Advertisement

Journal of Biomolecular NMR

, Volume 70, Issue 3, pp 187–202 | Cite as

Measuring the signs of the methyl 1H chemical shift differences between major and ‘invisible’ minor protein conformational states using methyl 1H multi-quantum spectroscopy

  • Anusha B. Gopalan
  • Pramodh Vallurupalli
Article
  • 456 Downloads

Abstract

Carr–Purcell–Meiboom–Gill (CPMG) type relaxation dispersion experiments are now routinely used to characterise protein conformational dynamics that occurs on the μs to millisecond (ms) timescale between a visible major state and ‘invisible’ minor states. The exchange rate(s) (\( k_{{{\text{ex}}}} \)), population(s) of the minor state(s) and the absolute value of the chemical shift difference \(|{\Delta \varpi }|\) (ppm) between different exchanging states can be extracted from the CPMG data. However the sign of \({\Delta \varpi }\) that is required to reconstruct the spectrum of the ‘invisible’ minor state(s) cannot be obtained from CPMG data alone. Building upon the recently developed triple quantum (TQ) methyl \( ^{1} {\text{H}} \) CPMG experiment (Yuwen in Angew Chem 55:11490–11494, 2016) we have developed pulse sequences that use carbon detection to generate and evolve single quantum (SQ), double quantum (DQ) and TQ coherences from methyl protons in the indirect dimension to measure the chemical exchange-induced shifts of the SQ, DQ and TQ coherences from which the sign of \({\Delta \varpi }\) is readily obtained for two state exchange. Further a combined analysis of the CPMG data and the difference in exchange induced shifts between the SQ and DQ resonances and between the SQ and TQ resonances improves the estimates of exchange parameters like the population of the minor state. We demonstrate the use of these experiments on two proteins undergoing exchange: (1) the ~ 18 kDa cavity mutant of T4 Lysozyme (\( k_{{{\text{ex}}}} \sim\,3500{\text{ s}}^{{ - 1}} \)) and (2) the \(\sim\,4.7\) kDa Peripheral Sub-unit Binding Domain (PSBD) from the acetyl transferase of Bacillus stearothermophilus (\(k_{ex} \sim\,13,000\hbox { s}^{-1}\)).

Keywords

Chemical/conformational exchange CPMG relaxation dispersion Multi quantum \(^{13}\hbox {CH}_3/^{12}\hbox {CD}_3\) ILV methyl labelling Carbon detection 

Notes

Acknowledgements

We thank Dr. Tairan Yuwen and Prof. Lewis E. Kay (University of Toronto) for useful discussions and for providing the Bruker TQ CPMG pulse sequence, Dr. G Bouvignies for providing ChemEx along with the source code, the national NMR facility at TIFR, Hyderabad for spectrometer time and Dr Krishna Rao for help with some of the experiments. The work was supported by generous startup funds from TCIS/TIFRH and Grant ECR/2016/001088 from SERB awarded to PV.

