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ARIA for Solution and Solid-State NMR

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Protein NMR Techniques

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

Abstract

In solution or solid-state, determining the three-dimensional structure of biomolecules by Nuclear ­Magnetic Resonance (NMR) normally requires the collection of distance information. The interpretation of the spectra containing this distance information is a critical step in an NMR structure determination. In this chapter, we present the Ambiguous Restraints for Iterative Assignment (ARIA) program for automated cross-peak assignment and determination of macromolecular structure from solution and solid-state NMR experiments. While the program was initially designed for the assignment of nuclear Overhauser effect (NOE) resonances, it has been extended to the interpretation of magic-angle spinning (MAS) solid-state NMR data. This chapter first details the concepts and procedures carried out by the program. Then, we describe both the general strategy for structure determination with ARIA 2.3 and practical aspects of the technique. ARIA 2.3 includes all recent developments. such as an extended integration of the Collaborative Computing Project for the NMR community (CCPN), the incorporation of the log-harmonic distance restraint potential and an automated treatment of symmetric oligomers.

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Acknowledgments

This work was supported by the EU grants SPINE (QLG2-CT-2002-00988) and ExtendNMR (LSHG-CT- 2005–018988). The Ministère de l’Enseignement Supérieur (ACI IMPBio, project ICMD-RMN) and Institut Pasteur are also acknowledged for financial support. The authors would like to thank Wolfgang Rieping, Michael Habeck, Aymeric Bernard, and the CCPN team for their active participation in the development of ARIA, as well as Anja Böckmann and Barth-Jan van Rossum for fruitful collaborations on solid-state NMR. Benjamin Bardiaux thanks Hartmut Oschkinat for support.

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Authors and Affiliations

  1. NMR-supported Structural Biology, Leibnitz-Institutfür Molekulare Pharmakologie (FMP), Berlin, Germany

    Benjamin Bardiaux

  2. Unité de Bioinformatique Structurale, CNRS URA 2185, Institut Pasteur, Paris, France

    Thérèse Malliavin & Michael Nilges

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  1. Benjamin Bardiaux
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  2. Thérèse Malliavin
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  3. Michael Nilges
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Correspondence to Benjamin Bardiaux .

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Editors and Affiliations

  1. University of Albany, State University of New York, Washington Avenue 1400, Albany, 12222, New York, USA

    Alexander Shekhtman

  2. University of Albany, State University of New York, Washington Avenue 1400, Albany, 12222, New York, USA

    David S. Burz

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Bardiaux, B., Malliavin, T., Nilges, M. (2012). ARIA for Solution and Solid-State NMR. 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_23

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