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Highly automated protein backbone resonance assignment within a few hours: the «BATCH» strategy and software package

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Abstract

Sequential resonance assignment represents an essential step towards the investigation of protein structure, dynamics, and interaction surfaces. Although the experimental sensitivity has significantly increased in recent years, with the availability of high field magnets and cryogenically cooled probes, resonance assignment, even of small globular proteins, still generally requires several days of data collection and analysis using standard protocols. Here we introduce the BATCH strategy for fast and highly automated backbone resonance assignment of 13C, 15N-labelled proteins. BATCH makes use of the fast data acquisition and analysis tools BEST, ASCOM, COBRA, and HADAMAC, recently developed in our laboratory. An improved Hadamard encoding scheme, presented here, further increases the performance of the HADAMAC experiment. A new software platform, interfaced to the NMRView software package, has been developed that enables highly automated NMR data processing and analysis, sequential resonance assignment, and 13C chemical shift extraction. We demonstrate for four small globular proteins that sequential resonance assignment can be routinely obtained within a few hours, or less, in a highly automated and robust way.

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Acknowledgments

This work was supported by the Commissariat à l’Energie Atomique, the Centre National de la Recherche Scientifique, the University Grenoble 1, the French Research Agency (ANR-JCJC-05-0077), and the European commission (I3, EU-NMR, Contract No. 026145). We thank I. Ayala for preparation of the ubiquitin sample, P. Gans for the calmodulin sample, and B. Bersch, K.-M. Derfoufi, G. Vandenbussche, R. Rasia, J. Boisbouvier, and M. Jamin, for making samples of HMR, Hyl1 and VSV-PCTD available for this study.

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Authors and Affiliations

  1. Laboratoire de Chimie et Biologie Structurales, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, 1, Avenue de la Terrasse, 91190, Gif-sur-Yvette, France

    Ewen Lescop

  2. Laboratoire de RMN, Institut de Biologie Structurale—Jean-Pierre Ebel, UMR5075 CNRS-CEA-UJF, 41, Rue Jules Horowitz, 38027, Grenoble Cedex, France

    Bernhard Brutscher

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  1. Ewen Lescop
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  2. Bernhard Brutscher
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Correspondence to Ewen Lescop or Bernhard Brutscher.

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Lescop, E., Brutscher, B. Highly automated protein backbone resonance assignment within a few hours: the «BATCH» strategy and software package. J Biomol NMR 44, 43–57 (2009). https://doi.org/10.1007/s10858-009-9314-2

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  • DOI: https://doi.org/10.1007/s10858-009-9314-2

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