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Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer

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Abstract

Although Chemical Exchange Saturation Transfer (CEST) type NMR experiments have been used to study chemical exchange processes in molecules since the early 1960s, there has been renewed interest in the past several years in using this approach to study biomolecular conformational dynamics. The methodology is particularly powerful for the study of sparsely populated, transiently formed conformers that are recalcitrant to investigation using traditional biophysical tools, and it is complementary to relaxation dispersion and magnetization transfer experiments that have traditionally been used to study chemical exchange processes. Here we discuss the concepts behind the CEST experiment, focusing on practical aspects as well, we review some of the pulse sequences that have been developed to characterize protein and RNA conformational dynamics, and we discuss a number of examples where the CEST methodology has provided important insights into the role of dynamics in biomolecular function.

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Fig. 1
Fig. 2
Fig. 3

Figure adapted from (Vallurupalli et al. 2012)

Fig. 4

Figure adapted from (Bouvignies et al. 2014)

Fig. 5

Figure adapted from Bouvignies and Kay (Bouvignies and Kay 2012b)

Fig. 6

Figure adapted from Yuwen et al. (Yuwen et al. 2016)

Fig. 7

Figure taken from (Long et al. 2015)

Fig. 8

Figure adapted from Long et al. (Long et al. 2014a)

Fig. 9

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References

  • Allard P, Helgstrand M, Hard T (1998) The complete homogeneous master equation for a heteronuclear two-spin system in the basis of Cartesian product operators. J Magn Reson 134:7–16

    Article  ADS  Google Scholar 

  • Allerhand A, Gutowsky HS (1964) Spin-echo NMR studies of chemical exchange 0.1. Some general aspects. J Chem Phys 41:2115–2126

    Article  ADS  Google Scholar 

  • Anderson WA (1956) Nuclear magnetic resonance spectra of some hydrocarbons. Phys Rev 102:151–167

    Article  ADS  Google Scholar 

  • Anderson WA, Freeman R (1962) Influence of a second radiofrequency field on high-resolution nuclear magnetic resonance spectra. J Chem Phys 37:85–103

    Article  ADS  Google Scholar 

  • Arnold JT, Dharmatti SS, Packard ME (1951) Chemical effects on nuclear induction signals from organic compounds. J Chem Phys 19:507–507

    Article  ADS  Google Scholar 

  • Austin RH, Beeson KW, Eisenstein L, Frauenfelder H, Gunsalus IC (1975) Dynamics of ligand binding to myoglobin. BioChemistry 14:5355–5373

    Article  Google Scholar 

  • Bai Y, Milne JS, Mayne L, Englander SW (1993) Primary structure effects on peptide group hydrogen exchange. Proteins 17:75–86

    Article  Google Scholar 

  • Bain AD (2003) Chemical exchange in NMR. Prog Nucl Magn Reson Spectrosc 43:63–103

    Article  Google Scholar 

  • Battiste JL, Wagner G (2000) Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data. BioChemistry 39:5355–5365

    Article  Google Scholar 

  • Bertini I, Luchinat C (1986) NMR of paramagnetic molecules in biological systems. Benjamin/Cummings, Menlo Park

    Google Scholar 

  • Bertini I, Ciurli S, Dikiy A, Gasanov R, Luchinat C, Martini G, Safarov N (1999) High-field NMR studies of oxidized blue copper proteins: the case of spinach plastocyanin. J Am Chem Soc 121:2037–2046

    Article  Google Scholar 

  • Bloch F, Hansen WW, Packard M (1946) Nuclear induction. Phys Rev 69:127–127

    Article  ADS  Google Scholar 

  • Bouvignies G (2012) Chemex (https://github.com/gbouvignies/chemex/releases)

  • Bouvignies G, Kay LE (2012a) A 2D C-13-CEST experiment for studying slowly exchanging protein systems using methyl probes: an application to protein folding. J Biomol NMR 53:303–310

    Article  Google Scholar 

  • Bouvignies G, Kay LE (2012b) Measurement of proton chemical shifts in invisible states of slowly exchanging protein systems by chemical exchange saturation transfer. J Phys Chem B 116:14311–14317

    Article  Google Scholar 

  • Bouvignies G, Vallurupalli P, Hansen DF, Correia BE, Lange O, Bah A, Vernon RM, Dahlquist FW, Baker D, Kay LE (2011) Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature 477:111–114

