We present NMRlib, a suite of jython-based tools designed for Bruker spectrometers (TopSpin versions 3.2–4.0) that allow easy setup, management, and exchange of NMR experiments. A NMR experiment can be set up and executed in a few clicks by navigating through the NMRlib GUI tree structure, without any further parameter adjustment. NMRlib is magnetic-field independent, and thus particularly helpful for laboratories operating multiple NMR spectrometers. NMRlib is easily personalized by adding, deleting, or reorganizing experiments. Additional tools are provided for data processing, visualization, and analysis. In particular, NMRlib contains all the polarization-enhanced fast-pulsing NMR experiments (SOFAST, BEST, HADAMAC,…) developed in our laboratory over the last decade. We also discuss some specific features that have been implemented to make these experiments most efficient and user friendly.
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Tax calculation will be finalised during checkout.
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
Tax calculation will be finalised during checkout.
Akoka S, Barantin L, Trierweiler M (1999) Concentration measurement by proton NMR using the ERETIC method. Anal Chem 71:2554–2557
Amero C, Schanda P, Durá MA et al (2009) Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies. J Am Chem Soc 131:3448–3449
Aue WP, Bartholdi E, Ernst RR (1976) 2-dimensional spectroscopy—application to nuclear magnetic-resonance. J Chem Phys 64:4226–4227
Bax A, Kontaxis G, Tjandra N (2001) Dipolar couplings in macromolecular structure determination. Methods Enzymol 339:127–174
Bersch B, Rossy E, Covès J, Brutscher B (2003) Optimized set of two-dimensional experiments for fast sequential assignment, secondary structure determination, and backbone fold validation of 13C/15 N-labelled proteins. J Biomol NMR 27:57–67
Brutscher B (2002) Intraresidue HNCA and COHNCA experiments for protein backbone resonance assignment. J Magn Reson 156:155–159
Brutscher B, Solyom Z (2017) Polarization-enhanced fast-pulsing techniques. In: Fast NMR data acquisition: beyond the Fourier transform. The Royal Society of Chemistry, pp 1–32
Christou NE, Brutscher B (2018) BEST and SOFAST experiments for resonance assignment of histidine and tyrosine side chains in 13C/15N labeled proteins. J Biomol NMR 72:115–124
Cordier F, Grzesiek S (1999) Direct observation of hydrogen bonds in proteins by interresidue 3hJNC’ scalar couplings. J Am Chem Soc 121:1601–1602
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
Dingley AJ, Cordier F, Grzesiek S (2001) An introduction to hydrogen bond scalar couplings. Concepts Magn Reson 13:103–127
Ernst RR, Anderson W (1966) Application of fourier transform spectroscopy to magnetic resonance. Rev Sci Instrum 37:93
Favier A, Brutscher B (2011) Recovering lost magnetization: polarization enhancement in biomolecular NMR. J Biomol NMR 49:9–15
Franco R, Gil-Caballero S, Ayala I et al (2017) Probing conformational exchange dynamics in a short-lived protein folding intermediate by real-time relaxation-dispersion NMR. J Am Chem Soc 139:1065–1068
Gal M, Kern T, Schanda P et al (2009) An improved ultrafast 2D NMR experiment: towards atom-resolved real-time studies of protein kinetics at multi-Hz rates. J Biomol NMR 43:1–10
Gil-Caballero S, Favier A, Brutscher B (2014) HNCA + , HNCO + , and HNCACB + experiments: improved performance by simultaneous detection of orthogonal coherence transfer pathways. J Biomol NMR 60:1–9
Helmus JJ, Jaroniec CP (2013) Nmrglue: an open source Python package for the analysis of multidimensional NMR data. J Biomol NMR 55:355–367
Hwang T-L, Shaka AJ (1995) Water suppression that works. excitation scultping using arbitrary waveforms and pulsed field gradients. J Magn Reson A 112:275–279
Kay LE, Keifer P, Saarinen T (1992) Pure absorption gradient enhanced heteronuclear single qauntum correlation spectroscopy with improved sensitivity. J Am Chem Soc 26:10663–10665
