Anisotropic intramolecular backbone dynamics of ubiquitin characterized by NMR relaxation and MD computer simulation

The anisotropy of rapid fluctuations of the peptide planes in ubiquitin is explored by combined N-15 and C-13' nuclear spin relaxation measurements and molecular dynamics (MD) computer simulation. T-1, T-2, and NOE data were collected at B-0-field strenghts corresponding to 400 and 600 MHz proton resonance. A 1.5-ns simulation of ubiquitin in an explicit water environment was performed using CHARMM 24,. The simulation suggests that, for 76% of the peptide planes, the relaxation-active motion of the backbone N-15 and C-13' spins is dominated by anisotropic Gaussian axial fluctuations of the peptide planes about three orthogonal axes. The dominant fluctuation axes are nearly parallel to the w(i-l)(alpha)-C-i(alpha) axes. The remaining peptide planes belong to more flexible regions of the backbone and cannot be described by this type of motion alone. Based on the results of the computer simulation, an analytical 3D GAF motional model (Bremi, T.; Bruschweiler, R. J. Am. Chem. Sec. 1997, 119, 6672-6673) was applied to the experimental relaxation data. The fluctuation amplitudes of the peptide planes show a significant anisotropy of the internal motion. This analysis demonstrates that a combined interpretation of N-15 and C-13' relaxation data by a model derived from a computer simulation may provide detailed insight into the fast time-scale backbone dynamics that goes beyond the results of a standard model-free analysis.