Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics.
Model-free parameters obtained from nuclear magnetic resonance (NMR) relaxation experiments and molecular dynamics (MD) simulations commonly are used to describe the intramolecular dynamical properties of proteins. To assess the relative accuracy and precision of experimental and simulated model-free parameters, three independent data sets derived from backbone 15N NMR relaxation experiments and two independent data sets derived from MD simulations of Escherichia-coli ribonuclease HI are compared. The widths of the distributions of the differences between the order parameters for pairs of NMR data sets are congruent with the uncertainties derived from statistical analyses of individual data sets; thus, current protocols for analyzing NMR data encapsulate random uncertainties appropriately. Large differences in order parameters for certain residues are attributed to systematic differences between samples for intralaboratory comparisons and unknown, possibly magnetic field-dependent, experimental effects for interlaboratory comparisons. The widths of distributions of the differences between the order parameters for two NMR sets are similar to widths of distributions for an NMR and an MD set or for two MD sets. The linear correlations between the order parameters for an MD set and an NMR set are within the range of correlations observed between pairs of NMR sets. These comparisons suggest that the NMR and MD generalized order parameters for the backbone amide N-H bond vectors are of comparable accuracy for residues exhibiting motions on a fast time scale (< 100 ps). Large discrepancies between NMR and MD order parameters for certain residues are attributed to the occurrence of "rare" motional events over the simulation trajectories, the disruption of an element of secondary structure in one of the simulations, and lack of consensus among the experimental data sets. Consequently, (easily detectable) severe distortions of local protein structure and infrequent motional events in MD simulations appear to be the most serious artifacts affecting the accuracy and precision, respectively, of MD order parameters relative to NMR values. In addition, MD order parameters for motions on a fast (< 100 ps) timescale are more precisely determined than their NMR counterparts, thereby permitting more detailed dynamic characterization of biologically important residues by MD simulation than is sometimes possible by experimental methods. Proteins 28:481-493, 1997.
Philippopoulos
M
M
Department of Chemistry, University of Toronto, Ontario, Canada.
Mandel
A M
AM
Palmer
A G
AG
Lim
C
C
D003198:Computer Simulation; D004926:Escherichia coli / Q000201:enzymology; D009682:Magnetic Resonance Spectroscopy; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D016914:Ribonuclease H / Q000737:chemistry
D011506:Proteins; D016914:Ribonuclease H; C078856:ribonuclease HI