Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray and NMR-resolved protein structures?
Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray and NMR-resolved protein structures?
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DOI：
10.1002/prot.20491
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发表时间：
2005-07-01
影响因子：
2.9
通讯作者：
Galzitskaya, OV
中科院分区：
文献类型：
--
作者：
Garbuzynskiy, SO;Melnik, BS;Galzitskaya, OV
我们比较了78个蛋白质的结构，这两种方法确定的NMR和X射线。结果表明，同一蛋白质的X射线和核磁共振结构比不同的X射线结构有更多的差异，甚至比不同的核磁共振结构的蛋白质。这78种蛋白质中有18种的X射线和NMR结构具有明显的大尺度结构差异，似乎反映了晶体和溶液结构的差异。其他60对结构只有小规模的差异，与蛋白质的各种X射线或各种NMR结构之间的差异相当;我们更仔细地分析了这些结构。NMR的主要区别之一。而X射线结构则与每个残基的接触数有关：（1）PDB中的NMR结构在3.0埃以下和4.5- 6.5埃的距离处比X射线结构具有更多的接触，而在3.0-4.5埃和6.5-8.0埃的距离处接触较少;（2）内部残基的这种接触数量的差异大于外部残基，并且含β蛋白质的这种接触数量的差异大于全α蛋白质。另一个显著的区别是在X射线和NMR结构中鉴定的主链氢键通常不同。相关性只有69%。然而，类似的差异被发现为精制和再精制的NMR结构，使我们能够表明，观察到的差异在残基间接触的X射线和NMR结构的相同的蛋白质主要是由于在数学处理的实验结果的差异。(c)2005 Wiley-Liss，Inc.
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 angstrom and 4.5- 6.5 angstrom, and fewer contacts at distances of 3.0-4.5 angstrom and 6.5-8.0 angstrom; (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. (c) 2005 Wiley-Liss, Inc.