Structure-Dynamics Relationships in Proteins: A multi-faceted characterizati

蛋白质的结构-动力学关系：多方面的表征

• 批准号: 8539027
• 负责人: MATTHIAS BUCK
• 金额: $ 28.5万
• 依托单位: CASE WESTERN RESERVE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-30 至 2014-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8539027
• 关键词: Address; Affect; Binding; Biophysics; Cells; Communication; Complex; Core Protein; Coupling; Data; Data Set; Development; Diagnostic; Distant; Docking; Drug Design; Event; Generations; Guanosine Triphosphate Phosphohydrolases; Information Theory; Investigation; Joints; Ligands; Link; Malignant Neoplasms; Measurement; Methods; Modeling; Motion; Neoplasm Metastasis; Play; Protein Dynamics; Protein Region; Proteins; Protocols documentation; Relaxation; Role; Sampling; Signal Transduction; Signaling Protein; Site; Solutions; Solvents; Structural Protein; Structure; Surface; Testing; Therapeutic Agents; Time; Ubiquitin; Validation; Viscosity; base; combat; conformer; design; feeding; improved; insight; methyl group; molecular dynamics; mutant; next generation; plexin; programs; protein complex; protein function; protein structure; protein structure function; public health relevance; research study; restraint; simulation; structural biology; tumorigenesis

DESCRIPTION (provided by applicant): Structure - Dynamics Relationships in Proteins: Multi-faceted characterization of structure and its fluctuations by NMR relaxation measurements and molecular dynamics simulations. Protein fluctuations and their relationship to protein structure and function continue to challenge biophysical measurements and simulations. All three aspects of proteins (dynamics, structure and function) are intimately linked. Recently it has become clear that alterations in protein dynamics alone can be used to communicate between distant sites in proteins. The structures and fluctuations that are involved in such communication conduits (and the coupling between them) are not yet well understood. We address several aspects of the structure-dynamics relationship. Aim 1: In a joint NMR experimental -computational refinement approach we seek to improve the representation of ps-ns timescale dynamics in protein structural ensembles. A statistical and an information theory based approach will be employed to evaluate the experimental restraints and the number of local conformers to be used in the structure refinement. The results will be compared to unrestrained molecular dynamics simulations and to order parameters derived from NMR relaxation measurements. The structural ensembles will be useful for ligand and protein docking calculations in drug design. Aim 2: Our study seeks to reveal design principles that allow a coupling between protein loops and the fluctuations of core structures. Again, both solution NMR experimental and computational strategies will be combined for several proteins, including for ubiquitin and for the RhoGTPase binding domain of plexin-B1 (RBD), which has a ubiquitin fold with long loop insertions. The loops as well as the protein core will be manipulated in order to probe possible dynamic coupling between the two. Possible motional coupling across a protein-protein interface will also be examined for the RBD-GTPase complex. Aim 3: The possibility that the global stochastic motion of the protein can affect the local, internal dynamics will be examined using NMR relaxation at different solvent viscosities and long time-scale Langevin/Brownian dynamics simulations. Aim 4: Methods for enhanced sampling of conformational space will be tested and a next generation force field for the molecular dynamics program CHARMM/NAMD will be validated against NMR data. Overall, in this project, several computational and experimental strategies will be brought together in order to provide deep insight into the relationship between protein structures, and internal as well as global protein dynamics. Several of the proteins studied have important roles in oncogenesis and cell metastasis and their further investigation will suggest new avenues for the design of diagnostic or therapeutic agents to combat cancer. PUBLIC HEALTH RELEVANCE: The joint experimental and computational project will provide detailed insight into the interrelationship between protein structure and protein internal and global dynamics. The basic questions addressed are fundamental to the field of protein biophysics and structural biology. The results of this study will help to understand protein function, here specifically of cell signaling proteins. Several of the proteins involved play important roles in cancer development and spreading, and their further investigation will suggest new avenues for the design of diagnostic or therapeutic agents.

