Multiscale simulations and NMR spectroscopy of ubiquitin chains: linkage chemistry and chain behavior (B09*)

我们的目标是揭开不同连接的泛素链的内在属性，它们决定了泛素化蛋白质的命运。高分辨率核磁共振波谱和多尺度分子动力学模拟的协同应用将获得原子水平上的结构和动态信息。这项拟议工作的一个优势在于，泛素三聚体和四聚体的实验可及性，以及链中单个泛素部分的高度特异的同位素标记。因此，我们将能够研究每个泛素单元的结构和动态性质、溶剂可及性、配体结合和结合亲和力。核磁共振数据的分子解释以及对构象行为和与结合伙伴的相互作用的耦合的机理洞察将通过附带的多尺度模拟提供。我们的组合核磁共振波谱/多尺度模拟方法为我们提供了一个强大的新工具来研究现有的各种泛素化，并更好地理解泛素化作为一个基本的蛋白质恒定过程。

We aim at unravelling the intrinsic properties of differently linked ubiquitin chains which dictate the fate of ubiquitylated proteins. Structural and dynamic information on an atomistic level will be obtained by the synergistic application of high-resolution NMR spectroscopy and multiscale molecular dynamics simulation. One strength of the proposed work lies in the experimental accessibility of ubiquitin tri- and tetramers with highly specific isotopic labeling of individual ubiquitin moieties in the chain. Thus we will be able to investigate structural and dynamic properties, solvent accessibility, ligand binding and binding affinities specifically for each ubiquitin unit. Molecular interpretation of the NMR data and mechanistic insight into coupling of conformational behavior and interactions with binding partners will be provided by accompanying multiscale simulations. Our combined NMR spectroscopic / multiscale-simulation approach gives us a powerful new tool to investigate the existing variety of ubiquitylation and to obtain a better understanding of ubiquitylation as one fundamental proteostatic process.