西亚试剂：Determining the architectures of macromolecular assemblies

1. Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, 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
2. Laboratory of Cellular and Structural Biology, and,
3. Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
4. These authors contributed equally to this work.
5. 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.).

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.

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