Speeding up the measurement of one-bond scalar ( 1J) and residual dipolar couplings ( 1D) by using non-uniform sampling (NUS)

Journal of Magnetic Resonance

Volumn 216, Issue , 2012, Pages 134-143

  Thiele, Christina M ^a   Bermel, Wolfgang ^b  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

^b BRUKER BIOSPIN GMBH   (Germany)

Author keywords

Compressed sensing; Coupling constant measurement; J scaling; NMR; Non uniform sampling; Partial alignment

Indexed keywords

COMPRESSED SENSING; COUPLING CONSTANTS; J-SCALING; NONUNIFORM SAMPLING; PARTIAL ALIGNMENT;

NUCLEAR MAGNETIC RESONANCE; SIGNAL RECONSTRUCTION; TENSORS;

MEASUREMENTS;

EID: 84858336677     PISSN: 10907807     EISSN: 10960856     Source Type: Journal    
DOI: 10.1016/j.jmr.2012.01.008     Document Type: Article

References (55)

1. N. Tjandra, and A. Bax Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium Science 278 1997 1111 1114 (Pubitemid 27517889)
2. For some reviews on the use of RDCs in biomolecular NMR see: M. Blackledge Recent progress in the study of biomolecular structure and dynamics in solution from residual dipolar couplings Prog. Nucl. Magn. Reson. Spectrosc. 46 2005 23 61 (Pubitemid 40357061)
3. J.R. Tolman, and K. Ruan NMR residual dipolar couplings as probes of biomolecular dynamics Chem. Rev. 106 2006 1720 1736 (Pubitemid 43792777)
4. A. Annila, and P. Permi Weakly aligned biological macromolecules in dilute aqueous liquid crystals Concepts Magn. Reson. 23A 2004 22 37 (Pubitemid 40646216)
5. A. Saupe Kernresonanzen in kristallinen Flüssigkeiten und in kristallinflüssigen Lösungen I Z. Naturforsch., A 19 1964 161 171
6. E.E. Burnell, and C.A. de Lange NMR of Ordered Liquids 2003 Kluwer Academic Publishers Dordrecht
7. C.M. Thiele, and S. Berger Probing the diastereotopicity of methylene protons in strychnine using residual dipolar couplings Org. Lett. 5 2003 705 708 (Pubitemid 37141084)
8. For some reviews on applications of RDCs see: C.M. Thiele Use of RDCs in rigid organic compounds and some practical considerations concerning alignment media Concepts Magn. Reson. A 30 2007 65 80
9. C.M. Thiele Residual dipolar couplings (RDCs) in organic structure determination Eur. J. Org. Chem. 34 2008 5673 5685
10. G. Kummerlöwe, and B. Luy Residual dipolar couplings as a tool in determining the structure of organic molecules Trends Anal. Chem. 28 2009 483 493
11. G. Kummerlöwe, and B. Luy Residual dipolar couplings for the configurational andconformational analysis of organic molecules Annu. Rep. NMR Spectrosc. 68 2009 193 232
12. B. Böttcher, C.M. Thiele, Determining the stereochemistry of molecules from residual dipolar couplings, in: D.M. Grant, R.K. Harris (Eds.), Encyclopedia of Magnetic Resonance, doi:10.1002/9780470034590.emrstm1194.pub2.
13. M. Ottiger, F. Delaglio, and A. Bax Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra J. Magn. Reson. 131 1998 373 378 (Pubitemid 128450579)
14. P. Andersson, J. Weigelt, and G. Otting Spin-state selection filters for the measurement of heteronuclear one-bond coupling constants J. Biomol. NMR 12 1998 435 441 (Pubitemid 128511309)
15. M.D. Sørensen, A. Meissner, and O.W. Sørensen 13C natural abundance S3E and S3CT experiments for measurement of J coupling constants between 13Cα or 1Hα and other protons in a protein J. Magn. Reson. 137 1999 237 242
16. T. Carlomagno, W. Peti, and C. Griesinger A new method for the simultaneous measurement of magnitude and sign of 1DCH and 1DHH dipolar couplings in methylene groups J. Biomol. NMR 17 2000 99 109 (Pubitemid 30452330)
17. P. Permi A spin-state selective experiment for measuring heteronuclear one-bond and homonuclear two-bond couplings from an HSQC-type spectrum J. Biomol. NMR 22 2002 27 35 (Pubitemid 34162449)