References

  1. Ahlner A, Carlsson M, Jonsson BH, Lundström P (2013) PINT: a software for integration of peak volumes and extraction of relaxation rates. J Biomol NMR 56(3):191–202CrossRefGoogle Scholar
  2. Allen MD, Broadhurst RW, Solomon RG, Perham RN (2005) Interaction of the E2 and E3 components of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. Use of a truncated protein domain in NMR spectroscopy. FEBS J 272(1):259–268CrossRefGoogle Scholar
  3. Anthis NJ, Clore GM (2015) Visualizing transient dark states by NMR spectroscopy. Q Rev Biophys 48(1):35–116CrossRefGoogle Scholar
  4. Auer R, Neudecker P, Muhandiram DR, Lundstrom P, Hansen DF, Konrat R, Kay LE (2009) Measuring the signs of 1H(alpha) chemical shift differences between ground and excited protein states by off-resonance spin-lock R1\(\rho \) NMR spectroscopy. J Am Chem Soc 131(31):10832–10833CrossRefGoogle Scholar
  5. Austin RH, Beeson KW, Eisenstein L, Frauenfelder H, Gunsalus I (1975) Dynamics of ligand binding to myoglobin. Biochemistry 14(24):5355–5373CrossRefGoogle Scholar
  6. Baase WA, Liu L, Tronrud DE, Matthews BW (2010) Lessons from the lysozyme of phage T4. Protein Sci 19(4):631–641CrossRefGoogle Scholar
  7. Baldwin AJ, Religa TL, Hansen DF, Bouvignies G, Kay LE (2010) (13)CHD(2) methyl group probes of millisecond time scale exchange in proteins by (1)H relaxation dispersion: an application to proteasome gating residue dynamics. J Am Chem Soc 132(32):10992–10995CrossRefGoogle Scholar
  8. Bermel W, Bertini I, Felli IC, Piccioli M, Pierattelli R (2006) C13-detected protonless NMR spectroscopy of proteins in solution. Prog Nucl Magn Reson Spectrosc 48(1):25–45CrossRefGoogle Scholar
  9. Bodenhausen G (1980) Multiple-quantum NMR. Progr Nucl Magn Reson Spectrosc 14:137–173CrossRefGoogle Scholar
  10. Boehr DD, Nussinov R, Wright PE (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 5(11):789–796CrossRefGoogle Scholar
  11. Bouvignies G (2011) ChemEx. https://github.com/gbouvignies/chemex
  12. Bouvignies G, Korzhnev DM, Neudecker P, Hansen DF, Cordes MH, Kay LE (2010) A simple method for measuring signs of (1)H (N) chemical shift differences between ground and excited protein states. J Biomol NMR 47(2):135–141CrossRefGoogle Scholar
  13. Bouvignies G, Hansen DF, Vallurupalli P, Kay LE (2011a) Divided-evolution-based pulse scheme for quantifying exchange processes in proteins: powerful complement to relaxation dispersion experiments. J Am Chem Soc 133(6):1935–1945CrossRefGoogle Scholar
  14. Bouvignies G, Vallurupalli P, Hansen DF, Correia BE, Lange O, Bah A, Vernon RM, Dahlquist FW, Baker D, Kay LE (2011b) Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature 477(7362):111ADSCrossRefGoogle Scholar
  15. Carr HY, Purcell EM (1954) Effects of diffusion on free precession in nuclear magnetic resonance experiments. Phys Rev 94(3):630ADSCrossRefGoogle Scholar
  16. Cavalli A, Salvatella X, Dobson CM, Vendruscolo M (2007) Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci USA 104(23):9615–9620ADSCrossRefGoogle Scholar
  17. Cavanagh J, Fairbrother WJ, Palmer AG, Rance M, Skelton NJ (2006) Protein NMR spectroscopy, principles and practice, 2nd edn. Academic Press, CambridgeGoogle Scholar
  18. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6(3):277–293CrossRefGoogle Scholar
  19. Ernst RR, Bodenhausen G, Wokaun A (1987) Principles of nuclear magnetic resonance in one and two dimensions, 1st edn. Oxford Science Publications, OxfordGoogle Scholar
  20. Fawzi NL, Ying J, Ghirlando R, Torchia DA, Clore GM (2011) Atomic-resolution dynamics on the surface of amyloid-beta protofibrils probed by solution NMR. Nature 480(7376):268–272ADSCrossRefGoogle Scholar
  21. Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T (2009) Hidden alternate structures of proline isomerase essential for catalysis. Nature 462(7273):669ADSCrossRefGoogle Scholar
  22. Frauenfelder H, Sligar SG, Wolynes PG (1991) The energy landscapes and motions of proteins. Science 254(5038):1598–1603ADSCrossRefGoogle Scholar
