Determining the conformational stability of NMR ensemble structures

描述(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。这些固有的非结构蛋白(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，为了理解IUPS的功能，产生现实的结构集合是至关重要的。在IUPS中，这样的系综很难产生，因为实验预测了经历大规模构象波动的广泛、不同种类的结构系综。结构蛋白中实验限制的环区系综也很难可靠地与平衡系综相比较。我们感兴趣的是通过使用计算和实验相结合的方法来检验两个假设：(I)基于平均测量的IUPS实验数据可以用来产生有用的结构集合。(Ii)这些系综必须在平衡分布中适当加权，才能有助于理解蛋白质的功能。为了扩大我们对实验限制的非结构蛋白质系综如何很好地代表平衡系综的理解，粗粒化将被用来产生大的系综，这些系综通过来自核磁共振(核磁共振)谱实验的平均距离和二面角测量来抑制。这些结构多样化的组合将通过更彻底地采样构象空间来扩展这一领域的先前工作。然后将使用基于小角x射线散射和剩余偶极耦合的拟合数据的非严格方法对这些集合进行重新加权。我们还将把一种严格的重新加权方法扩展到结构蛋白质中的环。这些目标将通过以下具体目标实现：目标1：使用粗粒化为IUP生成大型核磁共振集成。目的2：使用非严格方法对核磁共振谱进行重新加权。目标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。这项拟议的研究将对蛋白质环和IdP的结构和功能提供有价值的见解。由此产生的软件将为我们提供一种手段，以区分生物上相关的结构和不相关的结构。 与公共健康相关：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.