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Journal of Biomolecular NMR

, Volume 73, Issue 3–4, pp 105–116 | Cite as

Super resolution NOESY spectra of proteins

  • Charles F. DeLisle
  • H. Bhagya Mendis
  • Justin L. LorieauEmail author
Article

Abstract

Spectral resolution remains one of the most significant limitations in the NMR study of biomolecules. We present the srNOESY (super resolution nuclear overhauser effect spectroscopy) experiment, which enhances the resolution of NOESY cross-peaks at the expense of the diagonal peak line-width. We studied two proteins, ubiquitin and the influenza hemagglutinin fusion peptide in bicelles, and we achieved average resolution enhancements of 21–47% and individual peak enhancements as large as ca. 450%. New peaks were observed over the conventional NOESY experiment in both proteins as a result of these improvements, and the final structures generated from the calculated restraints matched published models. We discuss the impact of the experimental parameters, spin diffusion and the information content of the srNOESY lineshape.

Keywords

Solution-state NMR NOESY Resolution enhancement Proteins Signal improvement SRNOESY 

Notes

Acknowledgements

This work was supported by the National Science Foundation under Grant No. 1651598 and funds from the Department of Chemistry at the University of Illinois at Chicago. This study made use of NMRbox: National Center for Biomolecular NMR Data Processing and Analysis, a Biomedical Technology Research Resource (BTRR), which is supported by NIH Grant P41GM111135 (NIGMS).

Supplementary material

10858_2019_231_MOESM1_ESM.pdf (5.1 mb)
Supplementary material 1 (PDF 5231 KB)

