Abstract
A brief overview of theoretical and experimental aspects of the Dark state Exchange Saturation Transfer (DEST) and lifetime line broadening (\(\Delta R_{2}^{{}}\)) NMR methodologies is presented from a physico-chemical perspective. We describe how the field-dependence of \(\Delta R_{2}^{{}}\) can be used for determining the exchange regime on the transverse spin relaxation time-scale. Some limitations of DEST/\(\Delta R_{2}^{{}}\) methodology in applications to molecular systems with intermediate molecular weights are discussed, and the means of overcoming these limitations via the use of closely related exchange NMR techniques is presented. Finally, several applications of DEST/\(\Delta R_{2}^{{}}\) methodology are described from a methodological viewpoint, with an emphasis on providing examples of how kinetic and relaxation parameters of exchange can be reliably extracted from the experimental data in each particular case.
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References
Abragam A (1961) Principles of nuclear magnetism. Clarendon Press, Oxford
Anet FAL, Basus VJ (1969) Limiting equations for exchange broadening in two-site nmr systems with very unequal populations. J Magn Reson 32:339–343
Anthis NJ, Clore GM (2015) Visualizing transient dark states by NMR spectroscopy. Q Rev Biophys 48:35–116
Baldwin AJ (2014) An exact solution for R 2,eff in CPMG experiments in the case of two site chemical exchange. J Magn Reson 244:114–124
Baldwin AJ, Kay LE (2013) AR 1ρ expression for a spin in chemical exchange between two sites with unequal transverse relaxation rates. J Biomol NMR 55:211–218
Carver JP, Richards RE (1972) General two-site solution for chemical exchange produced dependence of T2 upon Carr–Purcell pulse separation. J Magn Reson 6:89–105
Ceccon A, Lelli M, D’Onofrio M, Molinari H, Assfalg M (2014) Dynamics of a globular protein adsorbed to liposomal nanoparticles. J Am Chem Soc 136:13158–13161
Ceccon A, Clore GM, Tugarinov V (2016a) Towards interpretation of intermolecular paramagnetic relaxation enhancement outside the fast exchange limit. J Biomol NMR 66:1–7
Ceccon A, Tugarinov V, Bax A, Clore GM (2016b) Global dynamics and exchange kinetics of a protein on the surface of nanoparticles revealed by relaxation-based solution NMR spectroscopy. J Am Chem Soc 138:5789–5792
Ceccon A, Tugarinov V, Boughton AJ, Fushman D, Clore GM (2017) Probing the binding modes of a multidomain protein to lipid-based nanoparticles by relaxation-based NMR. J Phys Chem Lett 8:2535–2540
Ceccon A, Clore GM, Tugarinov V (2018a) Decorrelating kinetic and relaxation parameters in exchange saturation transfer NMR: a case study of N-terminal huntingtin peptides binding to unilamellar lipid vesicles. J Phys Chem B 122:11271–11278
Ceccon A, Schmidt T, Tugarinov V, Kotler SA, Schwieters CD, Clore GM (2018b) Interaction of huntingtin exon-1 peptides with lipid-based micellar nanoparticles probed by solution NMR and Q-band pulsed EPR. J Am Chem Soc 140:6199–6202
Ceccon A, Tugarinov V, Clore GM (2019) TiO2 nanoparticles catalyze oxidation of huntingtin exon 1-derived peptides impeding aggregation: a quantitative NMR study of binding and kinetics. J Am Chem Soc 141:94–97
Conicella AE, Fawzi NL (2014) The C-terminal threonine of Aβ43 nucleates toxic aggregation via structural and dynamical changes in monomers and protofibrils. Biochemistry 53:3095–3105
Davis DG, Perlman ME, London RE (1994) Direct measurements of the dissociation-rate constant for inhibitor-enzyme complexes via the T1 and T2(CPMG) methods. J Magn Reson Ser B 104:266–275
Egner TK, Naik P, Nelson NC, Slowing II, Venditti V (2017) Mechanistic insight into nanoparticle surface adsorption by solution NMR spectroscopy in an aqueous gel. Angew Chem Int Ed Engl 56:9802–9806
Fawzi NL, Ying J, Torchia DA, Clore GM (2010) Kinetics of amyloid β monomer-to-oligomer exchange by NMR relaxation. J Am Chem Soc 132:9948–9951
Fawzi NL, Ying J, Ghirlando R, Torchia DA, Clore GM (2011) Atomic-resolution dynamics on the surface of amyloid-β protofibrils probed by solution NMR. Nature 480:268–272
Fawzi NL, Ying J, Torchia DA, Clore GM (2012) Probing exchange kinetics and atomic resolution dynamics in high-molecular-weight complexes using dark-state exchange saturation transfer NMR spectroscopy. Nat Protoc 7:1523–1533
Fawzi NL, Libich DS, Ying J, Tugarinov V, Clore GM (2014) Characterizing methyl-bearing side chain contacts and dynamics mediating amyloid β protofibril interactions using 13Cmethyl-DEST and lifetime line broadening. Angew Chem Int Ed Engl 53:10345–10349
Helgstrand M, Hard T, Allard P (2000) Simulations of NMR pulse sequences during equilibrium and non-equilibrium chemical exchange. J Biomol NMR 18:49–63
Libich DS, Fawzi NL, Ying J, 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
Libich DS, Tugarinov V, Clore GM (2015) Intrinsic unfoldase/foldase activity of the chaperonin GroEL directly demonstrated using multinuclear relaxation-basedNMR. Proc Natl Acad Sci USA 112:8817–8823
Libich DS, Tugarinov V, Ghirlando R, Clore GM (2017) Confinement and stabilization of Fyn SH3 folding intermediate mimetics within the cavity of the chaperonin GroEL demonstrated by relaxation-based NMR. Biochemistry 56:903–906
McConnell HM (1958) Reaction rates by nuclear magnetic resonance. J Chem Phys 28:430–431
Meiboom S, Gill D (1958) Modified spin-echo method for measuring nuclear relaxation times. Rev Sci Instrum 29:688–691
Millet O, Loria PJ, 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
Mulder FA, Hon B, Muhandiram DR, Dahlquist FW, Kay LE (2000) Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by multinuclear NMR. Biochemistry 39:12614–12622
Palmer AG (2014) Chemical exchange in biomacromolecules: past, present, and future. J Magn Reson 241:3–17
Skrynnikov NR, Dahlquist FW, Kay LE (2002) Reconstructing NMR spectra of “invisible” excited protein states using HSQC and HMQC experiments. J Am Chem Soc 124:12352–12360
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
Wälti MA, Steiner J, Meng F, Chung HS, Louis JM, Ghirlando R, Tugarinov V, Nath A, Clore GM (2018) Probing the mechanism of inhibition of amyloid-β(1–42)-induced neurotoxicity by the chaperonin GroEL. Proc Natl Acad Sci USA 115:E11924–E11932
Yuwen T, Brady JP, Kay LE (2018) Probing conformational exchange in weakly interacting, slowly exchanging protein systems via off-resonance R 1ρ experiments: Application to studies of protein phase separation. J Am Chem Soc 140:2115–2126
Acknowledgements
This mini-review is dedicated to our colleague and long-time friend, Dr. Dennis A. Torchia on the occasion of his 80th birthday. This work was supported by funds from the Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (G.M.C.).
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Tugarinov, V., Clore, G.M. Exchange saturation transfer and associated NMR techniques for studies of protein interactions involving high-molecular-weight systems. J Biomol NMR 73, 461–469 (2019). https://doi.org/10.1007/s10858-019-00244-6
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DOI: https://doi.org/10.1007/s10858-019-00244-6