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Gel chromatography and analytical ultracentrifugation to determine the extent of detergent binding and aggregation, and Stokes radius of membrane proteins using sarcoplasmic reticulum Ca2+–ATPase as an example

Nature Protocols volume 3, pages 17821795 (2008) | Download Citation

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Abstract

For structural studies of integral membrane proteins, including their 3D crystallization, the judicious use of detergent for solubilization and purification is required. Detergent binding by the solubilized protein is an important parameter to determine the hydrodynamic properties in terms of size and aggregational (monomeric/oligo(proto)meric) state of the protein. Detergent binding can be measured by gel filtration chromatography under equilibrium conditions and after separation from mixed micelles of solubilized lipid and detergent. Using sarcoplasmic reticulum Ca2+-ATPase as an example, we demonstrate in this protocol complete procedures for measurement of detergent binding using (i) radiolabeled n-dodecyl-β-D-maltoside (DM) or (ii) from measurements of the increase in refractive index due to the presence of bound detergent on the protein. The latter measurement can also be performed by sedimentation velocity (SV) analysis in the analytical ultracentrifuge which in addition allows determination of the sedimentation coefficient. In combination with estimation of Stokes radius by gel filtration calibration, the molecular mass and asymmetry of the solubilized protein can be calculated. In the proposed protocols, the gel chromatographic procedures require 1 d; SV experiments are performed just after size exclusion. The whole time for these experiments is 24 h. Data analysis of analytical ultracentrifugation requires a couple of days.

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Acknowledgements

This study was funded in part by grants from the Commissariat à l'Energie Atomique program Signalisation et transport membranaires (to M.l.M. and C.E.) and in part by an Agence Nationale de la Recherche grant (ANR-06-BLAN-0239-01) (to M.l.M.), by the Danish Medical Research Council, Aarhus University Research Foundation, and The Vilhelm Pedersen Foundation (to J.V.M.) and a Ph.D. stipend to C.O. from the Medical Faculty, Aarhus University. This protocol was improved over the years, in particular, thanks to the biennial EMBO Practical Course 'Current Methods in Membrane Protein Research' at The European Molecular Biology Laboratory, Heidelberg, Germany, organized in part by the late Matti Saraste to whom we would like to dedicate this work.

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Affiliations

  1. CEA, Institut de Biologie et Technologies de Saclay, F-91191 Gif-sur-Yvette, France.

    • Marc le Maire
    • , Bertrand Arnou
    •  & Dominique Georgin
  2. CNRS, Unité de Recherche Associée 2096, F-91191 Gif-sur-Yvette, France.

    • Marc le Maire
    •  & Bertrand Arnou
  3. Université Paris-Sud 11, LRA 17V, F-91191 Gif-sur-Yvette, France.

    • Marc le Maire
    •  & Bertrand Arnou
  4. Centre for Membrane Pumps in Cells and Disease—PUMPKIN, Danish National Research Foundation, Institute of Physiology and Biophysics, University of Aarhus, DK-8000 Aarhus C, Denmark.

    • Claus Olesen
    •  & Jesper V Møller
  5. CEA, Direction des Sciences du Vivant, Institut de Biologie Structurale, F-38027 Grenoble, France.

    • Christine Ebel
  6. CNRS, Institut de Biologie Structurale, Unite Mixte de Recherche 5075, F-38027 Grenoble, France.

    • Christine Ebel
  7. Université Joseph Fourier, Institut de Biologie Structurale, F-38027 Grenoble, France.

    • Christine Ebel

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Correspondence to Marc le Maire.

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https://doi.org/10.1038/nprot.2008.177

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