    Article  ADS  Google Scholar 

  • Bouvignies G, Vallurupalli P, Kay LE (2014) Visualizing side chains of invisible protein conformers by solution NMR. J Mol Biol 426:763–774

    Article  Google Scholar 

  • Capaldi AP, Shastry MCR, Kleanthous C, Roder H, Radford SE (2001) Ultrarapid mixing experiments reveal that Im7 folds via an on-pathway intermediate. Nat Struct Biol 8:68–72

    Article  Google Scholar 

  • Carneiro MG, Reddy JG, Griesinger C, Lee D (2015) Speeding-up exchange-mediated saturation transfer experiments by Fourier transform. J Biomol NMR 63:237–244

    Article  Google Scholar 

  • Carr HY, Purcell EM (1954) Effects of diffusion on free precession in nuclear magnetic resonance experiments. Phys Rev 94:630–638

    Article  ADS  Google Scholar 

  • Cavanagh J, Fairbrother WJ, Palmer AG, Rance M, Skelton NJ (2006) Protein NMR spectroscopy, principles and practice, 2nd edn. Academic Press, Boston

    Google Scholar 

  • Cayley PJ, Albrand JP, Feeney J, Roberts GC, Piper EA, Burgen AS (1979) Nuclear magnetic resonance studies of the binding of trimethoprim to dihydrofolate reductase. BioChemistry 18:3886–3895

    Article  Google Scholar 

  • Chacinska A, Koehler CM, Milenkovic D, Lithgow T, Pfanner N (2009) Importing mitochondrial proteins: machineries and mechanisms. Cell 138:628–644

    Article  Google Scholar 

  • Chakrabarti KS, Ban D, Pratihar S, Reddy JG, Becker S, Griesinger C, Lee D (2016) High-power (1)H composite pulse decoupling provides artifact free exchange-mediated saturation transfer (EST) experiments. J Magn Reson 269:65–69

    Article  ADS  Google Scholar 

  • Clore GM, Gronenborn AM (1982) Theory and applications of the transferred nuclear overhauser effect to the study of the conformations of small ligands bound to proteins. J Magn Reson 48:402–417

    ADS  Google Scholar 

  • Clore GM, Iwahara J (2009) Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem Rev 109:4108–4139

    Article  Google Scholar 

  • Clore GM, Roberts GCK, Gronenborn A, Birdsall B, Feeney J (1981) Transfer-of-saturation NMR-studies of protein-ligand complexes: 3-site exchange. J Magn Reson 45:151–161

    ADS  Google Scholar 

  • Deshmukh L, Louis JM, Ghirlando R, Clore GM (2016) Transient HIV-1 Gag-protease interactions revealed by paramagnetic NMR suggest origins of compensatory drug resistance mutations. Proc Natl Acad Sci USA 113:12456–12461

    Article  Google Scholar 

  • Deverell C, Morgan RE, Strange JH (1970) Studies of chemical exchange by nuclear magnetic relaxation in rotating frame. Mol Phys 18:553–559

    Article  ADS  Google Scholar 

  • Edgcomb SP, Murphy KP (2002) Variability in the pKa of histidine side-chains correlates with burial within proteins. Proteins Struct Funct Genet 49:1–6

    Article  Google Scholar 

  • Englander SW, Mayne L, Bai Y, Sosnick TR (1997) Hydrogen exchange: the modern legacy of Linderstrom-Lang. Protein Sci 6:1101–1109

    Article  Google Scholar 

  • Eriksson AE, Baase WA, Wozniak JA, Matthews BW (1992) A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene. Nature 355:371–373

    Article  ADS  Google Scholar 

  • Farrow NA, Muhandiram R, Singer AU, Pascal SM, Kay CM, Gish G, Shoelson SE, Pawson T, Forman-Kay JD, Kay LE (1994a) Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15 N NMR relaxation. BioChemistry 33:5984–6003

    Article  Google Scholar 

  • Farrow NA, Zhang O, Forman-Kay JD, Kay LE (1994b) A heteronuclear correlation experiment for simultaneous determination of 15 N longitudinal decay and chemical exchange rates of systems in slow equilibrium. J Biomol NMR 4:727–734

    Article  Google Scholar 

  • Fawzi NL, Ying JF, Torchia DA, Clore GM (2010) Kinetics of amyloid beta monomer-to-oligomer exchange by NMR relaxation. J Am Chem Soc 132:9948–9951

