Many proteins can adopt multiple conformations which are important for their function. This is also true for proteins and domains that are covalently linked to each other. One important example is ubiquitin, which can form chains of different conformations depending on which of its lysine side chains is used to form an isopeptide bond with the C-terminus of another ubiquitin molecule. Similarly, ubiquitin gets covalently attached to active-site residues of E2 ubiquitin-conjugating enzymes. Due to weak interactions between ubiquitin and its interaction partners, these covalent complexes adopt multiple conformations. Understanding the function of these complexes requires the characterization of the entire accessible conformation space and its modulation by interaction partners. Long-range (1.8–10 nm) distance restraints obtained by EPR spectroscopy in the form of probability distributions are ideally suited for this task as not only the mean distance but also information about the conformation dynamics is encoded in the experimental data. Here we describe a computational method that we have developed based on well-established structure determination software using NMR restraints to calculate the accessible conformation space using PELDOR/DEER data.

许多蛋白质可以采用对其功能很重要的多种构象。对于彼此共价连接的蛋白质和结构域来说也是如此。一个重要的例子是泛素，它可以形成不同构象的链，具体取决于其赖氨酸侧链用于与另一个泛素分子的 C 末端形成异肽键。同样，泛素共价连接到 E2 泛素结合酶的活性位点残基上。由于泛素与其相互作用伙伴之间的相互作用较弱，这些共价复合物采用多种构象。了解这些复合物的功能需要对整个可及构象空间及其相互作用伙伴的调节进行表征。 EPR 光谱以概率分布的形式获得的长程（1.8-10 nm）距离限制非常适合这项任务，因为实验数据中不仅编码了平均距离，而且还编码了有关构象动力学的信息。在这里，我们描述了一种基于完善的结构测定软件开发的计算方法，该软件使用 NMR 约束来使用 PELDOR/DEER 数据计算可访问的构象空间。