描述（由申请人提供）：蛋白质中的结构-动力学关系：通过核磁共振弛豫测量和分子动力学模拟对结构及其波动进行多方面表征。蛋白质波动及其与蛋白质结构和功能的关系继续挑战生物物理测量和模拟。蛋白质的所有三个方面（动力学、结构和功能）都是密切相关的。最近，人们已经清楚，仅蛋白质动力学的改变就可以用于蛋白质中遥远位点之间的通信。这种通信管道中涉及的结构和波动（以及它们之间的耦合）尚未得到很好的理解。我们讨论结构-动力学关系的几个方面。目标 1：在联合 NMR 实验-计算细化方法中，我们寻求改进蛋白质结构整体中 ps-ns 时间尺度动力学的表示。将采用基于统计和信息论的方法来评估实验限制和结构细化中使用的局部构象异构体的数量。结果将与无约束分子动力学模拟以及从 NMR 弛豫测量得出的有序参数进行比较。该结构整体将有助于药物设计中的配体和蛋白质对接计算。目标 2：我们的研究旨在揭示允许蛋白质环与核心结构波动之间耦合的设计原理。同样，解决方案 NMR 实验和计算策略将结合多种蛋白质，包括泛素和 plexin-B1 (RBD) 的 RhoGTPase 结合域，其具有带有长环插入的泛素折叠。将操纵环和蛋白质核心，以探测两者之间可能的动态耦合。还将检查 RBD-GTP 酶复合物跨蛋白质-蛋白质界面的可能运动耦合。目标 3：将使用不同溶剂粘度下的 NMR 弛豫和长时间尺度朗之万/布朗动力学模拟来检查蛋白质的全局随机运动影响局部内部动力学的可能性。目标 4：将测试增强构象空间采样的方法，并将根据 NMR 数据验证分子动力学程序 CHARMM/NAMD 的下一代力场。总体而言，在该项目中，将结合多种计算和实验策略，以便深入了解蛋白质结构、内部以及整体蛋白质动力学之间的关系。研究的几种蛋白质在肿瘤发生和细胞转移中具有重要作用，它们的进一步研究将为设计抗癌诊断或治疗剂提供新途径。 公共健康相关性：联合实验和计算项目将提供对蛋白质结构与蛋白质内部和整体动态之间相互关系的详细见解。所解决的基本问题是蛋白质生物物理学和结构生物学领域的基础。这项研究的结果将有助于了解蛋白质的功能，特别是细胞信号蛋白的功能。所涉及的几种蛋白质在癌症的发展和扩散中发挥着重要作用，它们的进一步研究将为诊断或治疗剂的设计提供新的途径。

项目成果

Structure and dynamics analysis on plexin-B1 Rho GTPase binding domain as a monomer and dimer.

• DOI: 10.1021/jp503668k
• 发表时间: 2014-07-03
• 期刊: The journal of physical chemistry. B
• 作者: Zhang L;Centa T;Buck M
• 通讯作者: Buck M

Analysis of 15N-1H NMR relaxation in proteins by a combined experimental and molecular dynamics simulation approach: picosecond-nanosecond dynamics of the Rho GTPase binding domain of plexin-B1 in the dimeric state indicates allosteric pathways.

通过实验和分子动力学模拟相结合的方法分析蛋白质中的 15N-1H NMR 弛豫：二聚体状态下 plexin-B1 的 Rho GTPase 结合域的皮秒-纳秒动力学表明变构途径。

• DOI: 10.1021/jp310142f
• 发表时间: 2013
• 期刊: The journal of physical chemistry. B
• 作者: Zerbetto,Mirco;Anderson,Ross;Bouguet-Bonnet,Sabine;Rech,Mariano;Zhang,Liqun;Meirovitch,Eva;Polimeno,Antonino;Buck,Matthias
• 通讯作者: Buck,Matthias