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Fast Protein Backbone NMR Resonance Assignment Using the BATCH Strategy

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 831)

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.

Key words

Protein Fast NMR Resonance assignment Chemical shift Amino acid type discrimination Algorithm 
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Notes

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.

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© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Institut de Biologie Structurale – Jean-Pierre Ebel, CNRS, CEA, UJF, UMR5075Grenoble CedexFrance
  2. 2.Laboratoire de Chimie et Biologie StructuralesInstitut de Chimie des Substances Naturelles, Centre de Recherche de Gif, CNRSGif-sur-YvetteFrance

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