NMR relaxation and protein mobility

Abstract The increased availability of isotope-enriched proteins and the high sensitivity of proton-detected heteronuclear experiments have stimulated studies of protein mobility via 15N and 13C relaxation. Developments during the past few years include new pulse sequences that yield more reliable values for relaxation rates, and pulse sequences that enable the measurement of new types of relaxation parameters. Methods with which to map distribution functions of motional frequencies (spectral density functions) from combinations of relaxation parameters have been suggested. Extensive measurements of 15N and 13C relaxation parameters have been made for a number of proteins and interpreted on the basis of the so-called ‘model-free’ approach; often, active sites of proteins are found to be mobile. In a few cases, molecular dynamics simulations have been carried out to simulate relaxation parameters.

[1]  Jeffrey W. Peng,et al.  Protein Mobility from Multiple 15N Relaxation Parameters , 1994 .

[2]  Yu-Sen Wang,et al.  NMR rotating‐frame relaxation measurements of conformational exchanges on the microsecond time scale. Part I: Theory , 1992 .

[3]  L. Kay,et al.  Pulse sequences for removal of the effects of cross correlation between dipolar and chemical-shift anisotropy relaxation mechanisms on the measurement of heteronuclear T1 and T2 values in proteins , 1992 .

[4]  A. Gronenborn,et al.  Analysis of the backbone dynamics of interleukin-1.beta. using two-dimensional inverse detected heteronuclear nitrogen-15-proton NMR spectroscopy , 1990 .

[5]  Jeffrey W. Peng,et al.  2D heteronuclear NMR measurements of spin-lattice relaxation times in the rotating frame of X nuclei in heteronuclear HX spin systems , 1991 .

[6]  R. Powers,et al.  Analysis of the backbone dynamics of the ribonuclease H domain of the human immunodeficiency virus reverse transcriptase using 15N relaxation measurements. , 1992, Biochemistry.

[7]  L. Kay,et al.  The effects of dipolar cross correlation on 13C methyl-carbon T1, T2, and NOE measurements in macromolecules , 1991 .

[8]  K. Dahlman-Wright,et al.  Backbone dynamics of the glucocorticoid receptor DNA-binding domain. , 1992, Biochemistry.

[9]  A. Palmer,et al.  Backbone dynamics of calcium-loaded calbindin D9k studied by two-dimensional proton-detected 15N NMR spectroscopy. , 1992, Biochemistry.

[10]  H. Dyson,et al.  Comparison of backbone and tryptophan side-chain dynamics of reduced and oxidized Escherichia coli thioredoxin using 15N NMR relaxation measurements. , 1993, Biochemistry.

[11]  M. Goldman,et al.  Interference effects in the relaxation of a pair of unlike spin-1/2 nuclei , 1984 .

[12]  M Ikura,et al.  Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible. , 1992, Biochemistry.

[13]  A. Wand,et al.  Model-independent and model-dependent analysis of the global and internal dynamics of cyclosporin A , 1989 .

[14]  L. Kay,et al.  The measurement of heteronuclear transverse relaxation times in ax3 spin systems via polarization-transfer techniques , 1992 .

[15]  R. Brüschweiler,et al.  Molecular dynamics monitored by cross‐correlated cross relaxation of spins quantized along orthogonal axes , 1992 .

[16]  P. Wright,et al.  Measurement of relaxation time constants for methyl groups by proton-detected heteronuclear NMR spectroscopy , 1991 .

[17]  Jyawei Cheng,et al.  Dynamics of a receptor-bound ligand by heteronuclear NMR: FK506 bound to FKBP-12 , 1993 .

[18]  T Szyperski,et al.  Protein dynamics studied by rotating frame 15N spin relaxation times , 1993, Journal of biomolecular NMR.

[19]  P. Wright,et al.  Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance carbon-13 heteronuclear NMR spectroscopy , 1991 .

[20]  D. Case,et al.  Molecular Dynamics Analysis of NMR Relaxation in a Zinc-Finger Peptide , 1992 .

[21]  O. Teleman,et al.  Backbone dynamics of calbindin D9k: comparison of molecular dynamics simulations and nitrogen-15 NMR relaxation measurements , 1992 .

[22]  G. Lipari.  Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules , 1982 .

[23]  A. Szabó,et al.  Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity , 1982 .

[24]  J. H. Strange,et al.  Studies of chemical exchange by nuclear magnetic relaxation in the rotating frame , 1970 .

[25]  A. Szabó,et al.  Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results , 1982 .

[26]  D. M. Schneider,et al.  Fast internal main-chain dynamics of human ubiquitin. , 1992, Biochemistry.

[27]  Paul C. Driscoll,et al.  Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins , 1990 .

[28]  Jeffrey W. Peng,et al.  Mapping of Spectral Density Functions Using Heteronuclear NMR Relaxation Measurements , 1992 .

[29]  H. Carr,et al.  The Principles of Nuclear Magnetism , 1961 .

[30]  G. Bodenhausen,et al.  Principles of nuclear magnetic resonance in one and two dimensions , 1987 .

[31]  M H Saier,et al.  Backbone dynamics of the Bacillus subtilis glucose permease IIA domain determined from 15N NMR relaxation measurements. , 1992, Biochemistry.

[32]  G. Wagner,et al.  Mapping of the spectral densities of N-H bond motions in eglin c using heteronuclear relaxation experiments. , 1992, Biochemistry.

[33]  L. Kay,et al.  Dynamics of methyl groups in proteins as studied by proton-detected 13C NMR spectroscopy. Application to the leucine residues of staphylococcal nuclease. , 1992, Biochemistry.

[34]  I. Campbell,et al.  Influence of cross-correlation between dipolar and anisotropic chemical shift relaxation mechanisms upon longitudinal relaxation rates of 15N in macromolecules , 1990 .

[35]  M. Karplus,et al.  Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution , 1992 .

[36]  L. Kay,et al.  Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. , 1989, Biochemistry.

[37]  Jeffrey W. Peng,et al.  Improved accuracy of heteronuclear transverse relaxation time measurements in macromolecules. elimination of antiphase contributions , 1991 .

[38]  Yu-Sen Wang.  NMR rotating-frame relaxation measurements of conformational exchanges on the microsecond time scale. Part II: Verification of the T1p method and analysis of experimental results , 1993 .

[39]  B. Brooks,et al.  A 500 ps molecular dynamics simulation study of interleukin-1 beta in water. Correlation with nuclear magnetic resonance spectroscopy and crystallography. , 1992, Journal of molecular biology.

[40]  P. Wright,et al.  Suppression of the effects of cross-correlation between dipolar and anisotropic chemical shift relaxation mechanisms in the measurement of spin-spin relaxation rates , 1992 .

[41]  R A Smith,et al.  Loop mobility in a four-helix-bundle protein: 15N NMR relaxation measurements on human interleukin-4. , 1992, Biochemistry.

[42]  G. Wagner,et al.  Measurement of 13C relaxation times in proteins by two-dimensional heteronuclear 1H-13C correlation spectroscopy , 1988 .