ANISOTROPIC INTRAMOLECULAR BACKBONE DYNAMICS OF UBIQUITIN CHARACTERIZED BY NMR RELAXATION AND MD COMPUTER-SIMULATION

The anisotropy of rapid fluctuations of the peptide planes in ubiquiti n is explored by combined N-15 and C-13' nuclear spin relaxation measu rements and molecular dynamics (MD) computer simulation. T-1, T-2, and NOE data were collected at B-0-field strenghts corresponding to 400 a nd 600 MHz proton resonance. A 1.5-ns simulation of ubiquitin in an ex plicit water environment was performed using CHARMM 24,. The simulatio n suggests that, for 76% of the peptide planes, the relaxation-active motion of the backbone N-15 and C-13' spins is dominated by anisotropi c Gaussian axial fluctuations of the peptide planes about three orthog onal axes. The dominant fluctuation axes are nearly parallel to the w( i-l)(alpha)-C-i(alpha) axes. The remaining peptide planes belong to mo re flexible regions of the backbone and cannot be described by this ty pe of motion alone. Based on the results of the computer simulation, a n analytical 3D GAF motional model (Bremi, T.; Bruschweiler, R. J. Am. Chem. Sec. 1997, 119, 6672-6673) was applied to the experimental rela xation data. The fluctuation amplitudes of the peptide planes show a s ignificant anisotropy of the internal motion. This analysis demonstrat es that a combined interpretation of N-15 and C-13' relaxation data by a model derived from a computer simulation may provide detailed insig ht into the fast time-scale backbone dynamics that goes beyond the res ults of a standard model-free analysis.