Automatic maximum entropy spectral reconstruction in NMR (original) (raw)

Abstract

Developments in superconducting magnets, cryogenic probes, isotope labeling strategies, and sophisticated pulse sequences together have enabled the application, in principle, of high-resolution NMR spectroscopy to biomolecular systems approaching 1 megadalton. In practice, however, conventional approaches to NMR that utilize the fast Fourier transform, which require data collected at uniform time intervals, result in prohibitively lengthy data collection times in order to achieve the full resolution afforded by high field magnets. A variety of approaches that involve nonuniform sampling have been proposed, each utilizing a non-Fourier method of spectrum analysis. A very general non-Fourier method that is capable of utilizing data collected using any of the proposed nonuniform sampling strategies is maximum entropy reconstruction. A limiting factor in the adoption of maximum entropy reconstruction in NMR has been the need to specify non-intuitive parameters. Here we describe a fully automated system for maximum entropy reconstruction that requires no user-specified parameters. A web-accessible script generator provides the user interface to the system.

Access this article

Log in via an institution

Subscribe and save

• Get 10 units per month
• Download Article/Chapter or eBook
• 1 Unit = 1 Article or 1 Chapter
• Cancel anytime Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

• Barna JCJ, Laue ED et al (1987) Exponential sampling: an alternative method for sampling in two dimensional NMR experiments. J Magn Reson 73:69–77
  Google Scholar
• Bodenhausen G, Ernst RR (1981) The accordion experiment, a simple approach to three dimensional NMR spectroscopy. J Magn Reson 45:367–373
  Google Scholar
• Chylla RA, Markley JL (1995) Theory and application of the maximum likelihood principle to NMR parameter estimation of multidimensional NMR data. J Biomol NMR 5:245–258
  Article Google Scholar
• Daniell GJ, Hore PJ (1989) Maximum entropy and NMR—A new approach. J Magn Reson 84:515–536
  Google Scholar
• Delaglio F, Grzesiek S et al (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293
  Article Google Scholar
• Gorbatyuk VY, Nosworthy NJ et al (2006) Mapping the phosphoinositide-binding site on chick cofilin explains how PIP2 regulates the cofilin-actin interaction. Mol Cell 24:511–522
  Article Google Scholar
• Hoch JC, Stern AS (1996) NMR data processing. Wiley-Liss, New York
  Google Scholar
• Hoch JC, Stern AS (2005) RNMR Toolkit, Version 3
• Hoch JC, Stern AS et al (1990) Maximum entropy reconstruction of complex (phase-sensitive) spectra. J Magn Reson 86:236–246
  Google Scholar
• Jaravine V, Ibraghimov I et al (2006) Removal of a time barrier for high-resolution multidimensional NMR spectroscopy. Nat Methods 3:605–607
  Article Google Scholar
• Jordan JB, Kovacs H et al (2006) Three-dimensional 13C-detected CH3-TOCSY using selectively protonated proteins: facile methyl resonance assignment and protein structure determination. J Am Chem Soc 128:9119–9128
  Article Google Scholar
• Kupče Ē, Freeman R (2003) New methods for fast multidimensional NMR. J Biomol NMR 27:101–113
  Article Google Scholar
• Malmodin D, Billeter M (2005) High-throughput analysis of protein NMR spectra. Prog Nuc Mag Res Spect 46:109–129
  Article Google Scholar
• Mobli M, Stern AS et al (2006) Spectral reconstruction methods in fast NMR: reduced dimensionality, random sampling and maximum entropy. J Magn Reson 182:95–105
  Article ADS Google Scholar
• Orekhov VY, Ibraghimov IV et al (2001) MUNIN: a new approach to multi-dimensional NMR spectra interpretation. J Biomol NMR 20:49–60
  Article Google Scholar
• Pons JL, Malliavin TE et al (1996) Gifa V4: a complete package for NMR data-set processing. J Biomol NMR 8:445–452
  Article Google Scholar
• Schmieder P, Stern AS et al (1993) Application of nonlinear sampling schemes to COSY-type spectra. J Biomol NMR 3:569–576
  Article Google Scholar
• Schmieder P, Stern AS et al (1994) Improved resolution in triple-resonance spectra by nonlinear sampling in the constant-time domain. J Biomol NMR 4:483–490
  Article Google Scholar
• Schmieder P, Stern AS et al (1997) Quantification of maximum entropy spectrum reconstructions. J Magn Reson 125:332–339
  Article Google Scholar
• Shimba N, Kovacs H et al (2004) Optimization of 13C direct detection NMR methods. J Biomol NMR 30:175–179
  Article Google Scholar
• Shimba N, Stern AS et al (2003) Elimination of 13Calpha splitting in protein NMR spectra by deconvolution with maximum entropy reconstruction. J Am Chem Soc 125:2382–2383
  Article Google Scholar
• Sibisi S, Skilling J et al (1984) Maximum entropy signal processing in practical NMR spectroscopy. Nature 311:446–447
  Article ADS Google Scholar
• Stern AS, Li K et al (2002) Modern spectrum analysis in multidimensional NMR spectroscopy: comparison of linear prediction extrapolation and maximum-entropy reconstruction. J Am Chem Soc 124:1982–1993
  Article Google Scholar
• Sun ZJ, Hyberts SG et al (2005) High-resolution aliphatic side-chain assignments in 3D HCcoNH experiments with joint H–C evolution and non-uniform sampling. J Biomol NMR 32:55–60
  Article Google Scholar
• Szyperski T, Wider G et al (1993) Reduced dimensionality in triple resonance NMR experiments. J Am Chem Soc 115:9307–9308
  Article Google Scholar
• Wishart DS, Bigam CG et al (1995) 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J Biomol NMR 6:135–140
  Article Google Scholar

Download references

Acknowledgements

This is a contribution from the NMRA Consortium. We thank Dr. Alan Stern for helpful discussions. This work was supported by grants from the National Institutes of Health GM-47467 (G. Wagner, PI), RR-20125 (J. Hoch, PI), GM-72000 (A. Ron, PI), and EB-001496 (M. Gryk, PI).

Author information

Authors and Affiliations

1. Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT, 06030-3305, USA
   Mehdi Mobli, Mark W. Maciejewski, Michael R. Gryk & Jeffrey C. Hoch

Authors

1. Mehdi Mobli
   You can also search for this author inPubMed Google Scholar
2. Mark W. Maciejewski
   You can also search for this author inPubMed Google Scholar
3. Michael R. Gryk
   You can also search for this author inPubMed Google Scholar
4. Jeffrey C. Hoch
   You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence toJeffrey C. Hoch.

Additional information

Mehdi Mobli and Mark W. Maciejewski contributed equally to this work.

Rights and permissions

About this article

Cite this article

Mobli, M., Maciejewski, M.W., Gryk, M.R. et al. Automatic maximum entropy spectral reconstruction in NMR.J Biomol NMR 39, 133–139 (2007). https://doi.org/10.1007/s10858-007-9180-8

Download citation

• Received: 22 May 2007
• Revised: 09 July 2007
• Accepted: 11 July 2007
• Published: 15 August 2007
• Issue Date: October 2007
• DOI: https://doi.org/10.1007/s10858-007-9180-8

Keywords