  23. Gardner KH, Kay LE (1998) The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins. Annu Rev Biophys Biomol Struct 27:357–406CrossRefGoogle Scholar
  24. Gardner KH, Konrat R, Rosen MK, Kay LE (1996) An (H)C(CO)NH-TOCSY pulse scheme for sequential assignment of protonated methyl groups in otherwise deuterated (15)N, (13)C-labeled proteins. J Biomol NMR 8(3):351–356CrossRefGoogle Scholar
  25. Gladkova C, Schubert AF, Wagstaff JL, Pruneda JN, Freund SMV, Komander D (2017) An invisible ubiquitin conformation is required for efficient phosphorylation by PINK1. EMBO J 36(24):3555–3572.  https://doi.org/10.15252/embj.201797876 CrossRefGoogle Scholar
  26. Goddard TD, Kneller DG (2008) SPARKY 3. University of California, San FranciscoGoogle Scholar
  27. Gopalan AB, Hansen DF, Vallurupalli P (2018) CPMG experiments for protein minor conformer structure determination. Methods Mol Biol 1688:223–242CrossRefGoogle Scholar
  28. Goto NK, Gardner KH, Mueller GA, Willis RC, Kay LE (1999) A robust and cost-effective method for the production of Val, Leu, Ile (\(\delta \)1) methyl-protonated 15N-, 13C-, 2H-labeled proteins. J Biomol NMR 13(4):369–374CrossRefGoogle Scholar
  29. Grey MJ, Wang C, Palmer AG (2003) Disulfide bond isomerization in basic pancreatic trypsin inhibitor: multisite chemical exchange quantified by CPMG relaxation dispersion and chemical shift modeling. J Am Chem Soc 125(47):14324–14335CrossRefGoogle Scholar
  30. Grutsch S, Bruschweiler S, Tollinger M (2016) NMR methods to study dynamic allostery. PLoS Comput Biol 12(3):e1004620ADSCrossRefGoogle Scholar
  31. Hansen AL, Kay LE (2014) Measurement of histidine pKa values and tautomer populations in invisible protein states. Proc Natl Acad Sci USA 111(17):E1705–E1712ADSCrossRefGoogle Scholar
  32. Hansen DF, Kay LE (2011) Determining valine side-chain rotamer conformations in proteins from methyl 13C chemical shifts: application to the 360 kDa half-proteasome. J Am Chem Soc 133(21):8272–8281CrossRefGoogle Scholar
  33. Hansen DF, Vallurupalli P, Kay LE (2008a) Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states. J Biomol NMR 41(3):113–120.  https://doi.org/10.1007/s10858-008-9251-5 CrossRefGoogle Scholar
  34. Hansen DF, Vallurupalli P, Lundstrom P, Neudecker P, Kay LE (2008b) Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do? J Am Chem Soc 130(8):2667–2675CrossRefGoogle Scholar
  35. Hansen DF, Neudecker P, Kay LE (2010a) Determination of isoleucine side-chain conformations in ground and excited states of proteins from chemical shifts. J Am Chem Soc 132(22):7589–7591CrossRefGoogle Scholar
  36. Hansen DF, Neudecker P, Vallurupalli P, Mulder FA, Kay LE (2010b) Determination of Leu side-chain conformations in excited protein states by NMR relaxation dispersion. J Am Chem Soc 132(1):42–43CrossRefGoogle Scholar
  37. 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(3):243–248CrossRefGoogle Scholar
  38. 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(40):10534–10542CrossRefGoogle Scholar
  39. Ishima R, Baber J, Louis JM, Torchia DA (2004) Carbonyl carbon transverse relaxation dispersion measurements and ms-micros timescale motion in a protein hydrogen bond network. J Biomol NMR 29(2):187–198CrossRefGoogle Scholar
  40. Kalia YN, Brocklehurst SM, Hipps DS, Appella E, Sakaguchi K, Perham RN (1993) The high-resolution structure of the peripheral subunit-binding domain of dihydrolipoamide acetyltransferase from the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. J Mol Biol 230(1):323–341CrossRefGoogle Scholar
  41. Kerfah R, Plevin MJ, Sounier R, Gans P, Boisbouvier J (2015) Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins. Curr Opin Struct Biol 32:113–122CrossRefGoogle Scholar
  42. Kloiber K, Konrat R (2000) Differential multiple-quantum relaxation arising from cross-correlated time-modulation of isotropic chemical shifts. J Biomol NMR 18(1):33–42CrossRefGoogle Scholar
  43. Korzhnev DM, Kloiber K, Kanelis V, Tugarinov V, Kay LE (2004a) Probing slow dynamics in high molecular weight proteins by methyl-TROSY NMR spectroscopy: application to a 723-residue enzyme. J Am Chem Soc 126(12):3964–3973CrossRefGoogle Scholar
