Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics

Abstract

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.

Protein conformational flexibility prediction using machine learning

“…Difficulties in controlling for differences in the models used to fit experimental data is a confounding factor in attempts to determine absolute accuracy of experimental values of S 2 [21]; consequently, whether further improvements in prediction accuracy are limited by the quality of the experimental S 2 data or merely by the size of the feature set that can be stably parameterized is unknown.…”

Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field

“…Ratios less than one for the AMBER99 simulations are consistent with a body of literature reporting that MD trajectories based on this and similar force fields often underestimate S 2 in loop regions. 1,10,[14][15][16]52 The trajectories using the two force fields exhibit differences in their internal motional correlation times, and therefore the total length of the trajectory, T MD , required to produce optimal agreement with experimental S 2 values is different for the two force fields. To demonstrate this effect, the order parameters were computed from the AMBER99 and AMBER99SB trajectories after 500 ps and 1, 5, 10, and 20 ns and compared against the experimental values ( Table 2).…”

“…Comparisons of MD simulations [6][7][8][9][10][11][12][13][14][15][16] with NMR relaxation data typically focus on the generalized N-H S 2 order parameter by Lipari and Szabo. 17,18 S 2 is a measure of the spatial restriction of the N-H vector in a molecule-fixed frame that takes values between 0 (large amounts of motion) and 1 (no motion) and which can be extracted from longitudinal T 1 , transverse T 2 , and heteronuclear Overhauser effect (NOE) data.…”

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

“…The comparison of three experimental sets of 15 N relaxation parameters along with two theoretical sets calculated from molecular dynamics simulations showed [301] that the NMR and MD generalized parameters are of comparable accuracy for residues exhibiting motions on a fast timescale. The comparison of the conformational entropy and the NMR order parameters on native and denatured staphylococcal nuclease [302] revealed that the general behavior of the experimental order parameters between native and unfolded states was reproduced by the simulations, but that the majority of theoretical order parameters disagree with the corresponding experimental ones.…”