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Recent Developments in 15N NMR Relaxation Studies that Probe Protein Backbone Dynamics

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NMR of Proteins and Small Biomolecules

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 326))

Abstract

Abstract

Nuclear Magnetic Resonance (NMR) relaxation is a powerful technique that provides information about internal dynamics associated with configurational energetics in proteins, as well as site-specific information involved in conformational equilibria. In particular, 15N relaxation is a useful probe to characterize overall and internal backbone dynamics of proteins because the relaxation mainly reflects reorientational motion of the N–H bond vector. Over the past 20 years, experiments and protocols for analysis of 15N R 1, R 2, and the heteronuclear 15N–{1H} NOE data have been well established. The development of these methods has kept pace with the increase in the available static–magnetic field strength, providing dynamic parameters optimized from data fitting at multiple field strengths. Using these methodological advances, correlation times for global tumbling and order parameters and correlation times for internal motions of many proteins have been determined. More recently, transverse relaxation dispersion experiments have extended the range of NMR relaxation studies to the milli- to microsecond time scale, and have provided quantitative information about functional conformational exchange in proteins. Here, we present an overview of recent advances in 15N relaxation experiments to characterize protein backbone dynamics.

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References

  1. Lipari G, Szabo A (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104:4546–4559

    Article  CAS  Google Scholar 

  2. Lipari G, Szabo A (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J Am Chem Soc 104:4559–4570

    Article  CAS  Google Scholar 

  3. Peng JW, Wagner G (1995) Frequency spectrum of NH bonds in eglin c from spectral density mapping at multiple fields. Biochemistry 34:16733–16752

    Article  CAS  Google Scholar 

  4. Farrow NA, Zhang O, Forman-Kay JD, Kay LE (1995) Comparison of the backbone dynamics of a folded and an unfolded SH3 domain existing in equilibrium in aqueous buffer. Biochemistry 34:868–878

    Article  CAS  Google Scholar 

  5. Ishima R, Nagayama K (1995) Protein backbone dynamics revealed by quasi spectral density function analysis of amide N-15 nuclei. Biochemistry 34:3162–3171

    Article  CAS  Google Scholar 

  6. Kay LE, Torchia DA, Bax A (1989) Backbone dynamics of proteins as studied by nitrogen-15 inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry 28:8972–8979

    Article  CAS  Google Scholar 

  7. Clore GM, Driscoll PC, Wingfield PT, Gronenborn AM (1990) Analysis of the backbone dynamics of interleukin-1 beta using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy. Biochemistry 29:7387–7401

    Article  CAS  Google Scholar 

  8. Palmer AG, Rance M, Wright PE (1991) Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance 13 C heteronuclear NMR spectroscopy. J Am Chem Soc 113:4371–4380

    Article  CAS  Google Scholar 

  9. Schneider DM, Dellwo MJ, Wand AJ (1992) Fast internal main-chain dynamics of human ubiquitin. Biochemistry 31:3645–3652

    Article  CAS  Google Scholar 

  10. Mandel AM, Akke M, Palmer AG (1995) Backbone dynamics of Escherichia-coli ribonuclease Hi – correlations with structure and function in an active enzyme. J Mol Biol 246:144–163

    Article  CAS  Google Scholar 

  11. Tjandra N, Kuboniwa H, Ren H, Bax A (1995) Rotational dynamics of calcium-free calmodulin studied by 15N-NMR relaxation measurements. Eur J Biochem 230:1014–1024

    Article  CAS  Google Scholar 

  12. Dayie KT, Wagner G, Lefevre JF (1996) Theory and practice of nuclear spin relaxation in proteins. Annu Rev Phys Chem 47:243–282

    Article  CAS  Google Scholar 

  13. Lee LK, Rance M, Chazin WJ, Palmer AGr (1997) Rotational diffusion anisotropy of proteins from simultaneous analysis of 15N and 13C alpha nuclear spin relaxation. J Biomol NMR 9:287–298

    Google Scholar 

  14. Kroenke CD, Loria JP, Lee LK, Rance M, Palmer AG (1998) Longitudinal and transverse H-1-N-15 dipolar N-15 chemical shift anisotropy relaxation interference: unambiguous determination of rotational diffusion tensors and chemical exchange effects in biological macromolecules. J Am Chem Soc 120:7905–7915

