[The difference between protein structures that are obtained by X-ray analysis and magnetic resonance spectroscopy]

We have analyzed the proteins whose structures were determined both by X-ray analysis (X-ray) and nuclear magnetic resonance (NMR) on condition that these structures do not differ greatly when spatially superimposed on each other (61 pairs of protein structures). Atom-atomic contacts (contact distances varied from 2 to 8 A) have been analyzed and it has been found that NMR structures (in comparison with X-ray ones) have more contacts in the range below 3.5 A and above 5.5 A. In the case of residue-residue contacts NMR structures have more contacts below 3 A and between 4.5 and 6.5 A. At all the other contact distances analyzed the X-ray structures have more contacts. The difference in the number of atom-atomic and residue-residue contacts is greater for internal residues, that are concealed from water, as compared to the surface residues. The other, not less important difference deals with the number of hydrogen bonds in the main chain: it is larger for the X-ray structures. The correlation between the hydrogen bonds identified in the structures obtained by both methods is no more than 32%. The consideration of a complete set of protein structures obtained by NMR results in the fact that the number of hydrogen bonds grows 1.2 times as compared to those obtained with the X-ray analysis, whereas the correlation increases only by 65%. We have also demonstrated that alpha-helices in the NMR structures are more distorted in comparison with the ideal alpha-helix, than alpha-helices in the X-ray structures.