Protein Structure and Dynamics from EPR Spectroscopy and MD Simulations

EPR 光谱和 MD 模拟的蛋白质结构和动力学

基本信息

批准号：
8277917
负责人：
TERRY P LYBRAND
金额：
$ 112.76万
依托单位：
VANDERBILT UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2008
资助国家：
美国
起止时间：
2008-05-01 至 2014-04-30
项目状态：
已结题

项目摘要

The long-term objectives of this program project are to develop computational tools that can be used to extract accurate structural and dynamical information from site-directed spin-labeling (SDSL) studies on proteins. These new tools constitute an essential enabling technology to determine the structures and functional dynamics for a wide range of soluble and membrane-bound proteins and their complexes. As such, these tools should have an immediate and significant impact on SDSL studies of proteins here at Vanderbilt and elsewhere, and we intend to make all software and computational protocols developed in this program project freely available to colleagues at other institutions. The specific aims of this program project are: 1) develop molecular dynamics and molecular modeling protocols to enable us to directly correlate EPR measurements of spin label mobility and accessibility with protein structure and structural fluctuations; 2) develop simulation tools and protocols so that EPR measurements of inter-probe distances can be related directly to protein structure; 3) develop a general computational protocol so that information obtained in Specific Aims 1 and 2 can be used to build and refine structural models; and 4) apply the tools and strategies developed in Aims 1-3 to SDSL data obtained for T4 lysozyme, a model protein of known structure, for CDB3, a more complex erythrocyte membrane protein that is to date only partially characterized structurally, and for amyloid precursor protein peptides that are not well characterized structurally at this time. These specific protein spectroscopic studies will provide the requisite experimental data necessary to develop and test the computational protocols. This program includes investigators with extensive eperience in EPR spectroscopy and SDSL studies of proteins (Beth and Hustedt), membrane protein structure-function studies (Beth, Lybrand, and Sanders), and use of molecular modeling and molecular simulation tools to refine three-dimensional protein structures from distance data obtained from spectroscopic and other biophysical studies (Lybrand and Smith).

该计划项目的长期目标是开发计算工具，可用于从蛋白质定点自旋标记（SDSL）研究中提取准确的结构和动态信息。这些新工具构成了确定各种可溶性和膜结合蛋白及其复合物的结构和功能动力学的重要使能技术。因此，这些工具应该对范德比尔特大学和其他地方的蛋白质 SDSL 研究产生直接而重大的影响，我们打算将该项目中开发的所有软件和计算协议免费提供给其他机构的同事。该计划项目的具体目标是：1）开发分子动力学和分子建模协议，使我们能够直接将自旋标签迁移率和可及性的 EPR 测量与蛋白质结构和结构波动相关联； 2) 开发模拟工具和协议，以便探针间距离的 EPR 测量可以直接与蛋白质结构相关； 3) 开发通用计算协议，以便在特定目标 1 和 2 中获得的信息可用于构建和完善结构模型； 4) 将目标 1-3 中开发的工具和策略应用于 T4 溶菌酶（一种已知结构的模型蛋白）、CDB3（一种更复杂的红细胞膜蛋白，迄今为止仅在结构上进行部分表征）和淀粉样蛋白获得的 SDSL 数据目前尚未在结构上得到很好的表征。这些特定的蛋白质光谱研究将提供开发和测试计算协议所需的实验数据。该计划包括在蛋白质 EPR 光谱和 SDSL 研究（Beth 和 Hustedt）、膜蛋白结构功能研究（Beth、Lybrand 和 Sanders）以及使用分子建模和分子模拟工具来完善三维模型方面具有丰富经验的研究人员。来自光谱和其他生物物理研究（Lybrand 和 Smith）获得的距离数据的蛋白质结构。