Abstract
Sparse sampling in biomolecular multidimensional NMR offers increased acquisition speed and resolution and, if appropriate conditions are met, an increase in sensitivity. Sparse sampling of indirectly detected time domains combined with the direct truly multidimensional Fourier transform has elicited particular attention because of the ability to generate a final spectrum amenable to traditional analysis techniques. A number of sparse sampling schemes have been described including radial sampling, random sampling, concentric sampling and variations thereof. A fundamental feature of these sampling schemes is that the resulting time domain data array is not amenable to traditional Fourier transform based processing and phasing correction techniques. In addition, radial sampling approaches offer a number of advantages and capabilities that are also not accessible using standard NMR processing techniques. These include sensitivity enhancement, sub-matrix processing and determination of minimal sets of sampling angles. Here we describe a new software package (Al NMR) that enables these capabilities in the context of a general NMR data processing environment.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Anderson E (1999) LAPACK Users’ Guide. Software, environments, tools, 3rd edn. Society for Industrial and Applied Mathematics, Philadelphia
Barber CB, Dobkin DP, Huhdanpaa H (1996) The quickhull algorithm for convex hulls. ACM T Math Software 22:469–483
Barkhuijsen H, Debeer R, Bovee WMMJ, Creyghton JHN, Vanormondt D (1985) Application of linear prediction and singular value decomposition (LPSVD) to determine NMR frequencies and intensities from the FID. Magn Reson Med 2:86–89
Bodenhausen G, Ernst R (1982) Direct determination of rate constants of slow dynamic processes by two-dimensional “Accordion” spectroscopy in nuclear magnetic resonance. J Am Chem Soc 104:1304–1309
Brutscher B, Morelle N, Cordier F, Marion D (1995) Determination of an initial set of NOE-derived distance constraints for the structure determination of 15 N/13C-labeled proteins. J Magn Reson B 109:238–242
Callaghan PT, Mackay AL, Pauls KP, Soderman O, Bloom M (1984) The high fidelity extraction of weak broad lines from NMR-spectra containing large solvent peaks. J Magn Reson 56:101–109
Coggins BE, Zhou P (2006) Polar Fourier transforms of radially sampled NMR data. J Magn Reson 182:84–95
Coggins BE, Zhou P (2007) Sampling of the NMR time domain along concentric rings. J Magn Reson 184:207–221
Coggins BE, Zhou P (2008) High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN. J Biomol NMR 42:225–239
Coggins BE, Venters RA, Zhou P (2005) Filtered backprojection for the reconstruction of a high-resolution (4, 2) D CH3-NHNOESY spectrum on a 29 kDa protein. J Am Chem Soc 127:11562–11563
Coggins BE, Venters RA, Zhou P (2010) Radial sampling for fast NMR: concepts and practices over three decades. Prog Nucl Magn Reson Spectrosc 57:381–419
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRpipe—A multidimensional spectral processing system based on unix pipes. J Biomol NMR 6:277–293
Eghbalnia HR, Bahrami A, Tonelli M, Hallenga K, Markley JL (2005) High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection. J Am Chem Soc 127:12528–12536
Freeman R, Kupce E (2003) New methods for fast multidimensional NMR. J Biomol NMR 27:101–113
Frigo M, Johnson SG (2005) The design and implementation of FFTW3. Proc IEEE 93:216–231
Gesmar H, Led JJ (1988) Spectral estimation of complex time-domain NMR signals by linear prediction. J Magn Reson 76:183–192
Gledhill JM, Wand AJ (2007) Phasing arbitrarily sampled multidimensional NMR data. J Magn Reson 187:363–370
Gledhill JM, Wand AJ (2008) Optimized angle selection for radial sampled NMR experiments. J Magn Reson 195:169–178
Gledhill JM, Wand AJ (2010) SEnD NMR: sensitivity enhanced n-dimensional NMR. J Magn Reson 202:250–258