Korzhnev DM, Kloiber K, Kanelis V et al (2004) Probing slow dynamics in high molecular weight proteins by methyl-TROSY NMR spectroscopy: application to a 723-residue enzyme. J Am Chem Soc 126:3964–3973
Lee D, Hilty C, Wider G, Wüthrich K (2006) Effective rotational correlation times of proteins from NMR relaxation interference. J Magn Reson 178:72–76
Lescop E, Schanda P, Brutscher B (2007a) A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. J Magn Reson 187:163–169
Lescop E, Schanda P, Rasia R, Brutscher B (2007b) Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. J Am Chem Soc 129:2756–2757
Lescop E, Rasia R, Brutscher B (2008) Hadamard amino-acid-type edited NMR experiment for fast protein resonance assignment. J Am Chem Soc 130:5014–5015
Lundström P, Vallurupalli P, Religa TL et al (2007) A single-quantum methyl 13C-relaxation dispersion experiment with improved sensitivity. J Biomol NMR 38:79–88
Mori S, Abeygunawardana C, O’Neil Johnson M, van Zijl PC (1995) Improved sensitivity of HSQC spectra of exchanhing protons at short interscan delays using a new fast HSQC (FHSQC) detection scheme that avoids water saturation. J Magn Reson, Ser B 108:94–98
Permi P (2002) Intraresidual HNCA: an experiment for correlating only intraresidual backbone resonances. J Biomol NMR 23:201–209
Pervushin K, Riek R, Wider G, Wüthrich K (1998) Transverse relaxation-optimized spectroscopy (TROSY) for NMR studies of aromatic spin systems in 13C-labeled proteins. J Am Chem Soc 120:6394–6400
Rasia RM, Lescop E, Palatnik JF et al (2011) Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins. J Biomol NMR 51:369–378
Schanda P (2009) Fast-pulsing longitudinal relaxation optimized techniques: enriching the toolbox of fast biomolecular NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 55:238–265
Schanda P, Brutscher B (2005) Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. J Am Chem Soc 127:8014–8015
Schanda P, Kupce E, Brutscher B (2005) SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds. J Biomol NMR 33:199–211
Schanda P, Forge V, Brutscher B (2006a) HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains. Magn Reson Chem 44:S177–S184
Schanda P, Van Melckebeke H, Brutscher B (2006b) Speeding up three-dimensional protein NMR experiments to a few minutes. J Am Chem Soc 128:9042–9043
Solyom Z, Schwarten M, Geist L et al (2013) BEST-TROSY experiments for time-efficient sequential resonance assignment of large disordered proteins. J Biomol NMR 55:311–321
Vallet A, Favier A, Brutscher B (2019) Aromatic SOFAST-HMBC for proteins at natural. J Magn Reson 300:95–102
Van Ingen H, Vuister GW, Tessari M (2002) A two-dimensional artifact from asynchronous decoupling a two-dimensional artifact from asynchronous decoupling. J Magn Reson 156:258–261
Van Melckebeke H, Simorre J-P, Brutscher B (2004) Amino acid-type edited NMR experiments for methyl-methyl distance measurement in 13C-labeled proteins. J Am Chem Soc 126:9584–9591
Weigelt J (1998) Single scan, sensitivity- and gradient-enhanced TROSY for multidimensional NMR experiments. J Am Chem Soc 120:10778–10779
Wu PSC, Otting G (2005) Rapid pulse length determination in high-resolution NMR. J Magn Reson 176:115–119
We thank Sergio Gil Caballero for his contributions during the early stages of the NMRlib development, Ewen Lescop for contributing the 2D ASCOM script, as well as Bruker BioSpin for financial support. This work used the NMR and isotope labeling platforms of the Grenoble Instruct center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05-02) and GRAL (ANR-10-LABX-49-01) within the Grenoble Partnership for Structural Biology (PSB).
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
Favier, A., Brutscher, B. NMRlib: user-friendly pulse sequence tools for Bruker NMR spectrometers. J Biomol NMR 73, 199–211 (2019). https://doi.org/10.1007/s10858-019-00249-1
- Protein NMR
- Pulse sequence