  44. Korzhnev DM, Kloiber K, Kay LE (2004b) Multiple-quantum relaxation dispersion NMR spectroscopy probing millisecond time-scale dynamics in proteins: theory and application. J Am Chem Soc 126(23):7320–7329CrossRefGoogle Scholar
  45. Korzhnev DM, Salvatella X, Vendruscolo M, Di Nardo AA, Davidson AR, Dobson CM, Kay LE (2004c) Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Nature 430(6999):586–590ADSCrossRefGoogle Scholar
  46. Korzhnev DM, Orekhov VY, Kay LE (2005) Off-resonance R1\(\rho \) NMR studies of exchange dynamics in proteins with low spin-lock fields: an application to a Fyn SH3 domain. J Am Chem Soc 127(2):713–721CrossRefGoogle Scholar
  47. Korzhnev DM, Religa TL, Banachewicz W, Fersht AR, Kay LE (2010) A transient and low-populated protein-folding intermediate at atomic resolution. Science 329(5997):1312–1316ADSCrossRefGoogle Scholar
  48. Kovrigin EL, Loria JP (2006) Characterization of the transition state of functional enzyme dynamics. J Am Chem Soc 128(24):7724–7725CrossRefGoogle Scholar
  49. Lee W, Tonelli M, Markley JL (2014) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31(8):1325–1327CrossRefGoogle Scholar
  50. Levitt MH (1982) Symmetrical composite pulse sequences for NMR population-inversion 2. Compensation of resonance offset. J Magn Reson 50(1):95–110ADSGoogle Scholar
  51. Li D, Bruschweiler R (2015) \(\text{ PPM }_{\rm One}\): a static protein structure based chemical shift predictor. J Biomol NMR 62(3):403–409CrossRefGoogle Scholar
  52. Li DW, Bruschweiler R (2012) PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles. J Biomol NMR 54(3):257–265CrossRefGoogle Scholar
  53. Lichtenecker RJ, Weinhaupl K, Reuther L, Schorghuber J, Schmid W, Konrat R (2013) Independent valine and leucine isotope labeling in Escherichia coli protein overexpression systems. J Biomol NMR 57(3):205–209CrossRefGoogle Scholar
  54. Liu LJ, Baase WA, Matthews BW (2009) Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I \(\cdot \cdot \cdot \) S and I \(\cdot \cdot \cdot \) Se halogen-bonding. J Mol Biol 385(2):595–605CrossRefGoogle Scholar
  55. Loria JP, Rance M, Palmer AG (1999a) A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy. J Am Chem Soc 121(10):2331–2332CrossRefGoogle Scholar
  56. Loria JP, Rance M, Palmer AG (1999b) A TROSY CPMG sequence for characterizing chemical exchange in large proteins. J Biomol NMR 15(2):151–155CrossRefGoogle Scholar
  57. Lundstrom P, Hansen DF, Vallurupalli P, Kay LE (2009a) Accurate measurement of alpha proton chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy. J Am Chem Soc 131(5):1915–1926CrossRefGoogle Scholar
  58. Lundstrom P, Lin H, Kay LE (2009b) Measuring 13C\(\beta \) chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy. J Biomol NMR 44(3):139–155CrossRefGoogle Scholar
  59. Mackenzie HW, Hansen DF (2017) A (13)C-detected (15)N double-quantum NMR experiment to probe arginine side-chain guanidinium (15)N(eta) chemical shifts. J Biomol NMR 69(3):123–132CrossRefGoogle Scholar
  60. Marion D, Ikura M, Tschudin R, Bax A (1989) Rapid Recording of 2D NMR-spectra without phase cycling—application to the study of hydrogen-exchange in proteins. J Magn Reson 85(2):393–399 ay905 Times Cited:1356 Cited References Count:18ADSGoogle Scholar
  61. McConnell HM (1958) Reaction rates by nuclear magnetic resonance. J Chem Phys 28(3):430–431ADSCrossRefGoogle Scholar
  62. Meiboom S, Gill D (1958) Modified spin-echo method for measuring nuclear relaxation times. Rev Sci Instrum 29(8):688–691ADSCrossRefGoogle Scholar
  63. Millet O, Loria JP, Kroenke CD, Pons M, Palmer AG (2000) The static magnetic field dependence of chemical exchange linebroadening defines the NMR chemical shift time scale. J Am Chem Soc 122(12):2867–2877CrossRefGoogle Scholar
  64. Morris GA, Freeman R (1979) Enhancement of nuclear magnetic-resonance signals by polarization transfer. J Am Chem Soc 101(3):760–762CrossRefGoogle Scholar
