Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement.
Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement.
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基于知识与实验获得的 NMR 结构细化距离和角度约束。
DOI：
10.1142/s0219720008003448
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发表时间：
2008
影响因子：
1
通讯作者：
Wu,Zhijun
中科院分区：
文献类型：
--
作者：
Cui,Feng;Jernigan,Robert;Wu,Zhijun
核奥弗豪泽效应（NOE）距离约束和扭转角约束是核磁共振（NMR）结构精化的主要构象约束。特别是，NOE约束的数量被认为是NMR结构质量的重要决定因素。当然，扭转角约束的可用性对于正确的局部构象的形成也是至关重要的。在我们最近的工作中，我们已经展示了一组基于知识的短程距离约束也可以用于NMR结构细化，作为NOE和扭转角约束的构象约束的互补集合。在本文中，我们展示了一系列的结构细化实验的结果，通过使用不同类型的构象约束- NOE，扭转角，或基于知识的约束-或它们的组合，并作出定量评估如何实验获得的约束有助于结构模型的质量，以及它们是否可以结合或取代基于知识的约束。我们已经进行了实验上的一个小的NMR结构。我们的初步计算表明，扭转角约束的结构质量有很大的贡献，但需要结合NOE约束是完全有效的。基于知识的约束在功能上可以与扭转角约束一样重要，尽管它们毕竟是统计约束，并且不意味着能够取代后者。
Nuclear Overhauser effects (NOE) distance constraints and torsion angle constraints are major conformational constraints for nuclear magnetic resonance (NMR) structure refinement. In particular, the number of NOE constraints has been considered as an important determinant for the quality of NMR structures. Of course, the availability of torsion angle constraints is also critical for the formation of correct local conformations. In our recent work, we have shown how a set of knowledge-based short-range distance constraints can also be utilized for NMR structure refinement, as a complementary set of conformational constraints to the NOE and torsion angle constraints. In this paper, we show the results from a series of structure refinement experiments by using different types of conformational constraints — NOE, torsion angle, or knowledge-based constraints — or their combinations, and make a quantitative assessment on how the experimentally acquired constraints contribute to the quality of structural models and whether or not they can be combined with or substituted by the knowledge-based constraints. We have carried out the experiments on a small set of NMR structures. Our preliminary calculations have revealed that the torsion angle constraints contribute substantially to the quality of the structures, but require to be combined with the NOE constraints to be fully effective. The knowledge-based constraints can be functionally as crucial as the torsion angle constraints, although they are statistical constraints after all and are not meant to be able to replace the latter.