Ahlner A, Carlsson M, Jonsson BH, Lundstrom P (2013) PINT: a software for integration of peak volumes and extraction of relaxation rates. J Biomol NMR 56:191–202

Article  Google Scholar 

Allen M, Friedler A, Schon O, Bycroft M (2002) The structure of an FF domain from human HYPA/FBP11. J Mol Biol 323:411–416

Article  Google Scholar 

Allerhand A, Thiele E (1966) Analysis of Carr-Purcell spin-echo NMR experiments on multiple-spin systems. II. The effect of chemical exchange. J Chem Phys 45:902–916

Article  ADS  Google Scholar 

Anthis NJ, Clore GM (2015) Visualizing transient dark states by NMR spectroscopy. Q Rev Biophys 48:35–116

Article  Google Scholar 

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 R(1rho) NMR spectroscopy. J Am Chem Soc 131:10832–10833

Article  Google Scholar 

Bahar I, Jernigan R, Dill KA (2017) Protein actions: principles and modeling. Garland Science, Taylor & Francis Group, New York

Google Scholar 

Bezsonova I, Korzhnev DM, Prosser RS, Forman-Kay JD, Kay LE (2006) Hydration and packing along the folding pathway of SH3 domains by pressure-dependent NMR. Biochemistry 45:4711–4719

Article  Google Scholar 

Bouvignies G (2011) ChemEx. https://github.com/gbouvignies/chemex

Bouvignies G, Kay LE (2012) A 2D (1)(3)C-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, 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 

Cabrera Allpas R, Hansen AL, Bruschweiler R (2023) ARCHE-NOAH: NMR supersequence with five different CEST experiments for studying protein conformational dynamics. Phys Chem Chem Phys 25:16217–16221

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, New York

Google Scholar 

Choy WY, Zhou Z, Bai Y, Kay LE (2005) An 15N NMR spin relaxation dispersion study of the folding of a pair of engineered mutants of apocytochrome b562. J Am Chem Soc 127:5066–5072

Article  Google Scholar 

Chung HS, Piana-Agostinetti S, Shaw DE, Eaton WA (2015) Structural origin of slow diffusion in protein folding. Science 349:1504–1510

Article  ADS  Google Scholar 

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 6:277–293

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

Article  ADS  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 

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 

Goddard TD, Kneller DG (2008) SPARKY 3. University of California, San Francisco

Google Scholar 

Gopalan AB, Vallurupalli P (2018) Measuring the signs of the methyl 1H chemical shift differences between major and ‘invisible’ minor protein conformational states using methyl 1H multi-quantum spectroscopy. J Biomol NMR 70:187–202

Article  Google Scholar 

Gopalan AB, Hansen DF, Vallurupalli P (2018a) CPMG experiments for protein minor conformer structure determination. Methods Mol Biol 1688:223–242

Article  Google Scholar 

Gopalan AB, Yuwen T, Kay LE, Vallurupalli P (2018b) A methyl (1)H double quantum CPMG experiment to study protein conformational exchange. J Biomol NMR 72:79–91

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 

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  ADS  Google Scholar 

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

Article  ADS  Google Scholar 

Hansen DF, Vallurupalli P, Kay LE (2008) An improved 15N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins. J Phys Chem B 112:5898–5904

Article  Google Scholar 

Hansen DF, Vallurupalli P, Kay LE (2009) Measurement of methyl group motional parameters of invisible, excited protein states by NMR spectroscopy. J Am Chem Soc 131:12745–12754

Article  Google Scholar 

Jemth P, Gianni S, Day R, Li B, Johnson CM, Daggett V, Fersht AR (2004) Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation. Proc Natl Acad Sci USA 101:6450–6455

Article  ADS  Google Scholar 

Jemth P, Johnson CM, Gianni S, Fersht AR (2008) Demonstration by burst-phase analysis of a robust folding intermediate in the FF domain. Protein Eng Des Sel 21:207–214

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 

Karunanithy G, Reinstein J, Hansen DF (2020) Multiquantum chemical exchange saturation transfer NMR to quantify symmetrical exchange: application to rotational dynamics of the guanidinium group in arginine side chains. J Phys Chem Lett 11:5649–5654

Article  Google Scholar 

Khandave NP, Sekhar A, Vallurupalli P (2023) Studying micro to millisecond protein dynamics using simple amide (15)N CEST experiments supplemented with major-state R(2) and visible peak-position constraints. J Biomol NMR 77(4):165–181

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, Neudecker P, Mittermaier A, Orekhov VY, Kay LE (2005) Multiple-site exchange in proteins studied with a suite of six NMR relaxation dispersion experiments: an application to the folding of a Fyn SH3 domain mutant. J Am Chem Soc 127:15602–15611

Article  Google Scholar 

Korzhnev DM, Religa TL, Lundstrom P, Fersht AR, Kay LE (2007) The folding pathway of an FF domain: characterization of an on-pathway intermediate state under folding conditions by (15)N, (13)C(alpha) and (13)C-methyl relaxation dispersion and (1)H/(2)H-exchange NMR spectroscopy. J Mol Biol 372:497–512

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 

Koss H, Rance M, Palmer AG (2017) General expressions for R1rho relaxation for N-site chemical exchange and the special case of linear chains. J Magn Reson 274:36–45

Article  ADS  Google Scholar 

Koss H, Crawley T, Palmer AG III (2023) Site-based description of R(1)(rho) relaxation in local reference frames. J Magn Reson 347:107366

Article  Google Scholar 

Kukic P, Pustovalova Y, Camilloni C, Gianni S, Korzhnev DM, Vendruscolo M (2017) Structural characterization of the early events in the nucleation-condensation mechanism in a protein folding process. J Am Chem Soc 139:6899–6910

Article  Google Scholar 

Lee W, Tonelli M, Markley JL (2015) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31:1325–1327

Article  Google Scholar 

Levitt MH (1982) Symmetrical composite pulse sequences for NMR population-inversion. 2. Compensation of resonance offset. J Magn Reson 50:95–110

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 Ed Engl 53:2358–2361

Article  Google Scholar 

Madhurima K, Nandi B, Munshi S, Naganathan AN, Sekhar A (2023) Functional regulation of an intrinsically disordered protein via a conformationally excited state. Sci Adv 9:eadh4591

Article  Google Scholar 

Massi F, Grey MJ, Palmer AG 3rd (2005) Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments. Protein Sci 14:735–742

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