    Article  CAS  Google Scholar 

  15. Fushman D, Tjandra N, Cowburn D (1999) An approach to direct determination of protein dynamics from N-15 NMR relaxation at multiple fields, independent of variable N-15 chemical shift anisotropy and chemical exchange contributions. J Am Chem Soc 121:8577–8582

    Article  CAS  Google Scholar 

  16. Andrec M, Montelione GT, Levy RM (1999) Estimation of dynamic parameters from NMR relaxation data using the Lipari-Szabo model-free approach and Bayesian statistical methods. J Magn Reson 139:408–421

    Article  CAS  Google Scholar 

  17. Lee AL, Wand AJ (1999) Assessing potential bias in the determination of rotational correlations times of proteins by NMR. J Biomol NMR 13:101–112

    Article  CAS  Google Scholar 

  18. Campbell AP, Spyracopoulos L, Irvin RT, Sykes BD (2000) Backbone dynamics of a bacterially expressed peptide from the receptor binding domain of Pseudomonas aeruginosa pilin strain PAK from heteronuclear 1H-15N NMR spectroscopy. J Biomol NMR 17:239–255

    Article  CAS  Google Scholar 

  19. Ishima R, Torchia DA (2000) Protein dynamics from NMR. Nat Struct Biol 7:740–743

    Article  CAS  Google Scholar 

  20. Fushman D, Cowburn D (2001) Nuclear magnetic resonance relaxation in determination of residue-specific N-15 chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Methods Enzymol Nucl Magn Reson Biol Macromol Pt B 339:109–126

    Google Scholar 

  21. Palmer AG 3rd (2001) NMR probes of molecular dynamics: overview and comparison with other. Annu Rev Biophys Biomol Struct 30:129–155

    Article  CAS  Google Scholar 

  22. Bruschweiler R (2003) New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins. Curr Opin Struct Biol 13:175–183

    Article  CAS  Google Scholar 

  23. d’Auvergne EJ, Gooley PR (2003) The use of model selection in the model-free analysis of protein dynamics. J Biomol NMR 25:25–39

    Google Scholar 

  24. Pelupessy P, Ravindranathan S, Bodenhausen G (2003) Correlated motions of successive amide N-H bonds in proteins. J Biomol NMR 25:265–280

    Article  CAS  Google Scholar 

  25. Idiyatullin D, Daragan VA, Mayo KH (2003) (NH)-N-15 backbone dynamics of protein GB1: comparison of order parameters and correlation times derived using various “model-free” approaches. J Phys Chem B 107:2602–2609

    Article  CAS  Google Scholar 

  26. Redfield C (2004) Using nuclear magnetic resonance spectroscopy to study molten globule states of proteins. Methods Mol Biol 34:121–132

    CAS  Google Scholar 

  27. Chen J, Brooks CLI, Wright PE (2004) Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. J Biomol NMR 29:243–257

    Article  CAS  Google Scholar 

  28. Korchuganov DS, Gagnidze IE, Tkach EN, Schulga AA, Kirpichnikov MP, Arseniev AS (2004) Determination of protein rotational correlation time from NMR relaxation data at various solvent viscosities. J Biomol NMR 30:431–442

    Article  CAS  Google Scholar 

  29. Kay LE (2005) NMR studies of protein structure and dynamics. J Magn Reson 173:193–207

    Article  CAS  Google Scholar 

  30. Jarymowycz VA, Stone MJ (2006) Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem Rev 106:1624–1671

    Article  CAS  Google Scholar 

  31. Igumenova TI, Frederick KK, Wand AJ (2006) Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem Rev 106:1672–1699

    Article  CAS  Google Scholar 

  32. Spyracopoulos L (2006) A suite of Mathematica notebooks for the analysis of protein main chain (15)N NMR relaxation data. J Biomol NMR 36:215–224

    Article  CAS  Google Scholar 

  33. Frederick KK, Sharp KA, Warischalk N, Wand AJ (2008) Re-evaluation of the model-free analysis of fast internal motion in proteins using NMR relaxation. J Phys Chem B 112:12095–12103

    Article  CAS  Google Scholar 

  34. Reddy T, Rainey JK (2010) Interpretation of biomolecular NMR spin relaxation parameters. Biochem Cell Biol 88:131–142