18. P. Nolis, J.F. Espinosa, and T. Parella Optimum spin-state selection for all multiplicities in the acquisition dimension of the HSQC experiment J. Magn. Reson. 180 2006 39 50
19. P. Tzvetkova, S. Simova, and B. Luy P.E: HSQC: a simple experiment for the simultaneous and sign-sensitive measurement of (1JCH + DCH) and (2JHH + DHH) couplings J. Magn. Reson. 186 2007 193 200 (Pubitemid 46880426)
20. W. Koźmiński, and D. Nanz Sensitivity improvement and new acquisition scheme of heteronuclear active-coupling-pattern-tilting spectroscopy J. Magn. Reson. 142 2000 294 299
21. J.L. Yan, A.D. Kline, H.P. Mo, M.J. Shapiro, and E.R. Zartler A novel method for the determination of stereochemistry in six-membered chairlike rings using residual dipolar couplings J. Org. Chem. 68 2003 1786 1795 (Pubitemid 36504830)
22. A. Enthart, J.C. Freudenberger, J. Furrer, H. Kessler, and B. Luy The CLIP/CLAP-HSQC: pure absorptive spectra for the measurement of one-bond couplings J. Magn. Reson. 192 2008 314 322
23. J.R. Tolman, and J.H. Prestegard Measurement of amide 15N-1H one-bond couplings in proteins using accordion heteronuclear-shift-correlation experiments J. Magn. Reson. B112 1996 269 274 (Pubitemid 126758734)
24. N. Tjandra, S. Grzesiek, and Bax Magnetic field dependence of nitrogen-proton J splittings in N-15-enriched human ubiquitin resulting from relaxation interference and residual dipolar coupling J. Am. Chem. Soc. 118 1996 6264 6272 (Pubitemid 26236864)
25. K. Fehér, S. Berger, and K.E. Kövér Accurate determination of small one-bond heteronuclear residual dipolar couplings by F1 coupled HSQC modified with a G-BIRD(r) module J. Magn. Reson. 163 2003 340 346
26. T.N. Pham, T. Liptaj, K. Bromek, and D. Uhrín Measurement of small one-bond proton-carbon residual dipolar coupling constants in partially oriented carbon-13 natural abundance oligosaccharide samples: analysis of heteronuclear (1)J(CH)-modulated spectra with the BIRD inversion pulse J. Magn. Reson. 157 2002 200 209
27. D. Uhrín, T. Liptaj, and K.E. Kövér Modified BIRD pulses and design of heteronuclear pulse sequences J. Magn. Reson. A101 1993 41 46
28. J.C.J. Barna, E.D. Laue, M.R. Mayger, J. Skilling, and S.J.P. Worrall Exponential sampling, an alternative method for sampling in two-dimensional NMR experiments J. Magn. Reson. 73 1987 69 77
29. P. Schmieder, A.S. Stern, G. Wagner, and J.C. Hoch Application of non-linear sampling schemes to COSY-type spectra J. Biomol. NMR 3 1993 569 576
30. V. Jaravine, A. Zhuravleva, P. Permi, I. Ibraghimov, and V.Y. Orekhov Hyperdimensional NMR spectroscopy with nonlinear sampling J. Am. Chem. Soc. 130 2008 3927 3936 (Pubitemid 351429859)
31. V. Jaravine, I. Ibraghimov, and V. Orekhov Removal of a time barrier for high-resolution multidimensional NMR spectroscopy Nat. Methods 3 2006 605 607 (Pubitemid 44123426)
32. M. Mobli, A.S. Stern, and J.C. Hoch Spectral reconstruction methods in fast NMR: reduced dimensionality, random sampling and maximum entropy J. Magn. Reson. 182 2006 96 105 (Pubitemid 44293436)
33. V.Y. Orekhov, and V.A. Jaravine Analysis of non-uniformly sampled spectra with multi-dimensional decomposition Prog. Nucl. Magn. Reson. 59 2011 271 292
34. V.Y. Orekhov, I. Ibraghimov, and M. Billeter Optimizing resolution in multidimensional NMR by three-way decomposition J. Biomol. NMR 27 2003 165 173 (Pubitemid 37045648)
35. T. Luan, V. Jaravine, A. Yee, C.H. Arrowsmith, and V.Y. Orekhov Optimization of resolution and sensitivity of 4D NOESY using multi-dimensional decomposition J. Biomol. NMR 33 2005 1 14 (Pubitemid 41573965)