  65. Mulder FA (2009) Leucine side-chain conformation and dynamics in proteins from 13C NMR chemical shifts. ChemBioChem 10(9):1477–1479CrossRefGoogle Scholar
  66. Mulder FA, Mittermaier A, Hon B, Dahlquist FW, Kay LE (2001a) Studying excited states of proteins by NMR spectroscopy. Nat Struct Biol 8(11):932–935CrossRefGoogle Scholar
  67. Mulder FA, Skrynnikov NR, Hon B, Dahlquist FW, Kay LE (2001b) 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(5):967–975CrossRefGoogle Scholar
  68. Neri D, Szyperski T, Otting G, Senn H, Wuthrich K (1989) Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling. Biochemistry 28(19):7510–7516CrossRefGoogle Scholar
  69. Neudecker P, Robustelli P, Cavalli A, Walsh P, Lundstrom P, Zarrine-Afsar A, Sharpe S, Vendruscolo M, Kay LE (2012) Structure of an intermediate state in protein folding and aggregation. Science 336(6079):362–366.  https://doi.org/10.1126/science.1214203 ADSCrossRefGoogle Scholar
  70. Orekhov VY, Korzhnev DM, Kay LE (2004) Double- and zero-quantum NMR relaxation dispersion experiments sampling millisecond time scale dynamics in proteins. J Am Chem Soc 126(6):1886–1891CrossRefGoogle Scholar
  71. Oyen D, Fenwick RB, Stanfield RL, Dyson HJ, Wright PE (2015) Cofactor-mediated conformational dynamics promote product release from Escherichia coli dihydrofolate reductase via an allosteric pathway. J Am Chem Soc 137(29):9459–9468CrossRefGoogle Scholar
  72. Palmer AG (2014) Chemical exchange in biomacromolecules: past, present, and future. J Magn Reson 241:3–17.  https://doi.org/10.1016/j.jmr.2014.01.008 ADSCrossRefGoogle Scholar
  73. Palmer AG, Massi F (2006) Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem Rev 106(5):1700–1719.  https://doi.org/10.1021/Cr0404287 CrossRefGoogle Scholar
  74. Piserchio A, Warthaka M, Kaoud TS, Callaway K, Dalby KN, Ghose R (2017) Local destabilization, rigid body, and fuzzy docking facilitate the phosphorylation of the transcription factor Ets-1 by the mitogen-activated protein kinase ERK2. Proc Natl Acad Sci USA 114(31):E6287–E6296CrossRefGoogle Scholar
  75. Rosenzweig R, Kay LE (2014) Bringing dynamic molecular machines into focus by methyl-TROSY NMR. Ann Rev Biochem 83(83):291–315CrossRefGoogle Scholar
  76. Rosenzweig R, Sekhar A, Nagesh J, Kay LE (2017) Promiscuous binding by Hsp70 results in conformational heterogeneity and fuzzy chaperone-substrate ensembles. Elife 14:6Google Scholar
  77. Sahakyan AB, Vranken WF, Cavalli A, Vendruscolo M (2011) Structure-based prediction of methyl chemical shifts in proteins. J Biomol NMR 50(4):331CrossRefGoogle Scholar
  78. Sanchez-Medina C, Sekhar A, Vallurupalli P, Cerminara M, Munoz V, Kay LE (2014) Probing the free energy landscape of the fast-folding gpW protein by relaxation dispersion NMR. J Am Chem Soc 136(20):7444–7451CrossRefGoogle Scholar
  79. Sauerwein A, Hansen DF (2015) Relaxation dispersion NMR spectroscopy. Springer, Boston, pp 75–132Google Scholar
  80. Sekhar A, Kay LE (2013) NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers. Proc Natl Acad Sci USA 110(32):12867–12874ADSCrossRefGoogle Scholar
  81. Serber Z, Richter C, Dotsch V (2001) Carbon-detected NMR experiments to investigate structure and dynamics of biological macromolecules. ChemBioChem 2(4):247–251CrossRefGoogle Scholar
  82. Shaka AJ, Keeler J, Frenkiel T, Freeman R (1983) An improved sequence for broad-band decoupling—WALTZ-16. J Magn Reson 52(2):335–338ADSGoogle Scholar
  83. Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu GH, Eletsky A, Wu YB, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105(12):4685–4690ADSCrossRefGoogle Scholar
  84. Skrynnikov NR, Mulder FA, Hon B, Dahlquist FW, Kay LE (2001) Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: application to methionine residues in a cavity mutant of T4 lysozyme. J Am Chem Soc 123(19):4556–4566CrossRefGoogle Scholar
  85. Skrynnikov NR, Dahlquist FW, Kay LE (2002) Reconstructing NMR spectra of invisible excited protein states using HSQC and HMQC experiments. J Am Chem Soc 124(41):12352–12360CrossRefGoogle Scholar
