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Analysis and Prediction of Protein Quaternary Structure

  • Anne Poupon
  • Joel Janin
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

oligomeric proteins protein molecular weight biomolecule molecular assembly protein–protein docking threading modeling 

Notes

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We are grateful to E. Levy (Cambridge) for the figure and for communicating unpublished data.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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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Anne Poupon
    • 1
  • Joel Janin
    • 1
  1. 1.Yeast Structural Genomics, IBBMC UMR 8619 CNRS, Université Paris-SudOrsayFrance

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