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Journal of Biomolecular NMR

, Volume 54, Issue 4, pp 343–353 | Cite as

Spectral editing of two-dimensional magic-angle-spinning solid-state NMR spectra for protein resonance assignment and structure determination

  • K. Schmidt-Rohr
  • K. J. Fritzsching
  • S. Y. Liao
  • Mei HongEmail author
Article

Abstract

Several techniques for spectral editing of 2D 13C–13C correlation NMR of proteins are introduced. They greatly reduce the spectral overlap for five common amino acid types, thus simplifying spectral assignment and conformational analysis. The carboxyl (COO) signals of glutamate and aspartate are selected by suppressing the overlapping amide N–CO peaks through 13C–15N dipolar dephasing. The sidechain methine (CH) signals of valine, lecuine, and isoleucine are separated from the overlapping methylene (CH2) signals of long-chain amino acids using a multiple-quantum dipolar transfer technique. Both the COO and CH selection methods take advantage of improved dipolar dephasing by asymmetric rotational-echo double resonance (REDOR), where every other π-pulse is shifted from the center of a rotor period tr by about 0.15 tr. This asymmetry produces a deeper minimum in the REDOR dephasing curve and enables complete suppression of the undesired signals of immobile segments. Residual signals of mobile sidechains are positively identified by dynamics editing using recoupled 13C–1H dipolar dephasing. In all three experiments, the signals of carbons within a three-bond distance from the selected carbons are detected in the second spectral dimension via 13C spin exchange. The efficiencies of these spectral editing techniques range from 60 % for the COO and dynamic selection experiments to 25 % for the CH selection experiment, and are demonstrated on well-characterized model proteins GB1 and ubiquitin.

Keywords

Spectral editing REDOR CH selection Protein secondary structure 

Notes

Acknowledgments

We thank Professor Chad Rienstra for providing the microcrystalline 13C, 15N-labeled GB1 and Tuo Wang for help with the experiments. This work was supported by the National Institutes of Health grant GM088204 (M. H., K.J. F and S.Y. L.) for the 600 MHz NMR experiments and by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award AL-90-360-001 (to K.S-R) for the 400 MHz NMR experiments.