  86. Sprangers R, Kay LE (2007) Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature 445(7128):618–622CrossRefGoogle Scholar
  87. Sugase K, Dyson HJ, Wright PE (2007) Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447(7147):1021–1025ADSCrossRefGoogle Scholar
  88. Takeuchi K, Gal M, Shimada G, Wagner G (2012) Low gamma nuclei detection experiments for biomolecular NMR. In: Clore M, Potts J (eds) Recent developments in biomolecular NMR. Royal Society of Chemistry, Cambridge, pp 25–52CrossRefGoogle Scholar
  89. Tamiola K, Acar B, Mulder FA (2010) Sequence-specific random coil chemical shifts of intrinsically disordered proteins. J Am Chem Soc 132(51):18000–18003CrossRefGoogle Scholar
  90. Torchia DA (2015) NMR studies of dynamic biomolecular conformational ensembles. Prog Nucl Magn Reson Spectrosc 84–85:14–32CrossRefGoogle Scholar
  91. Trott O, Palmer AG (2002) R1\(\rho \) relaxation outside of the fast-exchange limit. J Magn Reson 154:157–160ADSCrossRefGoogle Scholar
  92. Tugarinov V, Kay LE (2004) An isotope labeling strategy for methyl TROSY spectroscopy. J Biomol NMR 28(2):165–172CrossRefGoogle Scholar
  93. Tugarinov V, Kay LE (2007) Separating degenerate (1)H transitions in methyl group probes for single-quantum (1)H-CPMG relaxation dispersion NMR spectroscopy. J Am Chem Soc 129(30):9514–9521CrossRefGoogle Scholar
  94. Vallurupalli P, Hansen DF, Stollar E, Meirovitch E, Kay LE (2007) Measurement of bond vector orientations in invisible excited states of proteins. Proc Natl Acad Sci USA 104(47):473–477CrossRefGoogle Scholar
  95. Vallurupalli P, Hansen D, Kay LE (2008) Structures of invisible, excited protein states by relaxation dispersion nmr spectroscopy. Proc Natl Acad Sci USA 105(33):766–771.  https://doi.org/10.1073/pnas.0804221105 CrossRefGoogle Scholar
  96. Vallurupalli P, Hansen DF, Lundström P, Kay LE (2009) CPMG relaxation dispersion NMR experiments measuring glycine 1H\(\alpha \) and 13C\(\alpha \) chemical shifts in the invisible excited states of proteins. J Biomol NMR 45(1–2):45–55CrossRefGoogle Scholar
  97. Vallurupalli P, Bouvignies G, Kay LE (2011) Increasing the exchange time-scale that can be probed by CPMG relaxation dispersion NMR. J Phys Chem B 115(49):14891–14900CrossRefGoogle Scholar
  98. Vallurupalli P, Chakrabarti N, Pomes R, Kay LE (2016) Atomistic picture of conformational exchange in a T4 lysozyme cavity mutant: an experiment-guided molecular dynamics study. Chem Sci 7(6):3602–3613CrossRefGoogle Scholar
  99. van Ingen H, Vuister GW, Wijmenga S, Tessari M (2006) CEESY: characterizing the conformation of unobservable protein states. J Am Chem Soc 128(12):3856–3857CrossRefGoogle Scholar
  100. Velyvis A, Ruschak AM, Kay LE (2012) An economical method for production of (2)H, (13)CH3-threonine for solution NMR studies of large protein complexes: application to the 670 kDa proteasome. PLoS ONE 7(9):e43725ADSCrossRefGoogle Scholar
  101. Vugmeyster L, Kroenke CD, Picart F, Palmer AG, Raleigh DP (2000) 15N R1\(\rho \) measurements allow the determination of ultrafast protein folding rates. J Am Chem Soc 122(22):5387–5388CrossRefGoogle Scholar
  102. Wang CY, Palmer AG (2002) Differential multiple quantum relaxation caused by chemical exchange outside the fast exchange limit. J Biomol NMR 24(3):263–268CrossRefGoogle Scholar
  103. Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G (2008) CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucl Acids Res 36:W496–W502CrossRefGoogle Scholar
  104. Xie XS (2002) Single-molecule approach to dispersed kinetics and dynamic disorder: probing conformational fluctuation and enzymatic dynamics. J Chem Phys 117(24):24–32.  https://doi.org/10.1063/1.1521159 Google Scholar
  105. Yuwen T, Vallurupalli P, Kay LE (2016) Enhancing the sensitivity of CPMG relaxation dispersion to conformational exchange processes by multiple-quantum spectroscopy. Angew Chem 55(38):11490–11494CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research HyderabadHyderabadIndia

Personalised recommendations