在PSC HP GS1280机器上运行的，我们是我们是首选的用户组之一。 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，并且最适合McEll中的蒙特卡洛算法和运行时优化。具体而言，McEll模拟需要带有随机访问模式的大量内存。此外，该项目令人钦佩地证明了McEll在双分子相互作用中独特的蒙特卡洛算法的优势。 活动区的空间尺寸紧密限制，我们的模拟表明，囊泡结合位点附近的平均钙浓度对应于任何瞬间的小于单个离子。 尽管有这些条件，McEll仍能够在亚微秒尺度上以时间步长而不是次纳秒量表来准确模拟这些钙动力学（对于双分子相互作用的算法较不复杂的算法所需）。 因此，只有通过优化算法的组合和脱颖而出的结合才能实现该项目 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。在这项研究中，我们通常在任何给定时间运行一个“项目”。 每个“项目”都包含24套模拟，每个“集合”都需要500-1000个单独的（令人尴尬的平行）模拟，每个模拟都以3 gbytes的RAM运行。 由于Marvel的出色内存带宽和Mcell的频繁随机内存访问，我们的模拟即使与以更高的时钟速度运行的其他更新的处理器相比，我们的模拟也非常有效。 也许更重要的是，我们从未遇到过与编译器或操作系统问题有关的任何问题。 鉴于每个“项目”生成多达4800万个输出文件，这尤其令人印象深刻，这些文件最多可消耗2.4台磁盘空间，但我们可以在fly上进行后处理，从而在转移到质量存储之前获得了约1000倍的速度。 如果没有一个稳定的系统结合了大型内存，出色的内存带宽，快速的I/O以及可靠的转移到质量存储，我们的项目可能无法完成。 出版物： Pattillo，JM，Meriney，SD和Stiles，Jr。，2004年，在印刷中，在空间上逼真的蒙特卡洛模拟预测了在神经肌肉活性区的发射机释放的钙动力学。 Soc。 Neurosci。弃权。 脚注： 1。钙源通常不止一个通道，每个通道与恰好融合的囊泡的距离不同。 钙传感（结合）位点在每个囊泡的底部阵列。 从每个通道到每个传感器，钙梯度非常陡峭（在空间和时间上）不同。 因此，这与多个结合位点每个响应相同钙信号的情况大不相同。 明显的合作性还取决于我们如何定义融合模型，例如，结果不同，具体取决于我们是否要求〜6个站点同时绑定或只是在某个时间点绑定。