COMPARISON OF MD SIMULATIONS AND NMR EXPERIMENTS FOR HEN LYSOZYME - ANALYSIS OF LOCAL FLUCTUATIONS, COOPERATIVE MOTIONS, AND GLOBAL CHANGES

Three 1000 ps molecular dynamics simulations of hen lysozyme have been compared with a range of experimental NMR parameters in order to gain insight into the dynamical properties of the protein and to assess th e significance of the motional events observed in the simulations. The simulations, one in vacuum and two in water, were used to estimate in terproton distances (for comparison with NOE data), (3)J(HN alpha) and (3)J(alpha beta) coupling constants and H-1-N-15 order parameters. Co mparison of these values with experimental data, particularly NOEs, en abled force field-induced changes to the structure during the simulati ons to be recognized. It has been shown, however, that these changes c an be largely eliminated by slight modifications to the force field. U sing a simulation performed in water with this modified force field, i t has been found that H-1-N-15 order parameters calculated for side ch ain groups in particular correlate well with experimental values and r eflect the substantial dependence of these motional properties on the environment, particularly surface exposure, in which the side chain is found. In this case, the simulation then provides models for the moti onal processes giving rise to the observed experimental data. The resu lts indicate that the order parameter values reflect primarily the num ber of torsion angles about which rotameric interchange occurs. In add ition to local motions, the two different domains of lysozyme have bee n found to behave differently in the simulations. Possible implication s of these differences for the interpretation of unfolding simulations and experimental observations of folding intermediates for lysozyme a re discussed.