    Article  CAS  Google Scholar 

  35. Peng JW, Thanabal V, Wagner G (1991) Improved accuracy of heteronuclear transverse relaxation time measurements in macromolecules. elimination of antiphase contributions. J Magn Reson 95:421–427

    CAS  Google Scholar 

  36. Palmer AG, Skelton NJ, Chazin WJ, Wright PE, Rance M (1992) Suppression of the effects of cross-correlation between dipolar and anisotropic chemical-shift relaxation mechanisms in the measurement of spin relaxation rates. Mol Phys 75:699–711

    Article  CAS  Google Scholar 

  37. Kay LE, Nicholson LK, Delaglio F, Bax A, Torchia DA (1992) 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. J Magn Reson 97:359–375

    CAS  Google Scholar 

  38. Korzhnev DM, Skrynnikov NR, Millet O, Torchia DA, Kay LE (2002) An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates. J Am Chem Soc 124:10743–10753

    Article  CAS  Google Scholar 

  39. Massi F, Johnson E, Wang C, Rance M, Palmer AGr (2004) NMR R1 rho rotating-frame relaxation with weak radio frequency fields. J Am Chem Soc 126:2247–2256

    Google Scholar 

  40. Guenneugues M, Berthault P, Desvaux H (1999) A method for determining B1 field inhomogeneity. Are the biases assumed in heteronuclear relaxation experiments usually underestimated? J Magn Reson 136:118–126

    Article  CAS  Google Scholar 

  41. Ross A, Czisch M, King GC (1997) Systematic errors associated with the CPMG pulse sequence and their effect on motional analysis of biomolecules. J Magn Reson 124:355–365

    Article  CAS  Google Scholar 

  42. Korzhnev DM, Tischenko EV, Arseniev AS (2000) Off-resonance effects in N-15 T-2 CPMG measurements. J Biomol NMR 17:231–237

    Article  CAS  Google Scholar 

  43. Gullion T, Baker DB, Conradi MS (1990) New, compensated Carr-Purcell sequences. J Magn Reson 89:479–484

    CAS  Google Scholar 

  44. Yip GN, Zuiderweg ER (2004) A phase cycle scheme that significantly suppresses offset-dependent artifacts in the R2-CPMG 15 N relaxation experiment. J Magn Reson 171:25–36

    Article  CAS  Google Scholar 

  45. Long D, Liu M, Yang D (2008) Accurately probing slow motions on millisecond timescales with a robust NMR relaxation experiment. J Am Chem Soc 130:2432–2433

    Article  CAS  Google Scholar 

  46. Myint W, Gong Q, Ishima R (2009) Practical aspects of 15 N CPMG transverse relaxation experiments for proteins in solution. Concepts Magn Reson 34A:63–75

    Article  CAS  Google Scholar 

  47. Ishima R, Torchia DA (2003) Extending the range of amide proton relaxation dispersion experiments in proteins using a constant-time relaxation-compensated CPMG approach. J Biomol NMR 25:243–248

    Article  CAS  Google Scholar 

  48. Abragam A (1961) Principles of nuclear magnetism. Oxford University Press, Oxford

    Google Scholar 

  49. Freeman R, Hill HDW (1971) Fourier transform study of NMR spin-lattice relaxation by “progressive saturation”. J Chem Phys 54:3367–3377

    Article  CAS  Google Scholar 

  50. Markley JL, Horsley WJ, Klein MP (1971) Spin–lattice relaxation measurements in slowly relaxing complex spectra. J Chem Phys 55:3604–3605

    Article  CAS  Google Scholar 

  51. Chill JH, Louis JM, Baber JL, Bax A (2006) Measurement of 15N relaxation in the detergent-solubilized tetrameric KcsA potassium channel. J Biomol NMR 36:123–136

    Article  CAS  Google Scholar 

  52. Grzesiek S, Bax A (1993) The importance of not saturating H2O in protein NMR – application to sensitivity enhancement and NOE measurements. J Am Chem Soc 115:12593

    Article  CAS  Google Scholar 

  53. Li YC, Montelione GT (1994) Overcoming solvent saturation-transfer artifacts in protein NMR at neutral pH – application of pulsed-field gradients in measurements of H-1 N-15 Overhauser effects. J Magn Reson Ser B 105:45–51