References

  1. Baleja JD, Moult J, Sykes BD (1990) Distance measurement and structure refinement with NOE data. J Magn Reson 87:375–384ADSGoogle Scholar
  2. 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 39:5355–5365CrossRefGoogle Scholar
  3. Borgias BA, Gochin M, Kerwood DJ, James TL (1990) Relaxation matrix analysis of 2D NMR data. Prog Nucl Magn Reson Spectrosc 22:83–100CrossRefGoogle Scholar
  4. Cavanagh J, Fairbrother W, Palmer III, Rance M, Skelton N (2007) Protein NMR principles and practice. Academic Press, Cambridge.  https://doi.org/10.1093/cid/cis040 Google Scholar
  5. Chi CN, Strotz D, Riek R, Vögeli B (2018) NOE-derived methyl distances from a 360 kDa PROTEASOME Complex. Chemistry 24:2270–2276CrossRefGoogle Scholar
  6. Cole R, Loria JP, FAST-Modelfree (2003) A program for rapid automated analysis of solution NMR spin-relaxation data. J Biomol NMR 26:203–213CrossRefGoogle Scholar
  7. Cornilescu G, Marquardt JL, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120:6836–6837CrossRefGoogle Scholar
  8. Delaglio F et al (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293CrossRefGoogle Scholar
  9. Dobson C, Olejniczak E, Poulsen F, Ratcliffe R (1982) Time development of proton nuclear overhauser effects in proteins. J Magn Reson 48:97–110ADSGoogle Scholar
  10. Ellman JA, Volkman BF, Mendel D, Schulz PG, Wemmer DE (1992) Site-specific isotopic labeling of proteins for NMR studies. J Am Chem Soc 114:7959–7961CrossRefGoogle Scholar
  11. Farrow NA et al (1994) Backbone dynamics of a free and a phosphopeptide-complexed Src homology 2 domain studied by15N NMR relaxation. Biochemistry 33:5984–6003CrossRefGoogle Scholar
  12. Goddard TD, Kneller DG (2008) SPARKY 3. University of California, San FransiscoGoogle Scholar
  13. Kalbitzer HR, Leberman R, Wittinghofer A (1985) 1H-NMR spectroscopy on elongation factor Tu from Escherichia coli: resolution enhancement by perdeuteration. FEBS Lett 180:40–42CrossRefGoogle Scholar
  14. Kay LE, Keifer P, Saarinen T (1992) Pure absorption gradient enhanced heteronucler single quantum correlation spectroscopy with improved sensitivity. J Am Chem Soc 114:10663–10665CrossRefGoogle Scholar
  15. Lee W, Tonelli M, Markley JL (2015) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31:1325–1327CrossRefGoogle Scholar
  16. LeMaster DM (1989) Deuteration in protein proton magnetic resonance. Methods Enzymol 177:23–43CrossRefGoogle Scholar
  17. LeMaster DM, Richards FM (1988) NMR sequential assignment of Escherichia coli thioredoxin utilizing random fractional deuteriation. Biochemistry 27:142–150CrossRefGoogle Scholar
  18. Lipari G, Szabo A (1982a) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J Am Chem Soc 104:4559–4570CrossRefGoogle Scholar
  19. Lipari G, Szabo A (1982b) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104:4546–4559CrossRefGoogle Scholar
  20. Lorieau JL, Louis JM, Bax A The complete influenza hemagglutinin fusion domain adopts a tight helical hairpin arrangement at the lipid:water interface. Proc Natl Acad Sci 107:11341–11346 (2010)ADSCrossRefGoogle Scholar
  21. Maciejewski MW et al (2017) NMRbox: a resource for biomolecular NMR computation. Biophys J 112:1529–1534CrossRefGoogle Scholar
  22. Macura S, Wüthrich K, Ernst RR (1982a) The relevance of J cross-peaks in two-dimensional NOE experiments of macromolecules. J Magn Reson 47:351–357ADSGoogle Scholar
  23. Macura S, Wuthrich K, Ernst RR (1982b) Separation and suppression of coherent transfer effects in two-dimensional NOE and chemical exchange spectroscopy. J Magn Reson 46:269–282ADSGoogle Scholar
  24. Marley J, Lu M, Bracken C (2001) A method for efficient isotopic labeling of recombinant proteins. J Biomol NMR 20:71–75CrossRefGoogle Scholar
  25. Muhandiram R, Kay LE (2007) Three-Dimensional HMQC-NOESY, NOESY-HMQC, and NOESY-HSQC. Encycl Magn Reson.  https://doi.org/10.1002/9780470034590.emrstm0563 Google Scholar
  26. Nelson DL, Cox MM (2013) Lehninger principles of biochemistry. W. H. Freeman and Company, New YorkGoogle Scholar
  27. Neuhaus D, Williamson MP (2000) The nuclear overhauser effect in structural and conformational analysis. Wiley, New Jersey.  https://doi.org/10.1016/0022-2364(92)90256-7 Google Scholar
  28. Ollerenshaw JE, Tugarinov V, Kay LE, Methyl TROSY (2003) Explanation and experimental verification. Magn Reson Chem 41:843–852CrossRefGoogle Scholar
  29. Otten R, Chu B, Krewulak KD, Vogel HJ, Mulder FAA (2010) Comprehensive and cost-effective NMR spectroscopy of methyl groups in large proteins. J Am Chem Soc 132:2952–2960CrossRefGoogle Scholar
  30. 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 94:12366–12371ADSCrossRefGoogle Scholar
  31. Rieping W, Bardiaux B, Bernard A, Malliavin TE, Nilges M (2007) ARIA2: automated NOE assignment and data integration in NMR structure calculation. Bioinformatics 23:381–382CrossRefGoogle Scholar
  32. Schimmel PR, Cantor CR (1980) Biophysical chemistry, part II: techniques for the study of biological structure and function. W.H. Freeman, San FranciscoGoogle Scholar
  33. Schwieters CD, Kuszewski JJ Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Prog Nucl Magn Reson Spectrosc 48:47–62CrossRefGoogle Scholar
  34. Shaka AJ, Keeler J, Frenkiel T, Freeman R (1983) An improved sequence for broadband decoupling: WALTZ-16. J Magn Reson 52:335–338ADSGoogle Scholar
  35. Smrt ST, Draney AW, Lorieau JL (2015) The influenza hemagglutinin fusion domain is an amphipathic helical hairpin that functions by inducing membrane curvature. J Biol Chem 290:228–238CrossRefGoogle Scholar
  36. Tugarinov V, Kay LE (2005) Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins. ChemBioChem 6:1567–1577CrossRefGoogle Scholar
  37. Vögeli B et al (2009) Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups. J Am Chem Soc 131:17215–17225CrossRefGoogle Scholar
  38. Vögeli B, Friedmann M, Leitz D, Sobol A, Riek R (2010) Quantitative determination of NOE rates in perdeuterated and protonated proteins: Practical and theoretical aspects. J Magn Reson 204:290–302ADSCrossRefGoogle Scholar
  39. Vuister GW, Bax A (1992) Resolution enhancement and spectral editing of uniformly 13C-enriched proteins by homonuclear broadband 13C decoupling. J Magn Reson 98:428–435ADSGoogle Scholar
  40. Weigelt J (1998) Single scan, sensitivity- and gradient-enhanced TROSY for multidimensional NMR experiments. J Am Chem Soc 120:10778–10779CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of Illinois at ChicagoChicagoUSA

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