The difference between protein structures obtained by x-ray analysis and nuclear magnetic resonance

Abstract

We have analyzed the pairs of protein structures obtained by X-ray diffraction analysis and nuclear magnetic resonance (X-ray and NMR structures) that display no major differences when superimposed on one another (61 pairs). Analyzing atom-to-atom contacts (contact distances 2–8 A), it has been found that the NMR structures (compared to the X-ray structures) have more contacts at distances below 3.5 A and above 5.5 A. In the case of residue-to-residue contacts, the NMR structures have more contacts at distances below 3 A and between 4.5 and 6.5 A. At other distances analyzed, the X-ray structures have more contacts. The difference in the numbers of atom-to-atom and residue-to-residue contacts is greater for buried residues inaccessible to water than for surface residues. Another important difference is related to the number of hydrogen bonds in the main chain: this number is greater in the X-ray structures. The coefficient of correlation between the numbers of hydrogen bonds identified in the structures obtained by both methods is only 32%. If a complete set of NMR models of protein structure is considered, the total number of hydrogen bonds proves to be 1.2 times greater than in the X-ray structures, whereas the correlation coefficient increases to only 65%. We have also demon-strated that α-helices in the NMR structures are more distorted (compared to the ideal α-helix) than those in the X-ray structures.