    Article  Google Scholar 

  • 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 480:268–272

    Article  ADS  Google Scholar 

  • Fawzi NL, Libich DS, Ying JF, Tugarinov V, Clore GM (2014) Characterizing methyl-bearing side chain contacts and dynamics mediating amyloid beta protofibril interactions using C-13(methyl)-DEST and lifetime line broadening. Angew Chem Int Edit 53:10345–10349

    Article  Google Scholar 

  • Forsen S, Hoffman RA (1963) Study of moderately rapid chemical exchange reactions by means of nuclear magnetic double resonance. J Chem Phys 39:2892–2901

    Article  ADS  Google Scholar 

  • Frauenfelder H, Sligar SG, Wolynes PG (1991) The energy landscapes and motions of proteins. Science 254:1598–1603

    Article  ADS  Google Scholar 

  • Freeman R (1988) Handbook of nuclear magnetic resonance. Wiley, New York

    Google Scholar 

  • Goedert M, Spillantini MG (2006) A century of Alzheimer’s disease. Science 314:777–781

    Article  ADS  Google Scholar 

  • 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 13:369–374

    Article  Google Scholar 

  • Grey MJ, Wang C, Palmer AG 3rd (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 125:14324–14335

    Article  Google Scholar 

  • Grzesiek S, Bax A (1992) Correlating backbone amide and side-chain resonances in larger proteins by multiple relayed triple resonance NMR. J Am Chem Soc 114:6291–6293

    Article  Google Scholar 

  • Grzesiek S, Bax A (1993) Amino-acid type determination in the sequential assignment procedure of uniformly C-13/N-15-enriched proteins. J Biomol NMR 3:185–204

    Google Scholar 

  • Gu YN, Hansen AL, Peng Y, Bruschweiler R (2016) Rapid determination of fast protein dynamics from NMR chemical exchange saturation transfer data. Angew Chem Int Edit 55:3117–3119

    Article  Google Scholar 

  • Gupta RK, Redfield AG (1970a) Double nuclear magnetic resonance observation of electron exchange between ferri- and ferrocytochrome c. Science 169:1204–1206

    Article  ADS  Google Scholar 

  • Gupta RK, Redfield AG (1970b) NMR double resonance study of azidoferricytochrome C. Biochem Biophys Res Commun 41:273–281

    Article  Google Scholar 

  • Gutowsky HS, Holm CH (1956) Rate processes and nuclear magnetic resonance spectra 0.2. Hindered internal rotation of amides. J Chem Phys 25:1228–1234

    Article  ADS  Google Scholar 

  • Gutowsky HS, Saika A (1953) Dissociation, chemical exchange, and the proton magnetic resonance in some aqueous electrolytes. J Chem Phys 21:1688–1694

    Article  ADS  Google Scholar 

  • Hansen AL, Kay LE (2014) Measurement of histidine pK(a) values and tautomer populations in invisible protein states. Proc Natl Acad Sci USA 111:E1705–E1712

    Article  ADS  Google Scholar 

  • Hansen DF, Led JJ (2006) Determination of the geometric structure of the metal site in a blue copper protein by paramagnetic NMR. Proc Natl Acad Sci USA 103:1738–1743

    Article  ADS  Google Scholar 

  • Hansen DF, Vallurupalli P, Kay LE (2008) Quantifying two-bond 1HN–13CO and one-bond 1H(alpha)–13C(alpha) dipolar couplings of invisible protein states by spin-state selective relaxation dispersion NMR spectroscopy. J Am Chem Soc 130:8397–8405

    Article  Google Scholar 

  • Harbison GS (1993) Interference between J-couplings and cross-relaxation in solution NMR-spectroscopy: consequences for macromolecular structure determination. J Am Chem Soc 115:3026–3027

    Article  Google Scholar 

  • Hartl FU, Bracher A, Hayer-Hartl M (2011) Molecular chaperones in protein folding and proteostasis. Nature 475:324–332

    Article  Google Scholar 

  • Hasha DL, Eguchi T, Jonas J (1982) High-pressure NMR-study of dynamical effects on conformational isomerization of cyclohexane. J Am Chem Soc 104:2290–2296

    Article  Google Scholar 

  • Hass MAS, Ubbink M (2014) Structure determination of protein-protein complexes with long-range anisotropic paramagnetic NMR restraints. Curr Opin Struc Biol 24:45–53

