A novel approach to modeling side chain ensembles of the bifunctional spin label RX.
A novel approach to modeling side chain ensembles of the bifunctional spin label RX.
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一种对双功能自旋标签 RX 侧链整体进行建模的新颖方法。
DOI：
10.1101/2023.05.24.542139
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Stoll,Stefan
中科院分区：
文献类型：
--
作者：
Tessmer,MaxxH;Stoll,Stefan
我们介绍了一种新的方法来建模双功能自旋标签的侧链集成。该方法利用旋转体库生成侧链构象集成。由于双功能标签受到两个附着位点的约束，因此将标签分成两个单功能转子，分别附着在各自的位点上，然后在二面体空间中通过局部优化重新连接。我们使用双功能自旋标签RX对一组先前发表的实验数据验证了该方法。该方法相对快速，可以很容易地用于实验分析和蛋白质建模，与用分子动力学模拟建模双功能标签相比具有显着优势。使用双功能标签进行位点定向自旋标记（SDSL）电子顺磁共振（EPR）光谱分析可显著降低标签迁移率，从而显著提高蛋白质主链结构和动力学微小变化的分辨率。将双功能标签与侧链建模方法相结合，可以改进实验SDSL EPR数据在蛋白质建模中的定量应用。
We introduce a novel approach to modeling side chain ensembles of bifunctional spin labels. This approach utilizes rotamer libraries to generate side chain conformational ensembles. Because the bifunctional label is constrained by two attachment sites, the label is split into two monofunctional rotamers which are first attached to their respective sites, then rejoined by a local optimization in dihedral space. We validate this method against a set of previously published experimental data using the bifunctional spin label, RX. This method is relatively fast and can readily be used for both experimental analysis and protein modeling, providing significant advantages over modeling bifunctional labels with molecular dynamics simulations. Use of bifunctional labels for site directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy dramatically reduces label mobility, which can significantly improve resolution of small changes in protein backbone structure and dynamics. Coupling the use of bifunctional labels with side chain modeling methods allows for improved quantitative application of experimental SDSL EPR data to protein modeling.