Abstract
Probing protein structure, dynamics, and interaction surfaces by NMR requires initial backbone resonance assignment. The protocol for this step has been progressively developed in the last 15 years to provide robust assignments. However, even in the case of favorable conditions (high field magnets and cryogenically cooled probes, small globular proteins, high sample concentration), the assignment step generally takes several days of data collection and analysis, thus precluding studies of unstable proteins and limiting high-throughput applications. Recently, we have introduced the BATCH strategy for fast protein backbone resonance assignment. BATCH benefits from the combination of several tools (BEST/ASCOM/Targeted-Sampling/COBRA/HADAMAC) for time-optimized and highly automated NMR data acquisition, processing, and analysis. In this chapter, we discuss the individual steps of the BATCH method and describe its practical implementation to obtain the backbone resonance assignment of small globular proteins in a few hours of time.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Jaravine, V. A., Zhuravleva, A. V., Permi, P., Ibraghimov, I., and Orekhov, V. Y. (2008) Hyperdimensional NMR spectroscopy with nonlinear sampling. J. Am. Chem. Soc. 130, 3927–3936.
Hiller, S., Fiorito, F., Wuthrich, K., and Wider, G. (2005) Automated projection spectroscopy (APSY). Proc. Natl. Acad. Sci. USA 102, 10876–10881.
Lescop, E., and Brutscher, B. (2009) Highly automated protein backbone resonance assignment within a few hours: the “BATCH” strategy and software package. J. Biomol. NMR 44, 43–57.
Lescop, E., Rasia, R., and Brutscher, B. (2008) Hadamard amino-acid-type edited NMR experiment for fast protein resonance assignment. J. Am. Chem. Soc. 130, 5014–5015.
Lescop, E., and Brutscher, B. (2007) Hyperdimensional protein NMR spectroscopy in peptide-sequence space. J. Am. Chem. Soc. 129, 11916–11917.
Lescop, E., Schanda, P., and Brutscher, B. (2007) A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. J. Magn. Reson. 187, 163–169.
Schanda, P., Van Melckebeke, H., and Brutscher, B. (2006) Speeding up three-dimensional protein NMR experiments to a few minutes. J. Am. Chem. Soc. 128, 9042–9043.
Lescop, E., Schanda, P., Rasia, R., and Brutscher, B. (2007) Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. J. Am. Chem. Soc. 129, 2756–2757.
Deschamps, M., and Campbell, I. D. (2006) Cooling overall spin temperature: protein NMR experiments optimized for longitudinal relaxation effects. J. Magn. Reson. 178, 206–211.
Pervushin, K., Vogeli, B., and Eletsky, A. (2002) Longitudinal (1)H relaxation optimization in TROSY NMR spectroscopy. J. Am. Chem. Soc. 124, 12898–12902.
Diercks, T., Daniels, M., and Kaptein, R. (2005) Extended flip-back schemes for sensitivity enhancement in multidimensional HSQC-type out-and-back experiments. J. Biomol. NMR 33, 243–259.
Kupce, E., and Freeman, R. (1993) Polychromatic Selective Pulses. J. Magn. Reson. 102A, 122–126.
Geen, H., and Freeman, R. (1991) Band-selective radiofrequency pulses. J. Magn. Reson. 93, 93–141.
Smith, M. A., Hu, H., and Shaka, A. J. (2001) Improved Broadband Inversion Performance for NMR in Liquids. J. Magn. Reson. 151, 269–283.
Brutscher, B. (2002) Intraresidue HNCA and COHNCA experiments for protein backbone resonance assignment. J. Magn. Reson. 156, 155–159.
Blevins, R. A., and Johnson, B. A. (1994) NMRView: a computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603–614.
Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293.
Jung, Y. S., and Zweckstetter, M. (2004) Mars – robust automatic backbone assignment of proteins. J. Biomol. NMR 30, 11–23.
Slupsky, C. M., Boyko, R. F., Booth, V. K., and Sykes, B. D. (2003) Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments. J. Biomol. NMR 27, 313–321.
Rasia, R. M., Mateos, J., Bologna, N. G., Burdisso, P., Imbert, L., Palatnik, J. F., and Boisbouvier, J. (2010) Structure and RNA interactions of the plant MicroRNA processing-associated protein HYL1. Biochemistry 49, 8237–8239.
Wishart, D. S., and Sykes, B. D. (1994) The 13 C chemical-shift index: a simple method for the identification of protein secondary structure using 13 C chemical-shift data. J. Biomol. NMR 4, 171–180.
Acknowledgments
Special thanks to Rodolfo Rasia and Jérôme Boisbouvier (IBS, Grenoble) for allowing us to use their NMR data on Hyl1 to illustrate this book chapter.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Brutscher, B., Lescop, E. (2012). Fast Protein Backbone NMR Resonance Assignment Using the BATCH Strategy. In: Shekhtman, A., Burz, D. (eds) Protein NMR Techniques. Methods in Molecular Biology, vol 831. Humana Press. https://doi.org/10.1007/978-1-61779-480-3_21
Download citation
DOI: https://doi.org/10.1007/978-1-61779-480-3_21
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-479-7
Online ISBN: 978-1-61779-480-3
eBook Packages: Springer Protocols