References

  1. Bak M, Nielsen NC (1997) REPULSION, a novel approach to efficient powder averaging in solid-state NMR. J Magn Reson 125:132–139ADSCrossRefGoogle Scholar
  2. Bax A, Szeverenyi NM, Maciel GE (1983) Chemical shift anisotropy in powdered solids studied by 2D Fourier transform NMR with flipping of the spinning axis. J Magn Reson 55:494–497Google Scholar
  3. 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
  4. Castellani F, vanRossum 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
  5. De Vita E, Frydman L (2001) Spectral editing in (13)C MAS NMR under moderately fast spinning conditions. J Magn Reson 148:327–337ADSCrossRefGoogle Scholar
  6. Etzkorn M, Martell S, Andronesi OC, Seidel K, Engelhard M, Baldus M (2007) Secondary structure, dynamics, and topology of a seven-helix receptor in native membranes, studied by solid-state NMR spectroscopy. Angew Chem Int Ed Engl 46:459–462CrossRefGoogle Scholar
  7. Fang XW, Schmidt-Rohr K (2009) Fate of the amino acid in glucose-glycine melanoidins investigated by solid-state nuclear magnetic resonance. J Agric Food Chem 57:10701–10711CrossRefGoogle Scholar
  8. Franks WT, Zhou DH, Wylie BJ, Money BG, Graesser DT, Frericks HL, Sahota G, Rienstra CM (2005a) Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR. J Am Chem Soc 127:12291–12305CrossRefGoogle Scholar
  9. Franks WT, Zhou DH, Wylie BJ, Money BG, Graesser DT, Frericks HL, Sahota G, Rienstra CM (2005b) Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis. J Am Chem Soc 127:12291–12305CrossRefGoogle Scholar
  10. Franks WT, Wylie BJ, Schmidt HL, Nieuwkoop AJ, Mayrhofer RM, Shah GJ, Graesser DT, Rienstra CM (2008) Magic-angle spinning solid-state NMR spectroscopy of the β1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis. Proc Natl Acad Sci USA 105:4621–4626ADSCrossRefGoogle Scholar
  11. Frey MH, Opella SJ (1984) 13C spin exchange in amino acids and peptides. J Am Chem Soc 106:4942–4945CrossRefGoogle Scholar
  12. Gallagher T, Alexander P, Bryan P, Gilliland GL (1994) Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. Biochemistry 33:4721–4729CrossRefGoogle Scholar
  13. Goobes G, Goobes R, Schueler-Furman O, Baker D, Stayton PS, Drobny GP (2006) Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proc Natl Acad Sci USA 103:16083–16088ADSCrossRefGoogle Scholar
  14. Gullion T, Schaefer J (1989) Rotational echo double resonance NMR. J Magn Reson 81:196–200Google Scholar
  15. Heinig M, Frishman D (2004) STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res 32, Web Server IssueGoogle Scholar
  16. Hoang QQ, Sicheri F, Howard AJ, Yang DSC (2003) Bone recognition mechanism of porcine osteocalcin from crystal structure. Nature 425:977–980ADSCrossRefGoogle Scholar
  17. Hong M (2006) Oligomeric structure, dynamics, and orientation of membrane proteins from solid-state NMR. Structure 14:1731–1740CrossRefGoogle Scholar
  18. Hong M, Zhang Y, Hu F (2012) Membrane protein structure and dynamics from NMR spectroscopy. Annu Rev Phys Chem 63:1–24ADSCrossRefGoogle Scholar
  19. Huster D, Xiao LS, Hong M (2001) Solid-state NMR investigation of the dynamics of colicin Ia channel-forming domain. Biochemistry 40:7662–7674CrossRefGoogle Scholar
  20. Igumenova TI, McDermott AE, Zilm KW, Martin RW, Paulson EK, Wand AJ (2004) Assignments of carbon NMR resonances for microcrystalline ubiquitin. J Am Chem Soc 126:6720–6727CrossRefGoogle Scholar
  21. Jehle S, Hiller M, Rehbein K, Diehl A, Oschkinat H, van Rossum BJ (2006a) Spectral editing: selection of methyl groups in multidimensional solid-state magic-angle spinning NMR. J Biomol NMR 36:169–177CrossRefGoogle Scholar
  22. Jehle S, Rehbein K, Diehl A, van Rossum BJ (2006b) Amino-acid selective experiments on uniformly 13C and 15N labeled proteins by MAS NMR: filtering of lysines and arginines. J Magn Reson 183:324–328ADSCrossRefGoogle Scholar
  23. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637CrossRefGoogle Scholar
  24. Keeler C, Maciel GE (2000) 13C NMR spectral editing of humic material. J Mol Struct 550–551:297–305CrossRefGoogle Scholar
  25. Lesage A, Steuernagel S, Emsley L (1998) Carbon-13 spectral editing in solid-state NMR using heteronuclear scalar couplings. J Am Chem Soc 120:7095–7100CrossRefGoogle Scholar
  26. Lorieau JL, Day LA, McDermott AE (2008) Conformational dynamics of an intact virus: order parameters for the coat protein of Pf1 bacteriophage. Proc Natl Acad Sci USA 105:10366–10371ADSCrossRefGoogle Scholar
