Skip to main content
SpringerLink
Log in

SARA: a software environment for the analysis of relaxation data acquired with accordion spectroscopy

  • Article
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Abstract

We present SARA (Software for Accordion Relaxation Analysis), an interactive and user-friendly MATLAB software environment designed for analyzing relaxation data obtained with accordion spectroscopy. Accordion spectroscopy can be used to measure nuclear magnetic resonance (NMR) relaxation rates in a fraction of the time required by traditional methods, yet data analysis can be intimidating and no unified software packages are available to assist investigators. Hence, the technique has not achieved widespread use within the NMR community. SARA offers users a selection of analysis protocols spanning those presented in the literature thus far, with modifications permitting a more general application to crowded spectra such as those of proteins. We discuss the advantages and limitations of each fitting method and suggest a protocol combining the strengths of each procedure to achieve optimal results. In the end, SARA provides an environment for facile extraction of relaxation rates and should promote routine application of accordion relaxation spectroscopy.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Akke M, Brüschweiler R, Palmer AG (1993) NMR order parameters and free energy: an analytical approach and its application to cooperative calcium (2+) binding by calbindin D9 k. J Am Chem Soc 115:9832–9833

    Article  Google Scholar 

  • Barkhuijsen H, DeBeer R, VanOrmondt D (1987) Improved algorithm for noniterative time-domain model fitting to exponentially damped magnetic resonance signals. J Magn Reson 557:553–557

    ADS  Google Scholar 

  • Bodenhausen G (1982) Direct determination of rate constants of slow dynamic processes by two-dimensional “accordion” spectroscopy in nuclear magnetic resonance. J Am Chem Soc 3:1304–1309

    Article  Google Scholar 

  • Bodenhausen G, Ernst R (1981) The accordion experiment, a simple approach to three-dimensional NMR spectroscopy. J Magn Reson 45:367–373. doi:10.1016/0022-2364(81)90137-2

    ADS  Google Scholar 

  • Carr PA, Fearing DA, Palmer AG (1998) 3D accordion spectroscopy for measuring 15 N and 13CO relaxation rates in poorly resolved NMR spectra. J Magn Reson 132:25–33. doi:10.1006/jmre1998.1374

    Article  ADS  Google Scholar 

  • Chen K, Tjandra N (2009) Direct measurements of protein backbone 15 N spin relaxation rates from peak line-width using a fully-relaxed Accordion 3D HNCO experiment. J Magn Reson 197:71–76. doi:10.1016/j.jmr.2008.12.001

    Article  ADS  Google Scholar 

  • Delaglio F, Grzesiek S, Vuister GW et al (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293

    Article  Google Scholar 

  • Eisenmesser EZ, Millet O, Labeikovsky W et al (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438:117–121. doi:10.1038/nature04105

    Article  ADS  Google Scholar 

  • Guenneugues M, Gilquin B, Wolff N et al (1999) Internal motion time scales of a small, highly stable and disulfide-rich protein: a 15 N, 13C NMR and molecular dynamics study. J Biomol NMR 14:47–66

    Article  Google Scholar 

  • Gunther U, Ludwig C, Ruterjans H (2000) NMRLAB-advanced NMR data processing in matlab. J Magn Reson 145:201–208. doi:10.1006/jmre 2000.2071

    Article  ADS  Google Scholar 

  • Henzler-Wildman KA, Thai V, Lei M et al (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450:838–844. doi:10.1038/nature06410

    Article  ADS  Google Scholar 

  • Herman P, Lee JC (2012) The advantage of global fitting of data involving complex linked reactions. In: Fenton AW (ed) Allostery. Springer New York, New York, pp 399–421

    Chapter  Google Scholar 

  • Korzhnev DM, Kay LE (2008) Probing invisible, low-populated States of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding. Acc Chem Res 41:442–451. doi:10.1021/ar700189y

    Article  Google Scholar 

  • Mandel AM, Palmer AG (1994) Measurement of relaxation-rate constants using constant-time accordion NMR spectroscopy. J Magn Reson, Ser A 110:62–72. doi:10.1006/jmra1994.1182

    Article  ADS  Google Scholar 

  • Rabier P, Kieffer B, Koehl P, Lefèvre J-F (2001) Fast measurement of heteronuclear relaxation: frequency-domain analysis of NMR accordion spectroscopy. Magn Reson Chem 39:447–456. doi:10.1002/mrc.870

    Article  Google Scholar 

  • Sugase K, Dyson HJ, Wright PE (2007) Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447:1021–1025. doi:10.1038/nature05858

    Article  ADS  Google Scholar 

  • Wand AJ (2013) The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation. Curr Opin Struct Biol 23:75–81. doi:10.1016/j.sbi.2012.11.005

    Article  Google Scholar 

Download references

Acknowledgments

This work was supported by NIH, Grant R01-GM104257.

Author information

Authors and Affiliations

  1. Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 701 Hunterian, 725 North Wolfe St., Baltimore, MD, 21205, USA

    Bradley J. Harden & Dominique P. Frueh

Authors
  1. Bradley J. Harden
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dominique P. Frueh
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dominique P. Frueh.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 953 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Harden, B.J., Frueh, D.P. SARA: a software environment for the analysis of relaxation data acquired with accordion spectroscopy. J Biomol NMR 58, 83–99 (2014). https://doi.org/10.1007/s10858-013-9807-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-013-9807-x

Keywords

Search

Navigation