ASSESSMENT OF MULTI-MICROSECOND SIMULATIONS OF INTRINSICALLY DISORDERED PROTEIN

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其他NIH来源。 为子项目列出的总成本可能 代表子项目使用的中心基础设施的估计数量， NCRR赠款不直接向子项目或子项目工作人员提供资金。 本提案的目的是扩展国家的最先进的NMR为基础的轨迹评估协议微秒合奏计算的内在无序蛋白质（IDPs）。这项工作将能够严格评估编码在最佳电流力场中的蛋白质动力学的时间尺度及其振幅的限制。该项目还将允许获得国内流离失所者的高分辨率集合，目前难以用商业软件在单一实验室集群上进行计算。IDPs已经成为细胞系统的关键组成部分，有助于细胞信号传导和人类疾病。更好地了解它们的物理化学性质是必不可少的，因为IDPs的发现改变了科学家对蛋白质结构和功能之间关系的看法。虽然我们内部的计算基础设施足够短（< 1？s）模拟球状蛋白质，我们缺乏必要的本地资源来执行所有原子显式溶剂模拟的内在无序蛋白质。我请求50，000 CPU小时来计算大约40？使用AMBER 99 SB力场对人FCP 1（残基930-961）C-末端尾部的所有原子显式溶剂轨迹的总模拟时间。选择FCP 1作为模型系统是因为其在转录终止后促进RNA聚合酶II再循环中的关键作用。AMBER 99 SB将被使用，因为我过去成功地使用这个力场来模拟具有良好折叠蛋白质轨迹的各种NMR参数。我的实验室不断增长的内部收集的蛋白质FCP 1及其与TFIIF重链蛋白质RAP 74复合物的实验NMR数据将有助于使用已建立的协议计算的超长轨迹的定量集成评估和验证。该项目将为更广泛的IDP社区带来直接利益，因为FCP 1代表了大量的IDP，这些IDP在结合其他大分子后转变为更有序的构象。这使得该项目成为一个理想的机会，为具有已知生物学意义的折叠结合系统中所涉及的所有状态生成原子系综，从而使我们能够对结合事件进行前所未有的机械洞察。

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. The objective of this proposal is to extend state-of-the-art NMR based trajectory assessment protocols to microsecond ensembles calculated for intrinsically disordered proteins (IDPs). This work will enable a rigorous assessment of the timescale of protein dynamics encoded in the best current force fields and the restrictions to their amplitudes. This project will also allow access to high resolution ensembles of IDPs, which are currently intractable to calculate with commercial software on single-laboratory clusters. IDPs have emerged as critical components of cellular systems, contributing to cell signaling and human disease. A better understanding of their physico-chemical properties is imperative as the very discovery of IDPs has transformed scientists' view of the relationship between protein structure and function. While our in-house computational infrastructure is sufficient for short (< 1 ?s) simulations of globular proteins, we lack the local resources necessary to perform all atom explicit solvent simulations of intrinsically disordered proteins. I request 50,000 CPU-hours to calculate approximately 40 ?s total simulation time of all atom explicit solvent trajectories of the C-terminal tail of human FCP1 (residues 930-961) using the AMBER99SB force field. FCP1 is chosen as a model system because of its critical role in promoting RNA polymerase II recycling following the termination of transcription. AMBER99SB will be used due to my past success using this force field to model a variety of NMR parameters with trajectories of well folded proteins. My laboratory's ever growing body of in-house collected experimental NMR data for the protein FCP1 and its complex with the TFIIF heavy chain protein RAP74 will facilitate quantitative ensemble assessment and validation of the ultra-long trajectories computed using established protocols. This project will yield immediate benefit to the broader IDP community because FCP1 is representative of the large number of IDPs that transition to a more ordered conformation upon binding other macromolecules. This makes this project an ideal opportunity to generate atomistic ensembles for all states involved in a folding-upon-binding system with known biological significance, therefore allowing us unprecedented mechanistic insight into the binding event.