NEMD STUDY OF A MUTATED ION CHANNEL, ALPHA-HEMOLYSIN

突变离子通道、α-溶血素的 NEMD 研究

• 批准号: 8171882
• 负责人: ROB Duncan COALSON
• 金额: $ 0.11万
• 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/8171882
• 关键词: Anions; Architecture; Artificial Membranes; Cations; Chloride Ion; Chlorides; Computer Retrieval of Information on Scientific Projects Database; Data; Electrostatics; Equilibrium; Freezing; Funding; Grant; Hemolysin; Hour; Institution; Ion Channel; Ion Transport; Journals; Kale - dietary; Membrane Biology; Mutate; Physics; Point Mutation; Property; Proteins; Research; Research Personnel; Resources; Rest; Services; Site; Site-Directed Mutagenesis; Sodium Chloride; Solutions; Solvents; Source; Structure; Supercomputing; System; Testing; Time; United States National Institutes of Health; abstracting; base; molecular dynamics; preference; programs; simulation; sodium ion; 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. Abstract: We propose to perform voltage-driven non-equilibrium molecular dynamics (NEMD) simulations of a mutated alpha-hemolysin (a-HL) ion channel, using the molecular dynamics program NAMD (Kale et. al, 1999). The channel is first embedded in an artificial membrane, and solvated in 1M NaCl salt solution at neutral pH and equilibrated; then an external voltage potential is applied across the system. Additional constraints are placed on the system so that the residues at the protein-solvent interface are allowed to move freely while the rest of the protein remains frozen. These simulations are based on our previous calculations of the a-HL system, performed on the Lemieux Cluster at PSC (grant # mcb030021p), where we generated an I-V curve from -400mV to +400mV, in good correspondence with experimental results (Misakian and Kasianowicz, 2003). We collected concentration profiles as well as a 1-D potential of mean force (PMF) profile along the central pore axis for both chloride and sodium ions, which revealed a distinct preference for chloride ions in the narrow regions of the pore, including the most constricted section of the pore, which serves as a weak selectivity filter favoring anions. Additionally, the results revealed a site along the lining of the ion channel (at lys147) which might provide a good candidate for site-directed mutagenesis in order to change the permeant properties of the system from anion to cation selective. We would like to test this by generating I-V data at +200mV and -200 mV using mutated a-HL structures with one, three and seven lys147 -> ser point mutations. These calculations, consisting of equilibration and I-V calculations, would be most effectively carried out on the Bigben cluster at Pittsburgh Supercomputing Center, due to its scalable architecture and large number of available CPUs. Each of the I-V data points should require approximately 5000 hours of processor time on Bigben, for a total request of 30,000 service units. Kale, L., R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. 1999. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics 151: 283-312. Misakian M. and J. J. Kasianowicz. 2003. Electrostatic control of ion transport through the -hemolysin channel. Journal of Membrane Biology, 195 (3), 137-146.

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。 摘要：我们建议使用分子动力学程序NAMD（Kale et al，1999），对突变的α-溶血素（A-HL）离子通道进行电压驱动的非平衡分子动力学（NEMD）模拟。该通道首先嵌入人造膜中，并在中性pH下溶解在1M NaCl盐溶液中并平衡。然后在整个系统上应用外部电压电势。在系统上放置了其他约束，因此允许蛋白质溶剂界面的残基自由移动，而其余蛋白质保持冷冻。这些模拟基于我们先前对A-HL系统的计算，该系统在PSC的Lemieux群集上执行（授予＃MCB030021P），在该系统中，我们与实验结果（Misakian and Kasianowicz，2003）生成了I-V曲线从-400MV到 +400mV，从而从-400MV到 +400mV进行了良好的相对。我们沿着氯化物和钠离子的中央孔轴收集了平均力（PMF）曲线的1-D电位（PMF）的1-D电势，这揭示了孔狭窄区域中对氯离子的独特偏爱，包括孔中最狭窄的部分，这是最弱的选择性过滤性过滤性过滤性的偏爱。此外，结果揭示了沿离子通道衬里的位点（在LYS147处），该位点可能为位置定向诱变提供了良好的候选者，以便将系统的渗透性从阴离子从阴离子选择为阳离子选择性。我们希望通过使用一个，三个和七个Lys147-> Ser点突变的突变A -HL结构在 +200mV和-200 mV下生成I -V数据来测试这一点。这些计算由平衡和I-V计算组成，由于其可扩展的架构和大量可用CPU，将在匹兹堡超级计算中心的Bigben群集上最有效地进行。每个I-V数据点都应在Bigben上大约需要5000小时的处理器时间，总计30,000个服务单位。 Kale，L.，R。Skeel，M。Bhandarkar，R。Brunner，A。Gursoy，N。Krawetz，J。Phillips，A。Shinozaki，K。Varadarajan和K. Schulten。 1999。NAMD2：平行分子动力学的更大可伸缩性。计算物理杂志151：283-312。 Misakian M.和J. J. Kasianowicz。 2003。通过-脱糖蛋白通道的离子传输的静电控制。膜生物学杂志，195（3），137-146。