    Article  CAS  Google Scholar 

  54. Renner C, Schleicher M, Moroder L, Holak TA (2002) Practical aspects of the 2D N-15-{H-1}-NOE experiment. J Biomol NMR 23:23–33

    Article  CAS  Google Scholar 

  55. Freedberg DI, Ishima R, Jacob J, Wang YX, Kustanovich I, Louis JM, Torchia DA (2002) Rapid structural fluctuations of the free HIV protease flaps in solution. Protein Sci 11:221–232

    Article  CAS  Google Scholar 

  56. Gong Q, Ishima R (2007) 15 N-{1H} NOE experiment at high magnetic field strengths. J Biomol NMR 37:147–157

    Article  CAS  Google Scholar 

  57. Ferrage F, Piserchio A, Cowburn D, Ghose R (2008) On the measurement of 15 N-{1H} nuclear Overhauser effects. J Magn Reson 192:302–313

    Article  CAS  Google Scholar 

  58. Ferrage F, Cowburn D, Ghose R (2009) Accurate sampling of high-frequency motions in proteins by steady-state (15)N-{(1)H} nuclear Overhauser effect measurements in the presence of cross-correlated relaxation. J Am Chem Soc 131:6048–6049

    Article  CAS  Google Scholar 

  59. Rule GS, Hichens KT (2006) Fundamentals of protein NMR spectroscopy, vol 5. Springer, Dordrecht

    Google Scholar 

  60. Vugmeyster L, Raleigh DP, Palmer AGr, Vugmeister BE (2003) Beyond the decoupling approximation in the model free approach for the interpretation of NMR relaxation of macromolecules in solution. J Am Chem Soc 125:8400–8404

    Google Scholar 

  61. Vugmeyster L, McKnight CJ (2008) Slow motions in Chicken Villin headpiece subdomain probed by cross-correlated NMR relaxation of amide NH bonds in successive residues. Biophys J 95:5941–5950

    Article  CAS  Google Scholar 

  62. Goldman M (1984) Interference effects in the relaxation of a pair of unlike spin-1/2 nuclei. J Magn Reson 60:437–452

    CAS  Google Scholar 

  63. Boyd J, Hommel U, Campbell ID (1990) Influence of cross-correlation between dipolar and anisotropic chemical shift relaxation mechanisms upon longitudinal relaxation rates of 15 N in macromolecules. Chem Phys Lett 175:477–482

    Article  CAS  Google Scholar 

  64. Wang L, Kurochkin AV, Zuiderweg ER (2000) An iterative fitting procedure for the determination of longitudinal NMR cross-correlation rates. J Magn Reson 144:175–185

    Article  CAS  Google Scholar 

  65. Bouguet-Bonnet S, Mutzenhardt P, Canet D (2004) Measurement of 15 N csa/dipolar cross-correlation rates by means of spin state selective experiments. J Biomol NMR 30:133–142

    Article  CAS  Google Scholar 

  66. Tjandra N, Szabo A, Bax A (1996) Protein backbone dynamics and N-15 chemical shift anisotropy from quantitative measurement of relaxation interference effects. J Am Chem Soc 118:6986–6991

    Article  CAS  Google Scholar 

  67. Fushman D, Cowburn D (1998) Model-independent analysis of 15 N chemical shift anisotropy from NMR relaxation data. Ubiquitin as a test example. J Am Chem Soc 120:7109–7110

    Article  CAS  Google Scholar 

  68. Fushman D, Tjandra N, Cowburn D (1998) Direct measurement of N-15 chemical shift anisotropy in solution. J Am Chem Soc 120:10947–10952

    Article  CAS  Google Scholar 

  69. Kroenke CD, Rance M, Palmer AGr (1999) Variability of the 15N chemical shift anisotropy in Escherichia coli Ribonuclease H in Solution. J Am Chem Soc 121:10119–10125

    Google Scholar 

  70. Boyed J, Redfield C (1999) Characterization of 15 N chemical shift anisotropy from orientation-dependent changes to 15 N chemical shifts in dilute bicelle solutions. J Am Chem Soc 121:7441–7442

    Article  CAS  Google Scholar 

  71. Kurita J, Shimahara H, Utsunomiya-Tate N, Tate S (2003) Measurement of 15N chemical shift anisotropy in a protein dissolved in a dilute liquid crystalline medium with the application of magic angle sample spinning. J Magn Reson 163:163–173

