Vicinal coupling constants and protein dynamics.
The effects of motional averaging on the analysis of vicinal spin-spin coupling constants derived from proton NMR studies of proteins have been examined. Trajectories obtained from molecular dynamics simulations of bovine pancreatic trypsin inhibitor and of hen egg white lysozyme were used in conjunction with an expression for the dependence of the coupling constant on the intervening dihedral angle to calculate the time-dependent behavior of the coupling constants. Despite large fluctuations, the time-average values of the coupling constants are not far from those computed for the average structure in the cases where fluctuations occur about a single potential well. The calculated differences show a high correlation with the variation in the magnitude of the fluctuations of individual dihedral angles. For the cases where fluctuations involve multiple sites, large differences are found between the time-average values and the average structure values for the coupling constants. Comparison of the simulation results with the experimental trends suggests that side chains with more than one position are more common in proteins than is inferred from X-ray results. It is concluded that for the main chain, motional effects do not introduce significant errors where vicinal coupling constants are used in structure determinations; however, for side chains, the motional average can alter deductions about the structure. Accurately measured coupling constants are shown to provide information concerning the magnitude of dihedral angle fluctuations.
D000596:Amino Acids / Q000032:analysis; D000818:Animals; D002417:Cattle; D002645:Chickens; D004529:Egg White; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D009113:Muramidase; D010179:Pancreas; D011487:Protein Conformation; D014361:Trypsin Inhibitors; D014961:X-Ray Diffraction / Q000379:methods
D000596:Amino Acids; D014361:Trypsin Inhibitors; D009113:Muramidase