Advertisement

Journal of Biomolecular NMR

, Volume 63, Issue 3, pp 237–244 | Cite as

Speeding-up exchange-mediated saturation transfer experiments by Fourier transform

  • Marta G. Carneiro
  • Jithender G. Reddy
  • Christian Griesinger
  • Donghan LeeEmail author
Communication

Abstract

Protein motions over various time scales are crucial for protein function. NMR relaxation dispersion experiments play a key role in explaining these motions. However, the study of slow conformational changes with lowly populated states remained elusive. The recently developed exchange-mediated saturation transfer experiments allow the detection and characterization of such motions, but require extensive measurement time. Here we show that, by making use of Fourier transform, the total acquisition time required to measure an exchange-mediated saturation transfer profile can be reduced by twofold in case that one applies linear prediction. In addition, we demonstrate that the analytical solution for R1ρ experiments can be used for fitting the exchange-mediated saturation transfer profile. Furthermore, we show that simultaneous analysis of exchange-mediated saturation transfer profiles with two different radio-frequency field strengths is required for accurate and precise characterization of the exchange process and the exchanging states.

Keywords

CEST Chemical exchange DEST Fourier transform NMR Protein dynamics 

Notes

Acknowledgments

The authors thank L. M. I. Koharudin and A. M. Gronenborn for kindly providing 15N-labeled OAA sample. We also thank G. Bouvignies and L. E. Kay for providing a software to validate our in-house software for fitting CEST profiles. This work was supported by the James Graham Brown Foundation, the Max Planck Society and the EU (ERC Grant Agreement Number 233227 to CG).

Supplementary material

10858_2015_9985_MOESM1_ESM.docx (139 kb)
Supplementary material 1 (DOCX 140 kb)

References

  1. Baldwin A, Kay L (2013) An R1ρ expression for a spin in chemical exchange between two sites with unequal transverse relaxation rates. J Biomol NMR 55:211–218CrossRefGoogle Scholar
  2. Ban D et al (2011) Kinetics of conformational sampling in ubiquitin. Angw Chem Int Ed Engl 50:11437–11440CrossRefGoogle Scholar
  3. Ban D, Gossert AD, Giller K, Becker S, Griesinger C, Lee D (2012) Exceeding the limit of dynamics studies on biomolecules using high spin-lock field strengths with a cryogenically cooled probehead. J Magn Reson 221:1–4CrossRefADSGoogle Scholar
  4. Ban D et al (2013a) Enhanced accuracy of kinetic information from CT-CPMG experiments by transverse rotating-frame spectroscopy. J Biomol NMR 57:73–82MathSciNetCrossRefGoogle Scholar
  5. Ban D, Sabo T, Griesinger C, Lee D (2013b) Measuring dynamic and kinetic information in the previously inaccessible Supra-tc window of nanoseconds to microseconds by solution NMR spectroscopy. Molecules 18:11904–11937CrossRefGoogle Scholar
  6. Bhabha G et al (2011) A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 332:234–238CrossRefADSGoogle Scholar
  7. Carneiro MG et al (2015) Sampling of glycan-bound conformers by the anti-HIV lectin oscillatoria agardhii agglutinin in the absence of sugar. Angw Chem, Int Ed Engl 54:6462–6465CrossRefGoogle Scholar
  8. 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 6:277–293CrossRefGoogle Scholar
  9. 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 480:268–272CrossRefADSGoogle Scholar
  10. Helmus J, Jaroniec C (2013) Nmrglue: an open source Python package for the analysis of multidimensional NMR data. J Biomol NMR 55:355–367CrossRefGoogle Scholar
  11. Henzler-Wildman KA et al (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450:838–844CrossRefADSGoogle Scholar
  12. Hoch JC, Stern AS (1996) NMR data processing. Wiley-Liss, New YorkGoogle Scholar
  13. Keller RLJ (2004) The computer aided resonance assignment tutorial. CANTINA Verlag, GoldauGoogle Scholar
  14. Koharudin LMI, Furrey W, Gronenborn AM (2011) Novel fold and carbohydrate specificity of the potent anti-HIV cyanobacterial lectin from Oscillatoria agardhii. J Biol Chem 286:1588–1597CrossRefGoogle Scholar
  15. Lange OF et al (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320:1471–1475CrossRefADSGoogle Scholar
  16. Mayer M, Meyer B (1999) Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angw Chem Int Ed Engl 38:1784–1788CrossRefGoogle Scholar
  17. McConnell HM (1958) Reaction rates by nuclear magnetic resonance. J Chem Phys 28:430–431CrossRefADSGoogle Scholar
  18. Mittermaier AK, Kay LE (2009) Observing biological dynamics at atomic resolution using NMR. Trends Biochem Sci 34:601–611CrossRefGoogle Scholar
  19. Palmer AG III (2004) NMR characterization of the dynamics of biomacromolecules. Chem Rev 104:3623–3640CrossRefGoogle Scholar
  20. Palmer AG III (2014) Chemical exchange in biomacromolecules: past, present, and future. J Magn Reson 241:3–17CrossRefADSGoogle Scholar
  21. Smith CA et al (2015) Population shuffling of protein conformations. Angw Chem Int Ed Engl 54:207–210CrossRefGoogle Scholar
  22. Trott O, Palmer AG III (2002) R1ρ relaxation outside of the fast-exchange limit. J Magn Reson 154:157–160CrossRefADSGoogle Scholar
  23. Tzeng S-R, Kalodimos CG (2012) Protein activity regulation by conformational entropy. Nature 488:236–240CrossRefADSGoogle Scholar
  24. Vallurupalli P, Hansen DF, Kay LE (2008) Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. Proc Natl Acad Sci 105:11766–11771CrossRefADSGoogle Scholar
  25. Vallurupalli P, Bouvignies G, Kay LE (2012) Studying “Invisible” excited protein states in slow exchange with a major state conformation. J Am Chem Soc 134:8148–8161CrossRefGoogle Scholar
  26. 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 143:79–87CrossRefADSGoogle Scholar
  27. Zaiss M, Bachert P (2013) Exchange-dependent relaxation in the rotating frame for slow and intermediate exchange—modeling off-resonant spin-lock and chemical exchange saturation transfer. NMR Biomed 26:507–518CrossRefGoogle Scholar
  28. Zhao B, Hansen AL, Zhang Q (2014) Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R1ρ NMR spectroscopy. J Am Chem Soc 136:20–23CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Marta G. Carneiro
    • 1
  • Jithender G. Reddy
    • 1
  • Christian Griesinger
    • 1
  • Donghan Lee
    • 1
    • 2
    Email author
  1. 1.Department of NMR-based Structural BiologyMax-Planck Institute for Biophysical chemistryGoettingenGermany
  2. 2.Department of Medicine, James Graham Brown Cancer CenterUniversity of LouisvilleLouisvilleUSA

Personalised recommendations