DETERMINATION OF THE STRUCTURES OF SYMMETRIC PROTEIN OLIGOMERS FROM NMR CHEMICAL

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 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起着关键作用。然而，通过溶液NMR对低聚物系统进行结构研究可能是困难的，这是由于系统的缓慢翻滚以及难以识别跨蛋白质界面的NOE相互作用。在这里，我们提出了一个自动化的方法（RosettaOligomers），用于确定的解决方案的低聚物系统的结构，只使用化学位移，稀疏NOE，和域取向的限制，从残留偶极耦合（RDC），而不需要先前确定的单体亚基的结构。该方法集成了以前开发的Rosetta协议，用于解决单体蛋白质的结构，使用稀疏的NMR数据和预测两个非交织和交织的对称低聚物的结构。我们说明了该方法的性能，使用一个基准集的九个蛋白质二聚体，一个三聚体，和一个四聚体可用的实验数据和各种接口拓扑结构。最后收敛的结构被发现是在良好的协议与实验数据和以前发表的高分辨率结构。新的方法是更容易适用于大的低聚物系统比传统的结构测定方案，这往往需要大量的NOE，并可能会变得越来越相关，因为更多的高分子量系统的NMR研究。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. 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.