Advertisement

Journal of Biomolecular NMR

, Volume 52, Issue 1, pp 31–39 | Cite as

Assignment strategies for aliphatic protons in the solid-state in randomly protonated proteins

  • Sam Asami
  • Bernd ReifEmail author
Article

Abstract

Biological solid-state nuclear magnetic resonance spectroscopy developed rapidly in the past two decades and emerged as an important tool for structural biology. Resonance assignment is an essential prerequisite for structure determination and the characterization of motional properties of a molecule. Experiments, which rely on carbon or nitrogen detection, suffer, however, from low sensitivity. Recently, we introduced the RAP (Reduced Adjoining Protonation) labeling scheme, which allows to detect backbone and sidechain protons with high sensitivity and resolution. We present here a 1H-detected 3D (H)CCH experiment for assignment of backbone and sidechain proton resonances. Resolution is significantly improved by employing simultaneous 13CO and 13J-decoupling during evolution of the 13Cα chemical shift. In total, ~90% of the 1Hα-13Cα backbone resonances of chicken α-spectrin SH3 could be assigned.

Keywords

Magic angle spinning (MAS) solid-state NMR Perdeuteration 2H-labeling Side chain assignment strategies 

Notes

Acknowledgments

This research was supported by the Leibniz-Gemeinschaft, the Helmholtz-Gemeinschaft and the DFG (Re1435, SFB449, SFB740). We are grateful to the Center for Integrated Protein Science Munich (CIPS-M) for financial support. We thank W. Bermel for providing Bruker shaped files for scalar homonuclear carbon decoupling.

Supplementary material

10858_2011_9591_MOESM1_ESM.pdf (82 kb)
Supplementary material 1 (PDF 81 kb)