    Article  CAS  Google Scholar 

  72. Lipsitz RS, Tjandra N (2003) 15N chemical shift anisotropy in protein structure refinement and comparison with NH residual dipolar couplings. J Magn Reson 164:171–176

    Article  CAS  Google Scholar 

  73. Damberg P, Jarvet J, Gräslund A (2005) Limited variations in 15N CSA magnitudes and orientations in ubiquitin are revealed by joint analysis of longitudinal and transverse NMR relaxation. J Am Chem Soc 127:1995–2005

    Article  CAS  Google Scholar 

  74. Hansen DF, Yang D, Feng H, Zhou Z, Wiesner S, Bai Y, Kay LE (2007) An exchange-free measure of 15N transverse relaxation: an NMR spectroscopy application to the study of a folding intermediate with pervasive chemical exchange. J Am Chem Soc 129:11468–11478

    Article  CAS  Google Scholar 

  75. Hansen DF, Feng H, Zhou Z, Bai Y, Kay LE (2009) Selective characterization of microsecond motions in proteins by NMR relaxation. J Am Chem Soc 131:16257–16265

    Article  CAS  Google Scholar 

  76. Jeener J, Meier BH, Bachmann P, Ernst RR (1979) Investigation of exchange processes by two-dimensional NMR spectroscopy. J Chem Phys 71:4546–4553

    Article  CAS  Google Scholar 

  77. Sahu D, Clore GM, Iwahara J (2007) TROSY-based z-exchange spectroscopy: application to the determination of the activation energy for intermolecular protein translocation between specific sites on different DNA molecules. J Am Chem Soc 129:13232–13237

    Article  CAS  Google Scholar 

  78. Li Y, Palmer AG (2009) TROSY-selected ZZ-exchange experiment for characterizing slow chemical exchange in large proteins. J Biomol NMR 45:357–360

    Article  CAS  Google Scholar 

  79. Robson SA, Peterson R, Bouchard LS, Villareal VA, Clubb RT (2010) A heteronuclear zero quantum coherence Nz-exchange experiment that resolves resonance overlap and its application to measure the rates of heme binding to the IsdC protein. J Am Chem Soc 132:9522–9523

    Article  CAS  Google Scholar 

  80. Fite W II, Redfield AG (1967) Nuclear spin relaxation in superconduting mixed-state vanadium. Phys Rev 162:358–367

    Article  CAS  Google Scholar 

  81. Koenig SH, Schillinger WE (1969) Nuclear magnetic relaxation dispersion in protein solutions. J Biol Chem 244:3283–3289

    CAS  Google Scholar 

  82. Kimmich R (1979) Field cycling in NMR relaxation spectroscopy: applications in biological, chemical and polymer physics. Bull Magn Reson 1:195–218

    Google Scholar 

  83. Noack F (1986) NMR field-cycling spectroscopy: principles and applications. Prog NMR Spectrosc 18:171–276

    Article  CAS  Google Scholar 

  84. Bertini I, Briganti F, Xia ZC, Luchinat C (1993) Nuclear magnetic relaxation dispersion studies of hexaaquo Mn(II) ions in water-glycerol mixtures. J Magn Reson A 101:198–201

    Article  CAS  Google Scholar 

  85. Hodges MW, Cafiso DS, Polnaszek CF, Lester CC, Bryant RG (1997) Water translational motion at the bilayer interface: an NMR relaxation dispersion measurement. Biophys J 75:2575–2579

    Article  Google Scholar 

  86. Koenig SH, Brown RD (1990) Field-cycling relaxometry of protein solutions and tissue: implications for MRI. Prog NMR Spectrosc 22:487–567

    Google Scholar 

  87. Halle B, Denisov VP (1995) A new view of water dynamics in immobilized proteins. Biophys J 69:242–249

    Article  CAS  Google Scholar 

  88. Roberts MF, Redfield AG (2004) Phospholipid bilayer surface configuration probed quantitatively by P-31 field-cycling NMR. Proc Natl Acad Sci USA 101:17066–17071

