MOLECULAR DYNAMICS SIMULATIONS OF NATIVELY UNFOLDED PROTEINS

天然未折叠蛋白质的分子动力学模拟

• 批准号: 7956242
• 负责人: OLIVER MICHAEL COLVIN
• 金额: $ 0.08万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956242
• 关键词: Amber; Behavior; Biomedical Research; Computer Retrieval of Information on Scientific Projects Database; Development; Funding; Glycine; Goals; Grant; High Performance Computing; Institution; Metric; Modeling; Molecular Conformation; Nuclear Pore Complex Proteins; Phenylalanine; Play; Polymers; Property; Proteins; Research; Research Personnel; Resources; Role; Running; Solvents; Source; United States National Institutes of Health; molecular dynamics; mutant; nanosecond; nucleocytoplasmic transport; simulation

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. The FG-nucleoporins (FG-nups) are natively-unfolded domains with phenylalanine-glycine motifs that play key roles in nucleocytoplasmic transport. We are using classical molecular dynamics simulations using Amber to analyze the dynamical properties of a number of FG-nups and FG-nup mutants. Specifically we are running multiple replicate simulations of the FG-Nups starting from an extended conformation and then analyzing the trajectories using both established metrics for characterizing polymers and newly developed metrics for quantifying the rates of structural change and internal structural correlation. The goal of this development application is to continue the preliminary simulations begun with an AAP allocation, with a specific goal of determining the behavior of these nucleoporins for multiple 10's of nanoseconds using both implicit and explicit solvent models.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 FG-核孔蛋白（FG-nups）是天然未折叠的结构域，具有苯丙氨酸-甘氨酸基序，在核质转运中起关键作用。我们正在使用经典的分子动力学模拟琥珀分析一些FG-nup和FG-nup突变体的动力学性质。具体来说，我们正在运行多个重复模拟的FG-Nups从一个扩展的构象开始，然后分析的轨迹使用两个既定的指标表征聚合物和新开发的指标量化的结构变化率和内部结构相关性。该开发应用程序的目标是继续以AAP分配开始的初步模拟，具体目标是使用隐式和显式溶剂模型确定这些核孔蛋白在数十纳秒内的行为。