    Article  Google Scholar 

  • Hunkapiller MW, Smallcombe SH, Whitaker DR, Richards JH (1973) Carbon nuclear magnetic-resonance studies of histidine residue in alpha-lytic protease: implications for catalytic mechanism of serine proteases. BioChemistry 12:4732–4743

    Article  Google Scholar 

  • Hyberts SG, Heffron GJ, Tarragona NG, Solanky K, Edmonds KA, Luithardt H, Fejzo J, Chorev M, Aktas H, Colson K, Falchuk KH, Halperin JA, Wagner G (2007) Ultrahigh-resolution H-1-C-13 HSQC spectra of metabolite mixtures using nonlinear sampling and forward maximum entropy reconstruction. J Am Chem Soc 129:5108–5116

    Article  Google Scholar 

  • Hyberts SG, Arthanari H, Wagner G (2012) Applications of non-uniform sampling and processing. Top Curr Chem 316:125–148

    Article  Google Scholar 

  • Ikura M, Kay LE, Bax A (1990) A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. BioChemistry 29:4659–4667

    Article  Google Scholar 

  • 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 29:187–198

    Article  Google Scholar 

  • Jackman LM, Cotton FA (1975) Dynamic nuclear magnetic resonance spectroscopy. Academic Press, San Diego

    Google Scholar 

  • Jaravine V, Ibraghimov I, Orekhov VY (2006) Removal of a time barrier for high-resolution multidimensional NMR spectroscopy. Nat Methods 3:605–607

    Article  Google Scholar 

  • 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  ADS  Google Scholar 

  • Johnson MF, Forsberg JH (1972) Kinetics of exchange-reaction of beta, beta-′, beta-″-triaminotriethylamine with bis(beta, beta-′, beta-″-triaminotriethylamine)neodymium(III). Inorg Chem 11:2683–2686

    Article  Google Scholar 

  • Karplus M (2000) Aspects of protein reaction dynamics: deviations from simple behavior. J Phys Chem B 104:11–27

    Article  Google Scholar 

  • Karplus M, Kuriyan J (2005) Molecular dynamics and protein function. Proc Natl Acad Sci USA 102:6679–6685

    Article  ADS  Google Scholar 

  • Karplus M, Weaver DL (1979) Diffusion-collision model for protein folding. Biopolymers 18:1421–1437

    Article  Google Scholar 

  • Karplus M, Weaver DL (1994) Protein folding dynamics: the diffusion-collision model and experimental data. Protein Sci 3:650–668

    Article  Google Scholar 

  • Kasinath V, Valentine KG, Wand AJ (2013) A 13 C labeling strategy reveals a range of aromatic side chain motion in calmodulin. J Am Chem Soc 135:9560–9563

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Kay LE, Keifer P, Saarinen T (1992) Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J Am Chem Soc 114:10663–10665

    Article  Google Scholar 

  • 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 dispersion NMR. Nature 430:586–590

    Article  ADS  Google Scholar 

  • Korzhnev DM, Orekhov VY, Kay LE (2005) Off-resonance R(1rho) NMR studies of exchange dynamics in proteins with low spin-lock fields: an application to a Fyn SH3 domain. J Am Chem Soc 127:713–721

    Article  Google Scholar 

  • Korzhnev DM, Religa TL, Banachewicz W, Fersht AR, Kay LE (2010) A transient and low-populated protein-folding intermediate at atomic resolution. Science 329:1312–1316

    Article  ADS  Google Scholar 

  • Lauzon CB, van Zijl P, Stivers JT (2011) Using the water signal to detect invisible exchanging protons in the catalytic triad of a serine protease. J Biomol NMR 50:299–314

    Article  Google Scholar 

  • Levitt MH (1982a) Symmetrical composite pulse sequences for NMR population-inversion 0.1. Compensation of radiofrequency field inhomogeneity. J Magn Reson 48:234–264

    ADS  Google Scholar 

  • Levitt MH (1982b) Symmetrical composite pulse sequences for NMR population-inversion 0.2. Compensation of resonance offset. J Magn Reson 50:95–110

    ADS  Google Scholar 

  • Libich DS, Fawzi NL, Ying JF, Clore GM (2013) Probing the transient dark state of substrate binding to GroEL by relaxation-based solution NMR. Proc Natl Acad Sci USA 110:11361–11366

    Article  ADS  Google Scholar 

  • Lim J, Xiao TS, Fan JS, Yang DW (2014) An off-pathway folding intermediate of an acyl carrier protein domain coexists with the folded and unfolded states under native conditions**. Angew Chem Int Edit 53:2358–2361.

