Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
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.
Garbuzynskiy
Sergiy O
SO
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
Melnik
Bogdan S
BS
Lobanov
Michail Yu
MY
Finkelstein
Alexei V
AV
Galzitskaya
Oxana V
OV
D000818:Animals; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D006860:Hydrogen Bonding; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins