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Data Mining Techniques for the Life Sciences pp 349–364Cite as

Analysis and Prediction of Protein Quaternary Structure

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 609))

Abstract

The quaternary structure (QS) of a protein is determined by measuring its molecular weight in solution. The data have to be extracted from the literature, and they may be missing even for proteins that have a crystal structure reported in the Protein Data Bank (PDB). The PDB and other databases derived from it report QS information that either was obtained from the depositors or is based on an analysis of the contacts between polypeptide chains in the crystal, and this frequently differs from the QS determined in solution.

The QS of a protein can be predicted from its sequence using either homology or threading methods. However, a majority of the proteins with less than 30% sequence identity have different QSs. A model of the QS can also be derived by docking the subunits when their 3D structure is independently known, but the model is likely to be incorrect if large conformation changes take place when the oligomer assembles.

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Acknowledgments

We are grateful to E. Levy (Cambridge) for the figure and for communicating unpublished data. We acknowledge support of the 3D-Repertoire and SPINE2-Complexes programs of the European Union.

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Authors and Affiliations

  1. Yeast Structural Genomics, IBBMC UMR 8619 CNRS, Université Paris-Sud, Orsay, France

    Anne Poupon & Joel Janin

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  1. Anne Poupon
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  2. Joel Janin
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Editors and Affiliations

  1. Max F. Perutz Laboratories GmbH, Universität Wien, Dr. Bohr-Gasse 9, Wien, 1030, Austria

    Oliviero Carugo

  2. Research (A*STAR), Agency for Science & Technology, Biopolis Street 30, Singapore, 138671, Singapore

    Frank Eisenhaber

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Poupon, A., Janin, J. (2010). Analysis and Prediction of Protein Quaternary Structure. In: Carugo, O., Eisenhaber, F. (eds) Data Mining Techniques for the Life Sciences. Methods in Molecular Biology, vol 609. Humana Press. https://doi.org/10.1007/978-1-60327-241-4_20

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  • DOI: https://doi.org/10.1007/978-1-60327-241-4_20

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