36. K. Kazimierczuk, A. Zawadzka, and W. Koźmiński Optimisation of random time domain sampling in multidimensional NMR J. Magn. Reson. 192 2008 123 130 (Pubitemid 351609413)
37. K. Kazimierczuk, J. Stanek, A. Zawadzka-Kazimierczuk, and W. Koźmiński Random sampling in multidimensional NMR spectroscopy Prog. Nucl. Magn. Reson. 57 2010 420 434
38. J. Nováček, A. Zawadzka-Kazimierczuk, V. Papoušková, L. Žídek, H. Šanderova, L. Krásný, W. Koźmiński, and V. Sklenář 5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion J. Biomol. NMR 50 2011 1 11
39. J.A. Kubat, J.J. Chou, and D. Rovnyak Nonuniform sampling and maximum entropy reconstruction applied to the accurate measurement of residual dipolar couplings J. Magn. Reson. 186 2007 201 211 (Pubitemid 46880421)
40. K. Kazimierczuk, A. Zawadzka, W. Koźmiński, and I. Zhukov Determination of spin-spin couplings from ultrahigh resolution 3D NMR spectra obtained by optimized random sampling and multidimensional Fourier transformation J. Am. Chem. Soc. 130 2008 5404 5405 (Pubitemid 351612931)
41. K. Kazimierczuk, A. Zawadzka-Kazimierczuk, and W. Koźmiński Non-uniform frequency domain for optimal exploitation of non-uniform sampling J. Magn. Reson. 205 2010 286 292
42. M. Misiak, and W. Koźmiński Determination of heteronuclear coupling constants from 3D HSQC-TOCSY experiment with optimized random sampling of evolution time space Magn. Res. Chem. 47 2009 205 209
43. O. Lafon, B. Hu, J.-P. Amoureux, and P. Lesot Fast and high-resolution stereochemical analysis by nonuniform sampling and covariance processing of anisotropic natural abundance 2D 2H NMR datasets Chem. Eur. J. 17 2011 6716 6724
44. 13C HSQC spectra of metabolite mixtures using nonlinear sampling and forward maximum entropy reconstruction J. Am. Chem. Soc. 129 2007 5108 5116 (Pubitemid 46651389)
45. K. Kazimierczuk, and V.Y. Orekhov Accelerated NMR spectroscopy using compressed sensing Angew. Chem. Int. Ed. 123 2011 5556 5559
46. D.J. Holland, M.J. Bostock, L.F. Gladden, and D. Nietlispach Fast multidimensional NMR spectroscopy using compressed sensing Angew. Chem. Int. Ed. 123 2011 6548 6551
47. A. Marx, and C.M. Thiele Orientational properties of poly-γ-benzyl- l-glutamate: influence of molecular weight and solvent on order parameters of the solute Chem. Eur. J. 15 2009 254 260
48. V. Jaravine, and V. Orekhov Targeted acquisition for real-time NMR spectroscopy J. Am. Chem. Soc. 128 2006 13421 13426 (Pubitemid 44583026)
49. Both nussampler and compressed sensing are fully integrated in TopSpin 3.1 pl2 (Bruker Biospin GmbH).
50. K.E. Kövér, and K. Fehér Measurement of one-bond heteronuclear dipolar coupling contributions for amine and diastereotopic protons J. Magn. Reson. 168 2004 307 313
51. M.A. Smith, H. Hu, and A.J. Shaka Improved broadband inversion performance for NMR in liquids J. Magn. Reson. 151 2001 269 283
52. A.J. Shaka, P.B. Barker, and R. Freeman Computer-optimized decoupling scheme for wideband applications and low-level operation J. Magn. Reson. 64 1985 547 552
53. C.M. Thiele Poly-γ-ethyl-L-glutamate as alignment medium for the measurement of RDCs in organic substrates J. Org. Chem. 69 2004 7403 7413 (Pubitemid 39403324)
54. M. Mobli, A.S. Stern, W. Bermel, G.F. King, and J.C. Hoch A non-uniformly sampled 4D HCC(CO)NH-TOCSY experiment processed using maximum entropy for rapid protein sidechain assignment J. Magn. Reson. 204 2010 160 164
55. J. Furrer, M. John, H. Kessler, and B. Luy J-spectroscopy in the presence of residual dipolar couplings: determination of one-bond coupling constants and scalable resolution J. Biomol. NMR 37 2007 231 243 (Pubitemid 46477000)