  27. Luca S, Heise H, Baldus M (2003) High-resolution solid-state NMR applied to polypeptides and membrane proteins. Acc Chem Res 36:858–865CrossRefGoogle Scholar
  28. Mao JD, Schmidt-Rohr K (2004) Separation of aromatic-carbon C-13 NMR signals from di-oxygenated alkyl bands by a chemical-shift-anisotropy filter. Solid State Nucl Magn Reson 26:36–45CrossRefGoogle Scholar
  29. Mao J-D, Schmidt-Rohr K (2005) Methylene spectral editing in solid-state 13C NMR by three-spin coherence selection. J Magn Reson 176:1–6ADSCrossRefGoogle Scholar
  30. Mao J-D, Cory RM, McKnight DM, Schmidt-Rohr K (2007a) Characterization of a nitrogen-rich fulvic acid and its precursor algae by solid-state NMR. Org Geochem 38:1277–1292CrossRefGoogle Scholar
  31. Mao J-D, Tremblay L, Gagné J-P, Kohl S, Rice J, Schmidt-Rohr K (2007b) Natural organic matter in the Saguenay Fjord and the St. Lawrence Estuary investigated by advanced solid-state NMR. Geochim Cosmochim Acta 71:5483–5499ADSCrossRefGoogle Scholar
  32. Morcombe CR, Zilm KW (2003) Chemical shift referencing in MAS solid state NMR. J Magn Reson 162:479–486ADSCrossRefGoogle Scholar
  33. Pauli J, Baldus M, vanRossum B, Groot Hd, Oschkinat H (2001) Backbone and side-chain 13C and 15N signal assignments of the alpha-spectrin SH3 domain by magic-angle spinning solid-state NMR at 17.6 Tesla. ChemBioChem 2:272–281CrossRefGoogle Scholar
  34. Reggie L, Lopez JJ, Collinson I, Glaubitz C, Lorch M (2011) Dynamic nuclear polarization-enhanced solid-state NMR of a 13C-labeled signal peptide bound to lipid-reconstituted Sec translocon. J Am Chem Soc 133:19084–19086CrossRefGoogle Scholar
  35. Sakellariou D, Lesage A, Emsley L (2001) Spectral editing in solid-state NMR using scalar multiple quantum filters. J Magn Reson 151:40–47ADSCrossRefGoogle Scholar
  36. Schmidt-Rohr K, Mao J-D (2002a) Selective observation of nitrogen-bonded carbons in solid-state NMR by saturation-pulse induced dipolar exchange with recoupling. Chem Phys Lett 359:403–411ADSCrossRefGoogle Scholar
  37. Schmidt-Rohr K, Mao JD (2002b) Efficient CH-group selection and identification in C-13 solid-state NMR by dipolar DEPT and H-1 chemical-shift filtering. J Am Chem Soc 124:13938–13948CrossRefGoogle Scholar
  38. Schmidt-Rohr K, Spiess I HW (1994) Multidimensional solid-state NMR and polymers. Academic Press, San DiegoGoogle Scholar
  39. Schmidt-Rohr K, Mao JD, Olk DC (2004) Nitrogen-bonded aromatics in soil organic matter and their implications for a yield decline in intensive rice cropping. Proc Natl Acad Sci USA 101:6351–6354ADSCrossRefGoogle Scholar
  40. Sinha N, Schmidt-Rohr K, Hong H (2004) Compensation for pulse imperfections in rotational-echo double-resonance NMR by composite pulses and EXORCYCLE. J Magn Reson 168:358–365ADSCrossRefGoogle Scholar
  41. Su Y, Hong M (2011) Conformational disorder of membrane peptides investigated from solid-state NMR linewidths and lineshapes. J Phys Chem B 115:10758–10767CrossRefGoogle Scholar
  42. Takegoshi K, Nakamura S, Terao T (2001) C-13-H-1 dipolar-assisted rotational resonance in magic-angle spinning NMR. Chem Phys Lett 344:631–637ADSCrossRefGoogle Scholar
  43. Tycko R (2011) Solid-state NMR studies of amyloid fibril structure. Annu Rev Phys Chem 62:279–299ADSCrossRefGoogle Scholar
  44. Tycko R, Dabbagh G (1990) Measurement of nuclear magnetic dipole-dipole couplings in magic angle spinning NMR. Chem Phys Lett 173:461–465ADSCrossRefGoogle Scholar
  45. Veshtort M, Griffin RG (2006) SPINEVOLUTION: a powerful tool for the simulation of solid and liquid state NMR experiments. J Magn Reson 178:248–282ADSCrossRefGoogle Scholar
  46. Wishart DS, Sykes BD, Richards FM (1992) The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31:1647–1651CrossRefGoogle Scholar
  47. Wu XL, Zilm KW (1993) Spectral editing in CPMAS NMR. Generating subspectra based on proton multiplicities. J Magn Reson A 102:205–213CrossRefGoogle Scholar
  48. Wu X-L, Burns ST, Zilm KW (1994) Complete spectral editing in CPMAS NMR. J Magn Reson A 111:29–36CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • K. Schmidt-Rohr
    • 1
  • K. J. Fritzsching
    • 1
  • S. Y. Liao
    • 1
  • Mei Hong
    • 1
    Email author
  1. 1.Department of Chemistry and Ames LaboratoryIowa State UniversityAmesUSA

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