    Article  CAS  Google Scholar 

  89. Kimmich R, Anoardo E (2004) Field-cycling NMR relaxometry. Prog NMR Spectrosc 44:257–320

    Article  CAS  Google Scholar 

  90. Diakova G, Goddard YA, Korb JP, Bryant RG (2010) Water and backbone dynamics in a hydrated protein. Biophys J 98:138–146

    Article  CAS  Google Scholar 

  91. Wagner S, Dinesen TRJ, Rayner T, Bryant RG (1999) High-resolution magnetic relaxation dispersion measurements of solute spin probes using a dual-magnet system. J Magn Reson 140:172–178

    Article  CAS  Google Scholar 

  92. Redfield AG (2003) Shuttling device for high-resolution measurements of relaxation and related phenomena in solution at low field, using a shared commercial 500 MHz NMR instrument. Magn Reson Chem 41:753–768

    Article  CAS  Google Scholar 

  93. Victor K, Kavolius V, Bryant RG (2004) Magnetic relaxation dispersion probe. J Magn Reson 171:253–257

    Article  CAS  Google Scholar 

  94. McConnell HM (1958) Reaction rates by nuclear magnetic resonance. J Chem Phys 28:430–431

    Article  CAS  Google Scholar 

  95. Luz Z, Meiboom S (1963) Nuclear magnetic resonance study of the protolysis of trimethylammonium ion in aqueous solution – order of the reaction with respect to solvent. J Chem Phys 39:366–370

    Article  CAS  Google Scholar 

  96. Allerhand A, Gutowsky HS (1964) Spin-echo NMR studies of chemical exchange. 1. Some general aspects. J Chem Phys 41:2115

    Google Scholar 

  97. Gutowsky HS, Vold RL, Wells EJ (1965) Theory of chemical exchange effects in magnetic resonance. J Chem Phys 43:4107–4125

    Article  CAS  Google Scholar 

  98. Carver JP, Richards RE (1972) General 2-site solution for chemical exchange produced dependence of T2 upon Carr-Purcell pulse separation. J Magn Reson 6:89–105

    CAS  Google Scholar 

  99. Jen J (1978) Chemical exchange and NMR T2 relaxation – multisite case. J Magn Reson 30:111–128

    CAS  Google Scholar 

  100. Bleich HE, Day AR, Freer RJ, Glasel JA (1979) NMR rotating frame relaxation studies of intramolecular motion in peptides. Tyrosine ring motion in methionine-enkephalin. Biochem Biophys Res Commun 87:1146–1153

    Article  CAS  Google Scholar 

  101. Snyder GH, Rowan R III, Karplus S, Sykes BD (1979) NMR rotating frame relaxation studies of intramolecular motion in peptides. Tyrosine ring motion in methionine-enkephalin. Biochem Biophys Res Commun 87:1146–1153

    Article  Google Scholar 

  102. Bloom M, Reeves LW, Wells EJ (1965) Spin echoes and chemical exchange. J Chem Phys 42:1615–1624

    Article  CAS  Google Scholar 

  103. Davis DG, Perlman ME, London RE (1994) Direct measurements of the dissociation-rate constant for inhibitor-enzyme complexes via the T-1-Rho and T-2 (Cpmg) methods. J Magn Reson Ser B 104:266–275

    Article  CAS  Google Scholar 

  104. Szyperski S, Luginbühl P, Otting G, Güntert P, Wüthrich K (1993) Protein dynamics studied by rotating frame. J Biomol NMR 3:151–164

    CAS  Google Scholar 

  105. Orekhov VY, Pervushin KV, Arseniev AS (1994) Backbone dynamics of (1–71)bacterioopsin studied by two-dimensional 1H-15N NMR spectroscopy. Eur J Biochem 219:887–896

    Article  CAS  Google Scholar 

  106. Akke M, Palmer AGr (1996) Monitoring macromolecular motions on microsecond to millisecond time scales by R1ρ−R1 constant relaxation time NMR spectroscopy. J Am Chem Soc 118:911–912

    Google Scholar 

  107. Zinn-Justin S, Berthault P, Guenneugues M, Desvaus H (1997) Off-resonance rf fields in heteronuclear NMR. Application to the study of slow motions. J Biomol NMR 10:363–372

    Article  CAS  Google Scholar 

  108. Mulder FA, van Tilborg PJ, Kaptein R, Boelens R (1999) Microsecond time scale dynamics in the RXR DNA-binding domain from a combination of spin-echo and off-resonance rotating frame relaxation measurements. J Biomol NMR 13:275–288

