Jensen Pernille Rose, Axelsen Jacob Bock, Lerche Mathilde Hauge, Poulsen Flemming M
Institute of Molecular Biology, University of Copenhagen, Øster Farimagsgade 2A, DK-1353 Copenhagen K, Denmark.
J Biomol NMR. 2004 Jan;28(1):31-41. doi: 10.1023/B:JNMR.0000012865.35872.cc.
We have examined how the hydrogen bond geometry in three different proteins is affected when structural restraints based on measurements of residual dipolar couplings are included in the structure calculations. The study shows, that including restraints based solely on (1)H(N)-(15)N residual dipolar couplings has pronounced impact on the backbone rmsd and Ramachandran plot but does not improve the hydrogen bond geometry. In the case of chymotrypsin inhibitor 2 the addition of (13)CO-(13)C(alpha) and (15)N-(13)CO one bond dipolar couplings as restraints in the structure calculations improved the hydrogen bond geometry to a quality comparable to that obtained in the 1.8 A resolution X-ray structure of this protein. A systematic restraint study was performed, in which four types of restraints, residual dipolar couplings, hydrogen bonds, TALOS angles and NOEs, were allowed in two states. This study revealed the importance of using several types of residual dipolar couplings to get good hydrogen bond geometry. The study also showed that using a small set of NOEs derived only from the amide protons, together with a full set of residual dipolar couplings resulted in structures of very high quality. When reducing the NOE set, it is mainly the side-chain to side-chain NOEs that are removed. Despite of this the effect on the side-chain packing is very small when a reduced NOE set is used, which implies that the over all fold of a protein structure is mainly determined by correct folding of the backbone.
我们研究了在结构计算中纳入基于剩余偶极耦合测量的结构限制时，三种不同蛋白质中的氢键几何结构是如何受到影响的。研究表明，仅基于（1）H（N）-（15）N剩余偶极耦合纳入限制对主链均方根偏差和拉马钱德兰图有显著影响，但并未改善氢键几何结构。在胰凝乳蛋白酶抑制剂2的情况下，在结构计算中添加（13）CO-（13）C（α）和（15）N-（13）CO一键偶极耦合作为限制，可将氢键几何结构改善至与该蛋白质1.8埃分辨率X射线结构相当的质量。进行了一项系统的限制研究，其中四种类型的限制，即剩余偶极耦合、氢键、TALOS角和核Overhauser效应（NOE），在两种状态下被允许使用。这项研究揭示了使用多种类型的剩余偶极耦合以获得良好氢键几何结构的重要性。研究还表明，仅使用一小部分仅来自酰胺质子的NOE，再加上一整套剩余偶极耦合，可得到非常高质量的结构。当减少NOE集时，主要去除的是侧链到侧链的NOE。尽管如此，使用减少的NOE集时对侧链堆积的影响非常小，这意味着蛋白质结构的整体折叠主要由主链的正确折叠决定。
