Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
Sci Rep. 2021 Mar 11;11(1):5756. doi: 10.1038/s41598-021-85003-0.
Obtaining (dynamic) structure related information on proteins is key for understanding their function. Methods as single-molecule Förster Resonance Energy Transfer (smFRET) and Electron Paramagnetic Resonance (EPR) that measure distances between labeled residues to obtain dynamic information rely on selection of suitable residue pairs for chemical modification. Selection of pairs of amino acids, that show sufficient distance changes upon activity of the protein, can be a tedious process. Here we present an in silico approach that makes use of two or more structures (or structure models) to filter suitable residue pairs for FRET or EPR from all possible pairs within the protein. We apply the method for the study of the conformational dynamics of the substrate-binding domain of the osmoregulatory ATP-Binding Cassette transporter OpuA. This method speeds up the process of designing mutants, and because of its systematic nature, the chances of missing promising candidates are reduced.
获得蛋白质的（动态）结构相关信息是理解其功能的关键。测量标记残基之间距离以获取动态信息的方法，如单分子Förster 共振能量转移（smFRET）和电子顺磁共振（EPR），依赖于对适合化学修饰的残基对的选择。选择在蛋白质活性下显示出足够距离变化的氨基酸对可能是一个繁琐的过程。在这里，我们提出了一种基于计算的方法，该方法利用两个或多个结构（或结构模型）从蛋白质中的所有可能对中筛选适用于 FRET 或 EPR 的残基对。我们将该方法应用于渗透压调节 ATP 结合盒转运蛋白 OpuA 的底物结合域的构象动力学研究。该方法加快了设计突变体的过程，并且由于其系统性，减少了错过有前途的候选者的机会。