    Article  CAS  Google Scholar 

  109. Loria JP, Rance M, Palmer AG (1999) A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy. J Am Chem Soc 121:2331–2332

    Article  CAS  Google Scholar 

  110. Hansen DF, Vallurupalli P, Kay LE (2007) An improved (15)N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins. J Phys Chem B 112(19):5898–5904

    Google Scholar 

  111. Gadian DG, Robinson FNH (1979) Radiofrequency losses in NMR experiments on electrically conducting samples. J Magn Reson 34:449–455

    CAS  Google Scholar 

  112. Hoult DI, Lauterbur PC (1979) The sensitivity of the zeugmatographic experiment involving human samples. J Magn Reson 34:425–433

    CAS  Google Scholar 

  113. Kelly AE, Ou HD, Withers R, Dotsch V (2002) Low-conductivity buffers for high-sensitivity NMR measurements. J Am Chem Soc 124:12013–12019

    Article  CAS  Google Scholar 

  114. Horiuchi T, Takahashi M, Kikuchi J, Yokoyama S, Maeda H (2005) Effect of dielectric properties of solvents on the quality factor for a beyond 900 MHz cryogenic probe model. J Magn Reson 174:34–42

    Article  CAS  Google Scholar 

  115. Mulder FA, Skrynnikov NR, Hon B, Dahlquist FW, Kay LE (2001) Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme. J Am Chem Soc 123:967–975

    Article  CAS  Google Scholar 

  116. Tollinger M, Skrynnikov NR, Mulder FA, Forman-Kay JD, Kay LE (2001) Slow dynamics in folded and unfolded states of an SH3 domain. J Am Chem Soc 123:11341–11352

    Article  CAS  Google Scholar 

  117. Jones JA, Hodgkinson P, Barker AL, Hore PJ (1996) Optimal sampling strategies for the measurement of spin-spin relaxation times. J Magn Reson Seres B 113:25–34

    Article  CAS  Google Scholar 

  118. Jones JA (1997) Optimal sampling strategies for the measurement of relaxation times in proteins. J Magn Reson 126:283–286

    Article  CAS  Google Scholar 

  119. Czisch M, King GC, Ross A (1997) Removal of systematic errors associated with off-resonance oscillations in T2 measurements. J magn Reson 126:154–157

    Article  CAS  Google Scholar 

  120. Wang AC, Bax A (1993) Minimizing the effects of radio-frequency heating in multi-dimensional NMR experiments. J Biomol NMR 3:715–720

    Article  CAS  Google Scholar 

  121. Yip GN, Zuiderweg ER (2005) Improvement of duty-cycle heating compensation in NMR spin relaxation experiments. J Magn Reson 176:171–178

    Article  CAS  Google Scholar 

  122. Wang C, Grey MJ, Palmer AG 3rd (2001) CPMG sequences with enhanced sensitivity to chemical exchange. J Biomol NMR 21:361–366

    Article  CAS  Google Scholar 

  123. Loria JP, Rance M, Palmer AG (1999) A TROSY CPMG sequence for characterizing chemical exchange in large proteins. J Biomol NMR 15:151–155

    Article  CAS  Google Scholar 

  124. Wang CY, Palmer AG (2003) Solution NMR methods for quantitative identification of chemical exchange in N-15-labeled proteins. Magn Reson Chem 41:866–876

    Article  CAS  Google Scholar 

  125. Mulder FAA, de Graaf RA, Kaptein R, Boelens R (1998) An off-resonance rotating frame relaxation experiment for the investigation of macromolecular dynamics using adiabatic rotations. J Magn Reson 131:351–357

    Article  CAS  Google Scholar 

  126. Kempf JG, Jung JY, Sampson NS, Loria JP (2003) Off-resonance TROSY (R1 rho – R1) for quantitation of fast exchange processes in large proteins. J Am Chem Soc 125:12064–12065

    Article  CAS  Google Scholar 

  127. Kim S, Baum J (2004) An on/off resonance rotating frame relaxation experiment to monitor millisecond to microsecond timescale dynamics. J Biomol NMR 30:195–204