    Article  Google Scholar 

  • Long D, Bouvignies G, Kay LE (2014a) Measuring hydrogen exchange rates in invisible protein excited states. Proc Natl Acad Sci USA 111:8820–8825

    Article  ADS  Google Scholar 

  • Long D, Sekhar A, Kay LE (2014b) Triple resonance-based (1)(3)C(alpha) and (1)(3)C(beta) CEST experiments for studies of ms timescale dynamics in proteins. J Biomol NMR 60:203–208

    Article  Google Scholar 

  • Long D, Delaglio F, Sekhar A, Kay LE (2015) Probing invisible, excited protein states by non-uniformly sampled pseudo-4D CEST spectroscopy. Angew Chem Int Edit 54:10507–10511

    Article  Google Scholar 

  • Lundstrom P, Teilum K, Carstensen T, Bezsonova I, Wiesner S, Hansen DF, Religa TL, Akke M, Kay LE (2007) Fractional 13 C enrichment of isolated carbons using [1-13C]- or [2-13C]-glucose facilitates the accurate measurement of dynamics at backbone Calpha and side-chain methyl positions in proteins. J Biomol NMR 38:199–212

    Article  Google Scholar 

  • Lundstrom P, Hansen DF, Kay LE (2008) Measurement of carbonyl chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy: comparison between uniformly and selectively (13)C labeled samples. J Biomol NMR 42:35–47

    Article  Google Scholar 

  • Lundstrom P, Lin H, Kay LE (2009a) Measuring 13C beta chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy. J Biomol NMR 44:139–155

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  ADS  Google Scholar 

  • Lynden-Bell RM (1967) The calculation of line shapes by density matrix methods. Prog Nuc Magn Reson 2:163–204

    Article  Google Scholar 

  • Ma RS, Li QF, Wang AD, Zhang JH, Liu ZJ, Wu JH, Su XC, Ruan K (2016) Determination of pseudocontact shifts of low-populated excited states by NMR chemical exchange saturation transfer. Phys Chem Chem Phys 18:13794–13798

    Article  Google Scholar 

  • Markley JL (1975) Observation of histidine residues in proteins by means of nuclear magnetic-resonance spectroscopy. Accounts Chem Res 8:70–80

    Article  Google Scholar 

  • Matsuki Y, Eddy MT, Herzfeld J (2009) Spectroscopy by integration of frequency and time domain information for fast acquisition of high-resolution dark spectra. J Am Chem Soc 131:4648–4656

    Article  Google Scholar 

  • Matsuki Y, Eddy MT, Griffin RG, Herzfeld J (2010) Rapid three-dimensional MAS NMR spectroscopy at critical sensitivity. Angew Chem Int Edit 49:9215–9218

    Article  Google Scholar 

  • Mayer M, James TL (2002) Detecting ligand binding to a small RNA target via saturation transfer difference NMR experiments in D2O and H2O. J Am Chem Soc 124:13376–13377

    Article  Google Scholar 

  • Mayer M, Meyer B (1999) Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew Chem Int Edit 38:1784–1788

    Article  Google Scholar 

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

    Article  ADS  Google Scholar 

  • Meiboom S, Gill D (1958) Modified spin-echo method for measuring nuclear relaxation times. Rev Sci Instrum 29:688–691

    Article  ADS  Google Scholar 

  • 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 122:2867–2877

    Article  Google Scholar 

  • Milojevic J, Esposito V, Das R, Melacini G (2007) Understanding the molecular basis for the inhibition of the Alzheimer’s A beta-peptide oligomerization by human serum albumin using saturation transfer difference and off-resonance relaxation NMR spectroscopy. J Am Chem Soc 129:4282–4290

    Article  Google Scholar 

  • Milojevic J, Raditsis A, Melacini G (2009) Human serum albumin inhibits A beta fibrillization through a “monomer-competitor” mechanism. Biophys J 97:2585–2594

    Article  Google Scholar 

  • Miloushev VZ, Palmer AG 3rd (2005) R(1rho) relaxation for two-site chemical exchange: general approximations and some exact solutions. J Magn Reson 177:221–227

    Article  ADS  Google Scholar 

  • Min W, English BP, Luo G, Cherayil BJ, Kou SC, Xie XS (2005) Fluctuating enzymes: lessons from single-molecule studies. Acc Chem Res 38:923–931