Gledhill JM, Walters BT, Wand AJ (2009) AMORE-HX: a multidimensional optimization of radial enhanced NMR-sampled hydrogen exchange. J Biomol NMR 45:233–239
Hiller S, Fiorito F, Wuthrich K, Wider G (2005) Automated projection spectroscopy (APSY). Proc Natl Acad Sci USA 102:10876–10881
Hoch JC, Stern AS (1996) NMR data processing. Wiley-Liss, New York
Hoch JC, Maciejewski MW, Filipovic B (2008) Randomization improves sparse sampling in multidimensional NMR. J Magn Reson 193:317–320
Jaravine V, Ibraghimov I, Orekhov VY (2006) Removal of a time barrier for high-resolution multidimensional NMR spectroscopy. Nat Method 3:605–607
Kazimierczuk K, Kozminski W, Zhukov I (2006a) Two-dimensional Fourier transform of arbitrarily sampled NMR data sets. J Magn Reson 179:323–328
Kazimierczuk K, Zawadzka A, Kozminski W, Zhukov I (2006b) Random sampling of evolution time space and Fourier transform processing. J Biomol NMR 36:157–168
Kazimierczuk K, Zawadzka A, Kozminski W, Zhukov I (2007) Lineshapes and artifacts in multidimensional Fourier transform of arbitrary sampled NMR data sets. J Magn Reson 188:344–356
Kazimierczuk K, Zawadzka A, Kozminski W (2008) Optimization of random time domain sampling in multidimensional NMR. J Magn Reson 192:123–130
Kazimierczuk K, Stanek J, Zawadzka-Kazimierczuk A, Kozminski W (2010a) Random sampling in multidimensional NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 57:420–434
Kazimierczuk K, Zawadzka-Kazimierczuk A, Kozminski W (2010b) Non-uniform frequency domain for optimal exploitation of non-uniform sampling. J Magn Reson 205:286–292
Kim S, Szyperski T (2003) GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information. J Am Chem Soc 125:1385–1393
Kupce E, Freeman R (2003) Reconstruction of the three-dimensional NMR spectrum of a protein from a set of plane projections. J Biomol NMR 27:383–387
Kupce E, Freeman R (2004) Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy. J Am Chem Soc 126:6429–6440
Marion D (2006) Processing of ND NMR spectra sampled in polar coordinates: a simple Fourier transform instead of a reconstruction. J Biomol NMR 36:45–54
Marion D, Ikura M, Bax A (1989) Improved solvent suppression in one-dimensional and two-dimensional NMR-spectra by convolution of time-domain data. J Magn Reson 84:425–430
Otting G, Widmer H, Wagner G, Wuthrich K (1986) Origin of T1 and T2 ridges in 2d NMR-spectra and procedures for suppression. J Magn Reson 66:187–193
Pannetier N, Houben K, Blanchard L, Marion D (2007) Optimized 3D-NMR sampling for resonance assignment of partially unfolded proteins. J Magn Reson 186:142–149
Stern AS, Li KB, Hoch JC (2002) Modern spectrum analysis in multidimensional NMR spectroscopy: comparison of linear-prediction extrapolation and maximum-entropy reconstruction. J Am Chem Soc 124:1982–1993
Szyperski T, Wider G, Bushweller JH, Wuthrich K (1993) Reduced dimensionality in triple-resonance NMR experiments. J Am Chem Soc 115:9307–9308
Venters RA, Coggins BE, Kojetin D, Cavanagh J, Zhou P (2005) (4, 2)D projection-reconstruction experiments for protein backbone assignment: application to human carbonic anhydrase II and calbindin D-28 K. J Am Chem Soc 127:8785–8795
Zhu G, Bax A (1992) Improved linear prediction of damped NMR signals using modified forward backward linear prediction. J Magn Reson 100:202–207
Acknowledgments
We thank Vignesh Kasinath and Kathleen Valentine for helpful discussion. This work was supported by NIH grants DK 39806 and GM 081520, by NSF grants MCB 0842814 and DMR 05-20020 and by a grant from the Mathers Foundation.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Gledhill, J.M., Wand, A.J. Al NMR: a novel NMR data processing program optimized for sparse sampling. J Biomol NMR 52, 79–89 (2012). https://doi.org/10.1007/s10858-011-9584-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10858-011-9584-3