References

  1. Agarwal V, Reif B (2008) Residual methyl protonation in perdeuterated proteins for multi-dimensional correlation experiments in MAS solid-state NMR spectroscopy. J Magn Reson 194:16–24ADSCrossRefGoogle Scholar
  2. Agarwal V, Diehl A, Skrynnikov N, Reif B (2006) High resolution H-1 detected H-1, C-13 correlation spectra in MAS solid-state NMR using deuterated proteins with selective H-1, H-2 isotopic labeling of methyl groups. J Am Chem Soc 128:12620–12621CrossRefGoogle Scholar
  3. Agarwal V, Xue Y, Reif B, Skrynnikov NR (2008) Protein side-chain dynamics as observed by solution- and solid-state NMR spectroscopy: a similarity revealed. J Am Chem Soc 130:16611–16621CrossRefGoogle Scholar
  4. Agarwal V, Faelber K, Schmieder P, Reif B (2009) High-resolution double-quantum deuterium magic angle spinning solid-state NMR spectroscopy of perdeuterated proteins. J Am Chem Soc 131:2-+Google Scholar
  5. Agarwal V, Linser R, Fink U, Faelber K, Reif B (2010) Identification of hydroxyl protons, determination of their exchange dynamics, and characterization of hydrogen bonding in a microcrystallin protein. J Am Chem Soc 132:3187–3195CrossRefGoogle Scholar
  6. Akbey U, Lange S, Franks WT, Linser R, Rehbein K, Diehl A, van Rossum BJ, Reif B, Oschkinat H (2010) Optimum levels of exchangeable protons in perdeuterated proteins for proton detection in MAS solid-state NMR spectroscopy. J Biomol NMR 46:67–73CrossRefGoogle Scholar
  7. Akbey U, Camponeschi F, van Rossum BJ, Oschkinat H (2011) Triple resonance cross-polarization for more sensitive (13)C MAS NMR spectroscopy of deuterated proteins. ChemPhysChem 12:2092–2096CrossRefGoogle Scholar
  8. Asami S, Schmieder P, Reif B (2010) High resolution H-1-detected solid-state NMR spectroscopy of protein aliphatic resonances: access to tertiary structure information. J Am Chem Soc 132:15133–15135CrossRefGoogle Scholar
  9. Baldus M, Petkova AT, Herzfeld J, Griffin RG (1998) Cross polarization in the tilted frame: assignment and spectral simplification in heteronuclear spin systems. Mol Phys 95:1197–1207ADSCrossRefGoogle Scholar
  10. Bielecki A, Kolbert AC, Levitt MH (1989) Frequency-switched pulse sequences—homonuclear decoupling and dilute spin NMR in solids. Chem Phys Lett 155:341–346ADSCrossRefGoogle Scholar
  11. Bosman L, Madhu PK, Vega S, Vinogradov E (2004) Improvement of homonuclear dipolar decoupling sequences in solid-state nuclear magnetic resonance utilising radiofrequency imperfections. J Magn Reson 169:39–48ADSCrossRefGoogle Scholar
  12. Castellani F, van Rossum B, Diehl A, Schubert M, Rehbein K, Oschkinat H (2002) Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy. Nature 420:98–102ADSCrossRefGoogle Scholar
  13. Chevelkov V, van Rossum BJ, Castellani F, Rehbein K, Diehl A, Hohwy M, Steuernagel S, Engelke F, Oschkinat H, Reif B (2003) H-1 detection in MAS solid-state NMR Spectroscopy of biomacromolecules employing pulsed field gradients for residual solvent suppression. J Am Chem Soc 125:7788–7789CrossRefGoogle Scholar
  14. Chevelkov V, Rehbein K, Diehl A, Reif B (2006) Ultrahigh resolution in proton solid-state NMR spectroscopy at high levels of deuteration. Angew Chem Int Ed 45:3878–3881CrossRefGoogle Scholar
  15. Ferguson N, Becker J, Tidow H, Tremmel S, Sharpe TD, Krause G, Flinders J, Petrovich M, Berriman J, Oschkinat H, Fersht AR (2006) General structural motifs of amyloid protofilaments. Proc Natl Acad Sci USA 103:16248–16253ADSCrossRefGoogle Scholar
  16. Franks WT, Wylie BJ, Schmidt HLF, Nieuwkoop AJ, Mayrhofer RM, Shah GJ, Graesser DT, Rienstra CM (2008) Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR. Proc Natl Acad Sci USA 105:4621–4626ADSCrossRefGoogle Scholar
  17. Gardner KH, Rosen MK, Kay LE (1997) Global folds of highly deuterated, methyl-protonated proteins by multidimensional NMR. Biochemistry 36:1389–1401CrossRefGoogle Scholar
  18. Garrett DS, Seok YJ, Liao DI, Peterkofsky A, Gronenborn AM, Clore GM (1997) Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system by multidimensional NMR. Biochemistry 36:2517–2530CrossRefGoogle Scholar
  19. Hennig M, Bermel W, Schwalbe H, Griesinger C (2000) Determination of psi torsion angle restraints from (3)J(C-alpha, C-alpha) and 3 J(C-alpha, H-N) coupling constants in proteins. J Am Chem Soc 122:6268–6277CrossRefGoogle Scholar
  20. Huber M, Hiller S, Schanda P, Ernst M, Bockmann A, Verel R, Meier BH (2011) A proton-detected 4D solid-state NMR experiment for protein structure determination. ChemPhysChem 12:915–918CrossRefGoogle Scholar
  21. Jaroniec CP, MacPhee CE, Astrof NS, Dobson CM, Griffin RG (2002) Molecular conformation of a peptide fragment of transthyretin in an amyloid fibril. Proc Natl Acad Sci USA 99:16748–16753ADSCrossRefGoogle Scholar
  22. Kalbitzer HR, Leberman R, Wittinghofer A (1985) H-1-NMR spectroscopy on elongation-factor Tu from Escherichia coli—resolution enhancement by Perdeuteration. FEBS Lett 180:40–42CrossRefGoogle Scholar
  23. Laage S, Marchetti A, Sein J, Pierattelli R, Sass HJ, Grzesiek S, Lesage A, Pintacuda G, Emsley L (2008) Band-selective 1H–13C cross-polarization in fast magic angle spinning solid-state NMR spectroscopy. J Am Chem Soc 130:17216–17217CrossRefGoogle Scholar
  24. Lange A, Luca S, Baldus M (2002) Structural constraints from proton-mediated rare-spin correlation spectroscopy in rotating solids. J Am Chem Soc 124:9704–9705CrossRefGoogle Scholar
