Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B.
Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B.
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DOI：
10.7554/elife.84632
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发表时间：
2023-03-07
期刊：
影响因子：
7.7
通讯作者：
Cui, Qiang
中科院分区：
文献类型：
--
作者：
Skaist Mehlman, Tamar;Biel, Justin T.;Azeem, Syeda Maryam;Nelson, Elliot R.;Hossain, Sakib;Dunnett, Louise;Paterson, Neil G.;Douangamath, Alice;Talon, Romain;Axford, Danny;Orins, Helen;von Delft, Frank;Keedy, Daniel A.;Cui, Qiang
我们目前对小分子配体如何与蛋白质相互作用的理解，大部分来自于在低温下确定的x射线晶体结构。对于单独的蛋白质，室温（RT）晶体学可以揭示以前隐藏的，生物相关的替代构象。然而，人们对RT晶体学如何影响蛋白质配体复合物的构象景观知之甚少。先前，我们使用治疗靶点PTP1B的低温晶体学筛选显示，小分子片段在假定的变抗位点聚集（Keedy等人，2018）。在这里，我们使用许多相同的片段对PTP1B进行了两次RT晶体学筛选，代表了迄今为止各种配体库的最大RT晶体学筛选，并能够直接询问数据收集温度对蛋白质-配体相互作用的影响。我们表明，在RT下，更少的配体结合，通常更弱-但具有各种温度依赖性差异，包括独特的结合姿势，溶剂化的变化，新的结合位点和不同的蛋白质变构构象反应。总的来说，这项工作表明，大量现有的低温蛋白质配体结构可能提供了一个不完整的图像，并强调了RT晶体学通过揭示蛋白质配体系统的不同构象模式来帮助完成这一图像的潜力。我们的结果可能会启发未来使用RT晶体学来询问蛋白质配体构象集成在生物功能中的作用。
Much of our current understanding of how small-molecule ligands interact with proteins stems from X-ray crystal structures determined at cryogenic (cryo) temperature. For proteins alone, room-temperature (RT) crystallography can reveal previously hidden, biologically relevant alternate conformations. However, less is understood about how RT crystallography may impact the conformational landscapes of protein-ligand complexes. Previously, we showed that small-molecule fragments cluster in putative allosteric sites using a cryo crystallographic screen of the therapeutic target PTP1B (Keedy et al., 2018). Here, we have performed two RT crystallographic screens of PTP1B using many of the same fragments, representing the largest RT crystallographic screens of a diverse library of ligands to date, and enabling a direct interrogation of the effect of data collection temperature on protein-ligand interactions. We show that at RT, fewer ligands bind, and often more weakly – but with a variety of temperature-dependent differences, including unique binding poses, changes in solvation, new binding sites, and distinct protein allosteric conformational responses. Overall, this work suggests that the vast body of existing cryo-temperature protein-ligand structures may provide an incomplete picture, and highlights the potential of RT crystallography to help complete this picture by revealing distinct conformational modes of protein-ligand systems. Our results may inspire future use of RT crystallography to interrogate the roles of protein-ligand conformational ensembles in biological function.
影响因子：
3.7
作者：
Cole K;Roessler CG;Mulé EA;Benson-Xu EJ;Mullen JD;Le BA;Tieman AM;Birone C;Brown M;Hernandez J;Neff S;Williams D;Allaire M;Orville AM;Sweet RM;Soares AS
通讯作者：
Soares AS