    Article  Google Scholar 

  • Mittermaier A, Kay LE (2006) New tools provide new insights in NMR studies of protein dynamics. Science 312:224–228

    Article  ADS  Google Scholar 

  • Montelione GT, Wagner G (1989) 2D chemical-exchange NMR-spectroscopy by proton-detected heteronuclear correlation. J Am Chem Soc 111:3096–3098

    Article  Google Scholar 

  • Morris GA, Freeman R (1979) Enhancement of nuclear magnetic-resonance signals by polarization transfer. J Am Chem Soc 101:760–762

    Article  Google Scholar 

  • Mulder FA, Hon B, Mittermaier A, Dahlquist FW, Kay LE (2002) Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme. J Am Chem Soc 124:1443–1451

    Article  Google Scholar 

  • Narayanan S, Reif B (2005) Characterization of chemical exchange between soluble and aggregated states of beta-amyloid by solution-state NMR upon variation of salt conditions. BioChemistry 44:1444–1452

    Article  Google Scholar 

  • 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 336:362–366

    Article  ADS  Google Scholar 

  • Nielsen SO (1964) Use of hydrogen exchange in protein structural analysis. Biochem J 92:P12

    Article  Google Scholar 

  • Orekhov VY, Jaravine VA (2011) Analysis of non-uniformly sampled spectra with multi-dimensional decomposition. Prog Nucl Magn Reson Spectrosc 59:271–292

    Article  Google Scholar 

  • Palmer AG 3rd, Kroenke CD, Loria JP (2001) Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol 339:204–238

    Article  Google Scholar 

  • Palmer AG (2004) NMR characterization of the dynamics of biomacromolecules. Chem Rev 104:3623–3640

    Article  Google Scholar 

  • Palmer AG (2014) Chemical exchange in biomacromolecules: past, present, and future. J Magn Reson 241:3–17

    Article  ADS  Google Scholar 

  • Palmer AG, Massi F (2006) Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem Rev 106:1700–1719

    Article  Google Scholar 

  • Pelton JG, Torchia DA, Meadow ND, Roseman S (1993) Tautomeric states of the active-site histidines of phosphorylated and unphosphorylated III(Glc), a signal-transducing protein from Escherichia coli, using 2-dimensional heteronuclear NMR techniques. Protein Sci 2:543–558

    Article  Google Scholar 

  • Pervushin K, Riek R, Wider G, Wuthrich K (1997) Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci USA 94:12366–12371

    Article  ADS  Google Scholar 

  • Prestegard JH, al-Hashimi HM, Tolman JR (2000) NMR structures of biomolecules using field oriented media and residual dipolar couplings. Q Rev Biophys 33:371–424

    Article  Google Scholar 

  • Purcell EM, Torrey HC, Pound RV (1946) Resonance absorption by nuclear magnetic moments in a solid. Phys Rev 69:37–38

    Article  ADS  Google Scholar 

  • Querfurth HW, LaFerla FM (2010) Alzheimer’s disease. N Engl J Med 362:329–344

    Article  Google Scholar 

  • Ramsey NF (1952) Chemical effects in nuclear magnetic resonance and in diamagnetic susceptibility. Phys Rev 86:243–246

    Article  ADS  Google Scholar 

  • Rennella E, Huang R, Velyvis A, Kay LE (2015) (13)CHD2-CEST NMR spectroscopy provides an avenue for studies of conformational exchange in high molecular weight proteins. J Biomol NMR 63:187–199

    Article  Google Scholar 

  • Reynolds WF, Peat IR, Freedman MH, Lyerla JR (1973) Determination of tautomeric form of imidazole ring of l-histidine in basic solution by C-13 magnetic-resonance spectroscopy. J Am Chem Soc 95:328–331

    Article  Google Scholar 

  • Roberts JD (1959) Nuclear magnetic resonance applications to orgainc chemistry, 1st edn. McGraw-Hill, New York

    Google Scholar 

  • Rodriguez JC, Jennings PA, Melacini G (2004) Using chemical exchange to assign non-covalent protein complexes in slow exchange with the free state: enhanced resolution and efficient signal editing. J Biomol NMR 30:155–161

    Article  Google Scholar 

  • Rosenzweig R, Kay LE (2014) Bringing dynamic molecular machines into focus by methyl-TROSY NMR. Annu Rev Biochem 83(83):291–315

