Determining the conformational stability of NMR ensemble structures

确定 NMR 系综结构的构象稳定性

基本信息

批准号：
7932050
负责人：
Gary W Daughdrill
金额：
$ 18.78万
依托单位：
UNIVERSITY OF IDAHO
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-14 至 2012-02-29
项目状态：
已结题

项目摘要

DESCRIPTION (provided by applicant): An important outcome of the recent protein structure initiative is the discovery of numerous protein families that do not form compact rigid structures. These intrinsically unstructured proteins (IUPs) are common in nature and disrupting their function can also result in the onset of certain diseases. We believe that to understand the function of IUPs it is crucial to generate realistic structural ensembles. Such ensembles are difficult to generate for IUPs where experiments predict broad, heterogeneous ensembles of structures that undergo large-scale conformational fluctuations. Experimentally restrained ensembles of loop regions in structured proteins are also difficult to reliably compare to the equilibrium ensemble. We are interested in testing two hypotheses through the use of combined computational and experimental approaches: (i) Experimental data for IUPs which are based on average measurements can be used to generate useful structural ensembles. (ii) These ensembles must be properly weighted in the equilibrium distribution to be useful for understanding protein function. In an effort to expand our understanding of how well experimentally restrained ensembles of unstructured proteins represent the equilibrium ensemble, coarse-graining will be used to generate large ensembles that are restrained using average distance and dihedral angle measurements from nuclear magnetic resonance (NMR) spectroscopy experiments. These structurally diverse ensembles will extend previous work in this area by more thoroughly sampling conformational space. These ensembles will then be re-weighted using non-rigorous methods based on fitting data from small angle x-ray scattering and residual dipolar couplings. We will also extend a rigorous re-weighting approach to loops in structured proteins. These goals will be accomplished through the following Specific Aims: Aim 1: Generate large NMR ensembles for IUPs using coarse-graining. Aim 2: Re-weight NMR ensembles using non-rigorous methods. Aim 3: Extend rigorous re-weighting approach to protein loops. Aim 4: Create and maintain website. The proposed research will give valuable insight into the structure and function of protein loops and IDPs. The resulting software will provide us with a means to distinguish the biologically relevant structures from those that are not relevant. PUBLIC HEALTH RELEVANCE: The proposed research project will give insight into protein structure and function. Thus, our understanding of diseases caused by protein dysfunction will be enhanced.

描述（由申请人提供）：最近的蛋白质结构计划的重要结果是发现了许多不形成紧凑型刚性结构的蛋白质家族。这些本质上非结构化的蛋白质（IUP）在本质上很常见，并且破坏其功能也可能导致某些疾病的发作。我们认为，要了解IUP的功能，生成现实的结构合奏至关重要。对于实验预测经历大规模构象波动的结构的广泛，异质的结构，难以生成这样的合奏。结构化蛋白质中环区域的实验限制的集合也很难可靠地比较平衡集合。我们有兴趣通过使用合并的计算和实验方法来检验两个假设：（i）基于平均测量值的IUP的实验数据可用于生成有用的结构集合。（ii）这些集合必须在平衡分布中适当加权，以便理解蛋白质功能。为了扩展我们对非结构化蛋白的实验限制合成的理解，将使用平衡集合，将使用平均距离和二面角度测量的大集合来生成大型集合，这些集团是通过核磁共振（NMR）光谱实验来限制的。这些结构上不同的合奏将通过更彻底的采样构象空间来扩展该领域的先前工作。然后，这些集合将使用基于小角度X射线散射和残留偶极耦合的拟合数据的非辅助方法来重新加权。我们还将扩展一种严格的重新加权方法，以在结构化蛋白质中循环。这些目标将通过以下特定目的来实现：目标1：使用粗粒剂为IUP生成大型NMR合奏。 AIM 2：使用非符合方法的NMR合奏重新权重。 AIM 3：扩展严格的重新加权方法，以实现蛋白质环。目标4：创建和维护网站。拟议的研究将对蛋白质环和IDP的结构和功能有宝贵的见解。最终的软件将为我们提供一种将生物学相关结构与与无关相关的结构区分开的方法。公共卫生相关性：拟议的研究项目将深入了解蛋白质结构和功能。因此，将增强我们对蛋白质功能障碍引起的疾病的理解。