Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.
Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.
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DOI：
10.1021/ja111318m
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发表时间：
2011-04-27
影响因子：
15
通讯作者：
Baker, David
中科院分区：
文献类型：
--
作者：
Sgourakis, Nikolaos G.;Lange, Oliver F.;DiMaio, Frank;Andre, Ingemar;Fitzkee, Nicholas C.;Rossi, Paolo;Montelione, Gaetano T.;Bax, Ad;Baker, David
对称蛋白质二聚体、三聚体和高阶环状寡聚体在许多生物过程中发挥着关键作用。然而，由于系统翻滚缓慢且难以识别跨蛋白质界面的 NOE 相互作用，因此通过溶液 NMR 对寡聚系统进行结构研究可能很困难。在这里，我们提出了一种自动化方法（RosettaOligomers），仅使用化学位移、稀疏 NOE 和残余偶极耦合（RDC）的域方向限制来确定寡聚系统的溶液结构，而不需要先前确定的单体亚基结构。该方法集成了先前开发的 Rosetta 协议，用于使用稀疏 NMR 数据求解单体蛋白质的结构，并预测非缠结和缠结对称寡聚物的结构。我们使用九个蛋白质二聚体、一个三聚体和一个四聚体的基准集以及可用的实验数据和各种界面拓扑来说明该方法的性能。发现最终的收敛结构与实验数据和之前发布的高分辨率结构非常一致。与传统的结构测定方案相比，新方法更容易适用于大型低聚物系统，传统的结构测定方案通常需要大量 NOE，并且随着通过 NMR 研究更多高分子量系统，该方法可能会变得越来越重要。
Symmetric protein dimers, trimers, and higher-order cyclic oligomers play key roles in many biological processes. However, structural studies of oligomeric systems by solution NMR can be difficult due to slow tumbling of the system and the difficulty in identifying NOE interactions across protein interfaces. Here, we present an automated method (RosettaOligomers) for determining the solution structures of oligomeric systems using only chemical shifts, sparse NOEs, and domain orientation restraints from residual dipolar couplings (RDCs) without a need for a previously determined structure of the monomeric subunit. The method integrates previously developed Rosetta protocols for solving the structures of monomeric proteins using sparse NMR data and for predicting the structures of both nonintertwined and intertwined symmetric oligomers. We illustrated the performance of the method using a benchmark set of nine protein dimers, one trimer, and one tetramer with available experimental data and various interface topologies. The final converged structures are found to be in good agreement with both experimental data and previously published high-resolution structures. The new approach is more readily applicable to large oligomeric systems than conventional structure-determination protocols, which often require a large number of NOEs, and will likely become increasingly relevant as more high-molecular weight systems are studied by NMR.
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DOI：
10.1107/s0907444998003254
发表时间：
1998-09-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Brunger, AT;Adams, PD;Warren, GL
通讯作者：
Warren, GL
影响因子：
5.6
作者：
Gray, JJ;Moughon, S;Baker, D
通讯作者：
Baker, D
影响因子：
5.6
作者：
Dam, Julie;Baber, James;Mariuzza, Roy A.
通讯作者：
Mariuzza, Roy A.
影响因子：
2.7
作者：
Cornilescu, G;Cornilescu, CC;Markley, JL
通讯作者：
Markley, JL
影响因子：
2.7
作者：
Fitzkee NC;Bax A
通讯作者：
Bax A