FAST INTERNAL MAIN-CHAIN DYNAMICS OF HUMAN UBIQUITIN

The fast internal dynamics of human ubiquitin have been studied by the analysis of N-15 relaxation of backbone amide nitrogens. The amide N-15 resonances have been assigned by use of heteronuclear multiple-quantum spectroscopy. Spin lattice relaxation times at 60.8 and 30.4 MHz and the steady-state nuclear Overhauser effect at 60.8 MHz have been determined for 67 amide N-15 sites in the protein using two-dimensional spectroscopy. These data have been analyzed in terms of the model free treatment of Lipari and Szabo [Lipari, G., & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559]. The global motion of the protein is shown to be isotropic and is characterized by a correlation time of 4.1 ns rad-1. The generalized order parameters (S2) of backbone amide N-H vectors in the globular region of the protein range from 0.5 to 0.95. No apparent correlation between secondary structure and generalized order parameters is observed. There is, however, a strong correlation between the magnitude of the generalized order parameters of a given N-H vector and the presence of hydrogen bonding of the amide hydrogen or its peptide bond associated carbonyl. Using a chemical shift tensor breadth of 160 ppm, the N-H vectors of peptide linkages participating in one or more hydrogen bonds to the main chain show an average generalized order parameter of 0.80 (SD 0.06), while those amide NH of peptide linkages free of hydrogen-bonding interactions with the main chain show an average order parameter of 0.69 (SD 0.06). The last four residues of the C-terminus display a pattern of S2 values ranging from 0.13 to 0.63 consistent with restricted diffusion about phi and psi-rotation axes which is abruptly terminated at residue 72. These data suggest that molecular packing interactions provide the dominant restriction to internal motion on the subnanosecond time scale and that hydrogen-bonding interactions provide a significant but more modest damping of main-chain high-frequency dynamics.