    Article  CAS  Google Scholar 

  128. Igumenova TI, Palmer AG (2006) Off-resonance TROSY-selected R-1p experiment with improved sensitivity for medium- and high-molecular-weight proteins. J Am Chem Soc 128:8110–8111

    Article  CAS  Google Scholar 

  129. Trott O, Palmer AGr (2002) R1rho relaxation outside of the fast-exchange limit. J Magn Reson 154:157–160

    Google Scholar 

  130. Korzhnev DM, Orekhov VY, Dahlquist FW, Kay LE (2003) Off-resonance R1rho relaxation outside of the fast exchange limit: an experimental study of a cavity mutant of T4 lysozyme. J Biomol NMR 26:39–48

    Article  CAS  Google Scholar 

  131. Miloushev VZ, Palmer AGr (2005) R(1rho) relaxation for two-site chemical exchange: general approximations and some exact solutions. J Magn Reson 177:221–227

    Google Scholar 

  132. Vugmeyster L, Kroenke CD, Picart F, Palmer AG, Raleigh DP (2000) N-15 R-1 rho measurements allow the determination of ultrafast protein folding rates. J Am Chem Soc 122:5387–5388

    Article  CAS  Google Scholar 

  133. Massi F, Grey MJ, Palmer AGr (2005) Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments. Protein Sci 14:735–742

    Google Scholar 

  134. Ishima R, Torchia DA (1999) Estimating the time scale of chemical exchange of proteins from. J Biomol NMR 14:369–372

    Article  CAS  Google Scholar 

  135. Gardino AK, Kern D (2007) Functional dynamics of response regulators using NMR relaxation techniques. Methods Enzymol 423:195–205

    Google Scholar 

  136. Korzhnev DM, Salvatella X, Vendruscolo M, Di Nardo AA, Davidson AR, Dobson CM, Kay LE (2004) Low-populated folding intermediates of Fyn SH3 characterized by relaxation. Nature 430:586–590

    Google Scholar 

  137. Ishima R, Torchia DA (2005) Error estimation and global fitting in transverse-relaxation dispersion. J Biomol NMR 32:41–54

    Article  CAS  Google Scholar 

  138. Kovrigin EL, Kempf JG, Grey MJ, Loria JP (2006) Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements. J Magn Reson 180:83–104

    Article  CAS  Google Scholar 

  139. Hansen DF, Vallurupalli P, Lundström P, Neudecker P, Kay LE (2008) Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do? J Am Chem Soc 130:2667–2675

    Article  CAS  Google Scholar 

  140. Lundström P, Vallurupalli P, Hansen DF, Kay LE (2009) Isotope labeling methods for studies of excited protein states by relaxation dispersion NMR spectroscopy. Nat Protoc 4:1641–1648

    Article  CAS  Google Scholar 

  141. Nicholson LK, Yamazaki T, Torchia DA, Grzesiek S, Bax A, Stahl SJ, Kaufman JD, Wingfield PT, Lam PY, Jadhav PK, Hodge CN, Domaille PJ, Chong-Hwan C (1995) Flexibility and function in HIV-1 protease. Nat Struct Biol 2:274–280

    Article  CAS  Google Scholar 

  142. Ishima R, Wingfield PT, Stahl SJ, Kaufman JD, Torchia DA (1998) Using amide H-1 and N-15 transverse relaxation to detect millisecond time-scale motions in perdeuterated proteins: application to HIV-1 protease. J Am Chem Soc 120:10534–10542

    Article  CAS  Google Scholar 

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Acknowledgments

This study was supported by grants from the National Institutes of Health (AI077424 and GM066524), the National Science Foundation (MCB 0814905), and funds from the University of Pittsburgh. We thank Dennis Torchia and Robert Bryant for discussion and critical reading.

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  1. Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA

    Rieko Ishima

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  1. Rieko Ishima
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Correspondence to Rieko Ishima .

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  1. , Dept. of Biochemistry, Hong Kong University of Science and Tech, Clear Water Bay, Hong Kong, Kowloon, China, People's Republic

    Guang Zhu

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Ishima, R. (2011). Recent Developments in 15N NMR Relaxation Studies that Probe Protein Backbone Dynamics. In: Zhu, G. (eds) NMR of Proteins and Small Biomolecules. Topics in Current Chemistry, vol 326. Springer, Berlin, Heidelberg. https://doi.org/10.1007/128_2011_212

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