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

Journal of Biomolecular NMR

Volumn 52, Issue 1, 2012, Pages 31-39

  Asami, Sam ^a   Reif, Bernd ^a,b,c  

^a LEIBNIZ INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

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

Indexed keywords

ALIPHATIC COMPOUND; PROTON;

ARTICLE; CHEMICAL PROCEDURES; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; PROTON TRANSPORT; REDUCED ADJOINING PROTONATION; SOLID STATE; THREE DIMENSIONAL IMAGING;

ANIMALS; CARBON ISOTOPES; CHICKENS; FATTY ACIDS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTONS; SPECTRIN;

EID: 84856545466     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-011-9591-4     Document Type: Article

References (47)

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 194:16-24
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 128:12620-12621 (Pubitemid 44527720)
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 130:16611-16621
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 131:2-3
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 132:3187-3195
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 46:67-73
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 12:2092-2096
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 132:15133-15135
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 95:1197-1207 (Pubitemid 128495249)
10. Bielecki A, Kolbert AC, Levitt MH (1989) Frequency-switched pulse sequences-homonuclear decoupling and dilute spin NMR in solids. Chem Phys Lett 155:341-346
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 169:39-48
12. Castellani F, van RossumB,Diehl A, Schubert M, RehbeinK,Oschkinat H (2002) Structure of a protein determined by solid-state magicangle- spinning NMR spectroscopy. Nature 420:98-102 (Pubitemid 35291447)
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 125:7788-7789 (Pubitemid 36782141)
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 45:3878-3881 (Pubitemid 44098947)
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 103:16248-16253 (Pubitemid 44715182)
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 105:4621-4626 (Pubitemid 351753796)
17. Gardner KH, Rosen MK, Kay LE (1997) Global folds of highly deuterated, methyl-protonated proteins by multidimensional NMR. Biochemistry 36:1389-1401 (Pubitemid 27074963)
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 36:2517-2530 (Pubitemid 27106644)
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 122:6268-6277 (Pubitemid 30456860)
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 12:915-918
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 99:16748-16753 (Pubitemid 36034044)
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 180:40-42
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 solidstate NMR spectroscopy. J Am Chem Soc 130:17216-17217
24. Lange A, Luca S, Baldus M (2002) Structural constraints from proton-mediated rare-spin correlation spectroscopy in rotating solids. J Am Chem Soc 124:9704-9705
25. Lemaster DM, Richards FM (1988) NMR sequential assignment of escherichia-coli thioredoxin utilizing random fractional Deuteriation. Biochemistry 27:142-150
26. Leppert J, Heise B, Ohlenschlager O, Gorlach M, Ramachandran R (2003) Broadband RFDR with adiabatic inversion pulses. J Biomol NMR 26:13-24 (Pubitemid 36553449)
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 2:151-163
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 189:209-216 (Pubitemid 350051987)
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 193:89-93
30. Linser R, Fink U, Reif B (2010) Narrow carbonyl resonances in proton-diluted proteins facilitate NMR assignments in the solidstate. J Biomol NMR 47:1-6
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 50:4508-4512
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 2:373-388
33. Marion D, Wuthrich K (1983) Application of phase sensitive twodimensional correlated spectroscopy (Cosy) for measurements of H-1-H-1 spin-spin coupling-constants in proteins. Biochem Bioph Res Co 113:967-974
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 125:15831-15836 (Pubitemid 37553700)
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 125:1488-1489 (Pubitemid 36206224)
36. Sakellariou D, Lesage A, Hodgkinson P, Emsley L (2000) Homonuclear dipolar decoupling in solid-state NMR using continuous phase modulation. Chem Phys Lett 319:253-260
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 48:9322-9325
38. Shaka AJ, Keeler J, Frenkiel T, Freeman R (1983) An improved sequence for broad-band decoupling-Waltz-16. J Magn Reson 52:335-338
39. van Rossum BJ, Castellani F, Rehbein K, Pauli J, Oschkinat H (2001) Assignment of the nonexchanging protons of the alphaspectrin 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 2:906-914
40. Vinogradov E, Madhu PK, Vega S (1999) High-resolution proton solid-state NMR spectroscopy by phase-modulated Lee-Goldburg experiment. Chem Phys Lett 314:443-450 (Pubitemid 129594703)
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 98:428-435
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 319:1523-1526 (Pubitemid 351398180)
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 crosspolarization methods for solid-state H-2 MAS NMR of perdeuterated proteins. J Phys Chem Lett 2:1289-1294
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 6:215-218
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: 8618-8626 (Pubitemid 40868243)
46. Zhou DH, Rienstra CM (2008) High-performance solvent suppression for proton detected solid-state NMR. J Magn Reson 192:167-172
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 120:7617-7625 (Pubitemid 28383424)