Garbuzynskiy Sergiy O, Melnik Bogdan S, Lobanov Michail Yu, Finkelstein Alexei V, Galzitskaya Oxana V
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
Proteins. 2005 Jul 1;60(1):139-47. doi: 10.1002/prot.20491.
We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures of the same protein have more differences than various X-ray structures obtained for the protein, and even more than various NMR structures of the protein. X-ray and NMR structures of 18 of these 78 proteins have obvious large-scale structural differences that seem to reflect a difference of crystal and solution structures. The other 60 pairs of structures have only small-scale differences comparable with differences between various X-ray or various NMR structures of a protein; we have analyzed these structures more attentively. One of the main differences between NMR and X-ray structures concerns the number of contacts per residue: (1) NMR structures presented in PDB have more contacts than X-ray structures at distances below 3.0 A and 4.5-6.5 A, and fewer contacts at distances of 3.0-4.5 A and 6.5-8.0 A; (2) this difference in the number of contacts is greater for internal residues than for external ones, and it is larger for beta-containing proteins than for all-alpha proteins. Another significant difference is that the main-chain hydrogen bonds identified in X-ray and NMR structures often differ. Their correlation is 69% only. However, analogous difference is found for refined and rerefined NMR structures, allowing us to suggest that the observed difference in interresidue contacts of X-ray and NMR structures of the same proteins is due mainly to a difference in mathematical treatment of experimental results.
我们比较了通过核磁共振（NMR）和X射线方法测定的78种蛋白质的结构。结果表明，同一蛋白质的X射线结构和NMR结构之间的差异，比该蛋白质的各种X射线结构之间的差异更大，甚至比该蛋白质的各种NMR结构之间的差异还要大。这78种蛋白质中的18种，其X射线结构和NMR结构存在明显的大规模结构差异，这似乎反映了晶体结构和溶液结构的差异。另外60对结构只有小规模差异，与蛋白质的各种X射线结构或各种NMR结构之间的差异相当；我们对这些结构进行了更细致的分析。NMR结构和X射线结构之间的一个主要差异涉及每个残基的接触数：（1）蛋白质数据库（PDB）中呈现的NMR结构在距离低于3.0埃和4.5 - 6.5埃时比X射线结构有更多接触，而在3.0 - 4.5埃和6.5 - 8.0埃距离时接触较少；（2）内部残基的接触数差异比外部残基更大，含β折叠的蛋白质比全α螺旋蛋白质的差异更大。另一个显著差异是，在X射线结构和NMR结构中确定的主链氢键往往不同。它们的相关性仅为69%。然而，在精细和重新精细的NMR结构中也发现了类似差异，这使我们认为，同一蛋白质的X射线结构和NMR结构在残基间接触上观察到的差异，主要是由于实验结果数学处理方式的不同。
