Determining the conformational stability of NMR ensemble structures

描述（由申请人提供）：最近蛋白质结构倡议的一个重要成果是发现了许多不形成紧凑刚性结构的蛋白质家族。这些本质上非结构化的蛋白质（IUP）在自然界中很常见，破坏它们的功能也会导致某些疾病的发生。我们认为，要了解IUPs的功能，关键是要产生现实的结构合奏。这样的合奏是很难产生的IUP实验预测广泛的，异构合奏的结构，经历大规模的构象波动。实验上限制的环区结构蛋白质的系综也难以可靠地比较平衡系综。我们有兴趣通过使用计算和实验相结合的方法来测试两个假设：（i）基于平均测量的IUP的实验数据可以用来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，以有助于理解蛋白质功能。为了扩大我们对非结构化蛋白质的实验约束系综如何代表平衡系综的理解，粗粒化将用于生成使用来自核磁共振（NMR）光谱实验的平均距离和二面角测量来约束的大系综。这些结构多样的合奏将扩展以前的工作在这一领域更彻底的采样构象空间。然后，这些集合将使用基于来自小角度X射线散射和残余偶极耦合的拟合数据的非严格方法重新加权。我们还将扩展一个严格的重新加权的方法，在结构化蛋白质的循环。这些目标将通过以下具体目标来实现：目标1：使用粗粒化为IUP生成大型NMR合奏。目标2：使用非严格方法重新加权NMR系综。目的3：将严格的重加权方法扩展到蛋白质环。目标4：创建和维护网站。拟议的研究将提供有价值的深入了解蛋白质环和IDP的结构和功能。由此产生的软件将为我们提供一种区分生物相关结构和不相关结构的方法。 公共卫生相关性：拟议的研究项目将深入了解蛋白质的结构和功能。因此，我们对蛋白质功能障碍引起的疾病的理解将得到加强。

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.