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

描述(由申请人提供)：蛋白质中的结构-动力学关系：通过核磁共振松弛测量和分子动力学模拟对结构及其波动进行多方面的表征。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。最近已经清楚的是，仅蛋白质动力学的改变就可以用来在蛋白质中的远距离位置之间进行通信。这种通信渠道所涉及的结构和波动(以及它们之间的耦合)还没有被很好地理解。我们讨论了结构-动力学关系的几个方面。目的1：在一种联合的核磁共振实验-计算精化方法中，我们寻求改善蛋白质结构系综中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条件和用于结构优化的局部构象数量。结果将与自由分子动力学模拟和由核磁共振弛豫测量得到的有序参数进行比较。这些结构系综将对药物设计中的配体和蛋白质对接计算有用。目标2：我们的研究试图揭示允许蛋白质环和核心结构波动之间耦合的设计原则。再次，溶液核磁共振实验和计算策略将结合几种蛋白质，包括泛素和RhoGTPase结合域的丛蛋白-B1(RBD)，它有一个泛素折叠和长环插入。为了探测两者之间可能的动态耦合，将对环路以及蛋白质核心进行操作。对于RBD-GTPase复合体，也将研究跨越蛋白质-蛋白质界面的可能的运动耦合。目的3：利用不同溶剂粘度下的核磁共振弛豫和长时间尺度的朗之万布朗动力学模拟，研究蛋白质的全局随机运动影响局部和内部动力学的可能性。目的4：将测试加强构象空间采样的方法，并将根据核磁共振数据验证分子动力学程序CHARMM/NAMD的下一代力场。总体而言，在这个项目中，将把几种计算和实验策略结合在一起，以便深入了解蛋白质结构与内部和全球蛋白质动力学之间的关系。其中一些被研究的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药物提供新的途径。 公共卫生相关性：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全球动力学之间的相互关系的详细见解。所讨论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，这里特别是细胞信号蛋白。其中一些蛋白质在癌症的发展和扩散中扮演着重要的角色，他们的进一步研究将为诊断或治疗药物的设计提供新的途径。

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.