  25. Lemaster DM, Richards FM (1988) NMR sequential assignment of escherichia-coli thioredoxin utilizing random fractional Deuteriation. Biochemistry 27:142–150CrossRefGoogle Scholar
  26. Leppert J, Heise B, Ohlenschlager O, Gorlach M, Ramachandran R (2003) Broadband RFDR with adiabatic inversion pulses. J Biomol NMR 26:13–24CrossRefGoogle Scholar
  27. Levitt MH, Kolbert AC, Bielecki A, Ruben DJ (1993) High-resolution H-1-NMR in solids with frequency-switched multiple-pulse sequences. Solid State Nucl Mag 2:151–163CrossRefGoogle Scholar
  28. Linser R, Chevelkov V, Diehl A, Reif B (2007) Sensitivity enhancement using paramagnetic relaxation in MAS solid-state NMR of perdeuterated proteins. J Magn Reson 189:209–216ADSCrossRefGoogle Scholar
  29. Linser R, Fink U, Reif B (2008) Proton-detected scalar coupling based assignment strategies in MAS solid-state NMR spectroscopy applied to perdeuterated proteins. J Magn Reson 193:89–93ADSCrossRefGoogle Scholar
  30. Linser R, Fink U, Reif B (2010) Narrow carbonyl resonances in proton-diluted proteins facilitate NMR assignments in the solid-state. J Biomol NMR 47:1–6CrossRefGoogle Scholar
  31. Linser R, Dasari M, Hiller M, Higman V, Fink U, Lopez Del Amo JM, Markovic S, Handel L, Kessler B, Schmieder P, Oesterhelt D, Oschkinat H, Reif B (2011) Proton-detected solid-state NMR spectroscopy of fibrillar and membrane proteins. Angew Chem Int Ed Engl 50:4508–4512CrossRefGoogle Scholar
  32. Liu YJ, Zhao DQ, Altman R, Jardetzky O (1992) A systematic comparison of 3 structure determination methods from NMR data—dependence upon quality and quantity of data. J Biomol NMR 2:373–388CrossRefGoogle Scholar
  33. Marion D, Wuthrich K (1983) Application of phase sensitive two-dimensional correlated spectroscopy (Cosy) for measurements of H-1-H-1 spin–spin coupling-constants in proteins. Biochem Bioph Res Co 113:967–974CrossRefGoogle Scholar
  34. Paulson EK, Morcombe CR, Gaponenko V, Dancheck B, Byrd RA, Zilm KW (2003) Sensitive high resolution inverse detection NMR spectroscopy of proteins in the solid state. J Am Chem Soc 125:15831–15836CrossRefGoogle Scholar
  35. Reif B, van Rossum BJ, Castellani F, Rehbein K, Diehl A, Oschkinat H (2003) Characterization of H-1-H-1 distances in a uniformly H-2, N-15-labeled SH3 domain by MAS solid-state NMR spectroscopy. J Am Chem Soc 125:1488–1489CrossRefGoogle Scholar
  36. Sakellariou D, Lesage A, Hodgkinson P, Emsley L (2000) Homonuclear dipolar decoupling in solid-state NMR using continuous phase modulation. Chem Phys Lett 319:253–260ADSCrossRefGoogle Scholar
  37. Schanda P, Huber M, Verel R, Ernst M, Meier BH (2009) Direct detection of (3 h)J(NC ‘) hydrogen-bond scalar couplings in proteins by solid-state NMR spectroscopy. Angew Chem Int Ed 48:9322–9325CrossRefGoogle Scholar
  38. Shaka AJ, Keeler J, Frenkiel T, Freeman R (1983) An improved sequence for broad-band decoupling—Waltz-16. J Magn Reson 52:335–338Google Scholar
  39. van Rossum BJ, Castellani F, Rehbein K, Pauli J, Oschkinat H (2001) Assignment of the nonexchanging protons of the alpha-spectrin SH3 domain by two- and three-dimensional H-1-C-13 solid-state magic-angle spinning NMR and comparison of solution and solid-state proton chemical shifts. Chembiochem 2:906–914CrossRefGoogle Scholar
  40. Vinogradov E, Madhu PK, Vega S (1999) High-resolution proton solid-state NMR spectroscopy by phase-modulated Lee-Goldburg experiment. Chem Phys Lett 314:443–450ADSCrossRefGoogle Scholar
  41. Vuister GW, Bax A (1992) Resolution enhancement and spectral editing of uniformly C-13-enriched proteins by homonuclear broad-band C-13 decoupling. J Magn Reson 98:428–435Google Scholar
  42. Wasmer C, Lange A, Van Melckebeke H, Siemer AB, Riek R, Meier BH (2008) Amyloid fibrils of the HET-s(218–289) prion form a beta solenoid with a triangular hydrophobic core. Science 319:1523–1526ADSCrossRefGoogle Scholar
  43. Wei DX, Akbey U, Paaske B, Oschkinat H, Reif B, Bjerring M, Nielsen NC (2011) Optimal H-2 rf pulses and H-2-C-13 cross-polarization methods for solid-state H-2 MAS NMR of perdeuterated proteins. J Phys Chem Lett 2:1289–1294CrossRefGoogle Scholar
  44. Wickramasinghe NP, Parthasarathy S, Jones CR, Bhardwaj C, Long F, Kotecha M, Mehboob S, Fung LW, Past J, Samoson A, Ishii Y (2009) Nanomole-scale protein solid-state NMR by breaking intrinsic 1HT1 boundaries. Nat Methods 6:215–218CrossRefGoogle Scholar
  45. Zech SG, Wand AJ, McDermott AE (2005) Protein structure determination by high-resolution solid-state NMR spectroscopy: application to microcrystalline ubiquitin. J Am Chem Soc 127:8618–8626CrossRefGoogle Scholar
  46. Zhou DH, Rienstra CM (2008) High-performance solvent suppression for proton detected solid-state NMR. J Magn Reson 192:167–172ADSCrossRefGoogle Scholar
  47. Zwahlen C, Gardner KH, Sarma SP, Horita DA, Byrd RA, Kay LE (1998) An NMR experiment for measuring methyl–methyl NOEs in C-13-labeled proteins with high resolution. J Am Chem Soc 120:7617–7625CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Leibniz-Institut für Molekulare Pharmakologie (FMP)BerlinGermany
  2. 2.Department of Chemistry (CIPS-M), Munich Center for Integrated Protein ScienceTechnische Universität München (TUM)GarchingGermany
  3. 3.Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU)NeuherbergGermany

Personalised recommendations