Interpretation of NMR data on proteins by molecular dynamics simulations

The stability and the internal mobility of the recently determined solution structure of the activation domain of porcine procarboxypeptidase B (ADB; Vendrell J., Billeter M., Wider G., Avilés F.X., Wüthrich K.: EMBO J.10, 11–15 (1991)) was studied by unrestrained molecular dynamics. A 66 residue long polypeptide corresponding to the structurally well-defined fragment of ADB was immersed in a water bath and carefully equilibrated. A trajectory of 90 ps was then recorded at room temperature, using no constraints deduced from NMR distance measurements. The averages of the inverse third power of the proton-proton distances, for which NMR distance measurements are available, were calculated and converted to time averages of the distances. Comparison of these time averaged distances with the corresponding distance constraints used in the determination of the solution structure show that the dynamic structure described by the molecular dynamics trajectory is consistent with the NMR data for the polypeptide backbone and for most side chains. In the course of the 90 ps trajectory, the ß-sheet of ADB remains intact and well-defined. The last helix of the protein domain is also stable, but moves with respect to the rest of the protein, while the first helix shows increased instability. The structural fluctuations of the side chain do in general not exceed those observed among the 20 conformers describing the solution structure.