    Article  Google Scholar 

  • Sala D, Giachetti A, Luchinat C, Rosato A (2016) A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions. J Biomol NMR 66:175–185

    Article  Google Scholar 

  • Schleucher J, Sattler M, Griesinger C (1993) Coherence selection by gradients without signal attenuation: application to the 3-dimensional hnco experiment. Angew Chemie Int Ed 32:1489–1491

    Article  Google Scholar 

  • Schmitz C, Vernon R, Otting G, Baker D, Huber T (2012) Protein structure determination from pseudocontact shifts using ROSETTA. J Mol Biol 416:668–677

    Article  Google Scholar 

  • 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 110:12867–12874

    Article  ADS  Google Scholar 

  • Sekhar A, Rosenzweig R, Bouvignies G, Kay LE (2015a) Mapping the conformation of a client protein through the Hsp70 functional cycle. Proc Natl Acad Sci USA 112:10395–10400

    Article  ADS  Google Scholar 

  • Sekhar A, Rumfeldt JAO, Broom HR, Doyle CM, Bouvignies G, Meiering EM, Kay LE (2015b) Thermal fluctuations of immature SOD1 lead to separate folding and misfolding pathways. Elife 4:e07296

    Article  Google Scholar 

  • Sekhar A, Rosenzweig R, Bouvignies G, Kay LE (2016) Hsp70 biases the folding pathways of client proteins. Proc Natl Acad Sci USA 113:E2794–E2801

    Article  ADS  Google Scholar 

  • Shaka AJ, Keeler J, Frenkiel T, Freeman R (1983) An improved sequence for broad-band decoupling: Waltz-16. J Magn Reson 52:335–338

    ADS  Google Scholar 

  • Spera S, Bax A (1991) Empirical correlation between protein backbone conformation and C-alpha and C-beta C-13 nuclear-magnetic-resonance chemical-shifts. J Am Chem Soc 113:5490–5492

    Article  Google Scholar 

  • Stanek J, Kozminski W (2010) Iterative algorithm of discrete Fourier transform for processing randomly sampled NMR data sets. J Biomol NMR 47:65–77

    Article  Google Scholar 

  • Takahashi H, Nakanishi T, Kami K, Arata Y, Shimada I (2000) A novel NMR method for determining the interfaces of large protein-protein complexes. Nat Struct Biol 7:220–223

    Article  Google Scholar 

  • Teilum K, Brath U, Lundstrom P, Akke M (2006) Biosynthetic 13 C labeling of aromatic side chains in proteins for NMR relaxation measurements. J Am Chem Soc 128:2506–2507

    Article  Google Scholar 

  • Tjandra N, Bax A (1997) Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278:1111–1114

    Article  ADS  Google Scholar 

  • 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  Google Scholar 

  • Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH (1997) NMR evidence for slow collective motions in cyanometmyoglobin. Nat Struct Biol 4:292–297

    Article  Google Scholar 

  • Trott O, Palmer AG 3rd (2002) R1rho relaxation outside of the fast-exchange limit. J Magn Reson 154:157–160

    Article  ADS  Google Scholar 

  • Tugarinov V, Kay LE (2005) Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins. Chembiochem 6:1567–1577

    Article  Google Scholar 

  • Tugarinov V, Hwang PM, Ollerenshaw JE, Kay LE (2003) Cross-correlated relaxation enhanced 1H[bond]13 C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes. J Am Chem Soc 125:10420–10428

    Article  Google Scholar 

  • Tycko R (1994) Nuclear magnetic resonance probes of molecular dynamics. Kluwer Academic Publishers, Dordrecht

    Book  Google Scholar 

  • Vallurupalli P, Kay LE (2013) Probing slow chemical exchange at carbonyl sites in proteins by chemical exchange saturation transfer NMR spectroscopy. Angew Chem Int Ed Engl 52:4156–4159

    Article  Google Scholar 

  • 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 104:18473–18477

    Article  ADS  Google Scholar 

  • Vallurupalli P, Hansen DF, Kay LE (2008) Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. Proc Natl Acad Sci USA 105:11766–11771

    Article  ADS  Google Scholar 

  • 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 115:14891–14900

    Article  Google Scholar 

  • Vallurupalli P, Bouvignies G, Kay LE (2012) Studying “invisible” excited protein states in slow exchange with a major state conformation. J Am Chem Soc 134:8148–8161

