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Determining the architectures of macromolecular assemblies

Author

Listed:
  • Frank Alber

    (and California Institute for Quantitative Biosciences, Byers Hall, Suite 503B, 1700 4th Street, University of California at San Francisco, San Francisco, California 94158-2330, USA)

  • Svetlana Dokudovskaya

    (Laboratory of Cellular and Structural Biology, and,
    Present addresses: Laboratory of Nucleocytoplasmic Transport, Institut Jacques Monod, 2 place Jussieu, Tour 43, Paris 75251, France (S.D.); Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands (L.M.V.); German Aerospace Center (PT-DLR), Heinrich-Konen-Strasse 1, D-53227 Bonn, Germany (J.K.); Structural Bioinformatics, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany (D.D.); Office of Technology Transfer, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA (A.S.); Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA (O.K.-S.).)

  • Liesbeth M. Veenhoff

    (Laboratory of Cellular and Structural Biology, and,
    Present addresses: Laboratory of Nucleocytoplasmic Transport, Institut Jacques Monod, 2 place Jussieu, Tour 43, Paris 75251, France (S.D.); Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands (L.M.V.); German Aerospace Center (PT-DLR), Heinrich-Konen-Strasse 1, D-53227 Bonn, Germany (J.K.); Structural Bioinformatics, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany (D.D.); Office of Technology Transfer, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA (A.S.); Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA (O.K.-S.).)

  • Wenzhu Zhang

    (Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA)

  • Julia Kipper

    (Laboratory of Cellular and Structural Biology, and,
    Present addresses: Laboratory of Nucleocytoplasmic Transport, Institut Jacques Monod, 2 place Jussieu, Tour 43, Paris 75251, France (S.D.); Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands (L.M.V.); German Aerospace Center (PT-DLR), Heinrich-Konen-Strasse 1, D-53227 Bonn, Germany (J.K.); Structural Bioinformatics, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany (D.D.); Office of Technology Transfer, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA (A.S.); Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA (O.K.-S.).)

  • Damien Devos

    (and California Institute for Quantitative Biosciences, Byers Hall, Suite 503B, 1700 4th Street, University of California at San Francisco, San Francisco, California 94158-2330, USA
    Present addresses: Laboratory of Nucleocytoplasmic Transport, Institut Jacques Monod, 2 place Jussieu, Tour 43, Paris 75251, France (S.D.); Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands (L.M.V.); German Aerospace Center (PT-DLR), Heinrich-Konen-Strasse 1, D-53227 Bonn, Germany (J.K.); Structural Bioinformatics, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany (D.D.); Office of Technology Transfer, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA (A.S.); Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA (O.K.-S.).)

  • Adisetyantari Suprapto

    (Laboratory of Cellular and Structural Biology, and,
    Present addresses: Laboratory of Nucleocytoplasmic Transport, Institut Jacques Monod, 2 place Jussieu, Tour 43, Paris 75251, France (S.D.); Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands (L.M.V.); German Aerospace Center (PT-DLR), Heinrich-Konen-Strasse 1, D-53227 Bonn, Germany (J.K.); Structural Bioinformatics, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany (D.D.); Office of Technology Transfer, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA (A.S.); Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA (O.K.-S.).)

  • Orit Karni-Schmidt

    (Laboratory of Cellular and Structural Biology, and,
    Present addresses: Laboratory of Nucleocytoplasmic Transport, Institut Jacques Monod, 2 place Jussieu, Tour 43, Paris 75251, France (S.D.); Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands (L.M.V.); German Aerospace Center (PT-DLR), Heinrich-Konen-Strasse 1, D-53227 Bonn, Germany (J.K.); Structural Bioinformatics, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany (D.D.); Office of Technology Transfer, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA (A.S.); Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA (O.K.-S.).)

  • Rosemary Williams

    (Laboratory of Cellular and Structural Biology, and,)

  • Brian T. Chait

    (Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA)

  • Michael P. Rout

    (Laboratory of Cellular and Structural Biology, and,)

  • Andrej Sali

    (and California Institute for Quantitative Biosciences, Byers Hall, Suite 503B, 1700 4th Street, University of California at San Francisco, San Francisco, California 94158-2330, USA)

Abstract

To understand the workings of a living cell, we need to know the architectures of its macromolecular assemblies. Here we show how proteomic data can be used to determine such structures. The process involves the collection of sufficient and diverse high-quality data, translation of these data into spatial restraints, and an optimization that uses the restraints to generate an ensemble of structures consistent with the data. Analysis of the ensemble produces a detailed architectural map of the assembly. We developed our approach on a challenging model system, the nuclear pore complex (NPC). The NPC acts as a dynamic barrier, controlling access to and from the nucleus, and in yeast is a 50 MDa assembly of 456 proteins. The resulting structure, presented in an accompanying paper, reveals the configuration of the proteins in the NPC, providing insights into its evolution and architectural principles. The present approach should be applicable to many other macromolecular assemblies.

Suggested Citation

  • Frank Alber & Svetlana Dokudovskaya & Liesbeth M. Veenhoff & Wenzhu Zhang & Julia Kipper & Damien Devos & Adisetyantari Suprapto & Orit Karni-Schmidt & Rosemary Williams & Brian T. Chait & Michael P. , 2007. "Determining the architectures of macromolecular assemblies," Nature, Nature, vol. 450(7170), pages 683-694, November.
    • Handle: RePEc:nat:nature:v:450:y:2007:i:7170:d:10.1038_nature06404
    DOI: 10.1038/nature06404
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    Cited by:

    1. Daniel Russel & Keren Lasker & Ben Webb & Javier Velázquez-Muriel & Elina Tjioe & Dina Schneidman-Duhovny & Bret Peterson & Andrej Sali, 2012. "Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies," PLOS Biology, Public Library of Science, vol. 10(1), pages 1-5, January.
    2. V V Krishnan & Edmond Y Lau & Justin Yamada & Daniel P Denning & Samir S Patel & Michael E Colvin & Michael F Rexach, 2008. "Intramolecular Cohesion of Coils Mediated by Phenylalanine–Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin," PLOS Computational Biology, Public Library of Science, vol. 4(8), pages 1-13, August.

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