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Science 337 (6100): 1348-1352

Copyright © 2012 by the American Association for the Advancement of Science

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

Franz Herzog,1,* Abdullah Kahraman,1,* Daniel Boehringer,2,* Raymond Mak,1 Andreas Bracher,4 Thomas Walzthoeni,1 Alexander Leitner,1 Martin Beck,3 Franz-Ulrich Hartl,4 Nenad Ban,2 Lars Malmström,1 Ruedi Aebersold1,{dagger}

Abstract: The identification of proximate amino acids by chemical cross-linking and mass spectrometry (XL-MS) facilitates the structural analysis of homogeneous protein complexes. We gained distance restraints on a modular interaction network of protein complexes affinity-purified from human cells by applying an adapted XL-MS protocol. Systematic analysis of human protein phosphatase 2A (PP2A) complexes identified 176 interprotein and 570 intraprotein cross-links that link specific trimeric PP2A complexes to a multitude of adaptor proteins that control their cellular functions. Spatial restraints guided molecular modeling of the binding interface between immunoglobulin binding protein 1 (IGBP1) and PP2A and revealed the topology of TCP1 ring complex (TRiC) chaperonin interacting with the PP2A regulatory subunit 2ABG. This study establishes XL-MS as an integral part of hybrid structural biology approaches for the analysis of endogenous protein complexes.

1 Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland.
2 Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Schafmattstrasse 20, 8093 Zurich, Switzerland.
3 European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
4 Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: aebersold{at}imsb.biol.ethz.ch

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