    Article  Google Scholar 

  • Vallurupalli P, Bouvignies G, Kay LE (2013) A computational study of the effects of C-13-C-13 scalar couplings on C-13 CEST NMR spectra: towards studies on a uniformly C-13-labeled protein. Chembiochem 14:1709–1713

    Article  Google Scholar 

  • van Zijl PCM, Yadav NN (2011) Chemical exchange saturation transfer (CEST): what is in a name and what isn’t? Magn Reson Med 65:927–948

    Article  Google Scholar 

  • Varani G, Aboulela F, Allain FHT (1996) NMR investigation of RNA structure. Prog Nucl Magn Reson Spectrosc 29:51–127

    Article  Google Scholar 

  • Velyvis A, Schachman HK, Kay LE (2009) Assignment of Ile, Leu, and Val methyl correlations in supra-molecular systems: an application to aspartate transcarbamoylase. J Am Chem Soc 131:16534–16543

    Article  Google Scholar 

  • Walsh DM, Selkoe DJ (2007) A beta oligomers: a decade of discovery. J Neurochem 101:1172–1184

    Article  Google Scholar 

  • Ward KM, Aletras AH, Balaban RS (2000) A new class of contrast agents for MRI based on proton chemical exchange dependent saturation transfer (CEST). J Magn Reson 143:79–87

    Article  ADS  Google Scholar 

  • Wasylishen RE, Tomlinson G (1975) Ph-dependence of C-13 chemical-shifts and C-13, H coupling-constants in imidazole and l-histidine. Biochem J 147:605–607

    Article  Google Scholar 

  • Wishart DS, Sykes BD, Richards FM (1991) Relationship between nuclear-magnetic-resonance chemical-shift and protein secondary structure. J Mol Biol 222:311–333

    Article  Google Scholar 

  • Wuthrich K (1986) NMR of proteins and nucleic acids, 1st edn. Wiley, New York

    Google Scholar 

  • Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM (2016) Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nat Commun 7:11768

    Article  ADS  Google Scholar 

  • Yuwen T, Sekhar A, Kay LE (2016) Separating dipolar and chemical exchange magnetization transfer processes in 1H-CEST. Angew Chem Int Ed Engl. doi:10.1002/anie.201610759

    Google Scholar 

  • Zaiss M, Bachert P (2013) Chemical exchange saturation transfer (CEST) and MR Z-spectroscopy in vivo: a review of theoretical approaches and methods. Phys Med Biol 58:R221–R269

    Article  ADS  Google Scholar 

  • Zhang Y-Z (1995) Thesis: Protein and peptide structure and interactions studied by hydrogen exchange and NMR, University of Pennsylvania, PA, USA

  • Zhao B, Zhang Q (2015) Measuring residual dipolar couplings in excited conformational states of nucleic acids by CEST NMR spectroscopy. J Am Chem Soc 137:13480–13483

    Article  Google Scholar 

  • Zhao B, Hansen AL, Zhang Q (2014) Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R-1 rho NMR spectroscopy. J Am Chem Soc 136:20–23

    Article  Google Scholar 

  • Zhou Y, Yang DW (2014) Effects of J couplings and unobservable minor states on kinetics parameters extracted from CEST data. J Magn Reson 249:118–125

    Article  ADS  Google Scholar 

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Acknowledgements

This work was supported by grants from the Canadian Institutes of Health Research. L.E.K holds a Canada Research Chair in Biochemistry. P.V. is grateful to TIFR Centre for Interdisciplinary Sciences for funding. This paper is dedicated to the memory of Professor Alex Bain, McMaster University, whose pioneering contributions to the NMR chemical exchange field were highly inspirational to the authors.

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Authors and Affiliations

  1. TIFR Centre for Interdisciplinary Sciences, Hyderabad, India

    Pramodh Vallurupalli

  2. Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada

    Ashok Sekhar, Tairan Yuwen & Lewis E. Kay

  3. Hospital for Sick Children, Program in Molecular Structure and Function, Toronto, ON, Canada

    Lewis E. Kay

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  1. Pramodh Vallurupalli
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  2. Ashok Sekhar
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  3. Tairan Yuwen
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  4. Lewis E. Kay
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Correspondence to Pramodh Vallurupalli or Lewis E. Kay.

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Vallurupalli , P., Sekhar, A., Yuwen, T. et al. Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer. J Biomol NMR 67, 243–271 (2017). https://doi.org/10.1007/s10858-017-0099-4

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