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Article
Nature Biotechnology  22, 724 - 731 (2004)
Published online: 16 May 2004; | doi:10.1038/nbt969

Time-controlled transcardiac perfusion cross-linking for the study of protein interactions in complex tissues

Gerold Schmitt-Ulms1, 2, 8, Kirk Hansen3, Jialing Liu4, Cynthia Cowdrey5, Jian Yang5, Stephen J DeArmond1, 5, Fred E Cohen1, 6, 7, Stanley B Prusiner1, 2, 7 & Michael A Baldwin1, 2, 3

1  Institute for Neurodegenerative Disease, 513 Parnassus Ave., San Francisco, California 94143, USA.

2  Department of Neurology, 513 Parnassus Ave., San Francisco, California 94143, USA.

3  Department of Pharmaceutical Chemistry, 521 Parnassus Ave., San Francisco, California 94143, USA.

4  Departments of Neurological Surgery and Pathology, 513 Parnassus Ave., San Francisco, California 94143, USA.

5  Departments of Neurological Surgery and Pathology, 513 Parnassus Ave., San Francisco, California 94143, USA.

6  Department of Cellular and Molecular Pharmacology, 600 16th St., San Francisco, California 94143, USA.

7  Department of Biochemistry and Biophysics, 513 Parnassus Ave., University of California, San Francisco, California 94143, USA.

8  Present address: Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario M5S 3H2, Canada.

Correspondence should be addressed to Gerold Schmitt-Ulms g.schmittulms@utoronto.ca or Michael A Baldwin mikeab@itsa.ucsf.edu
Because of their sensitivity to solubilizing detergents, membrane protein assemblies are difficult to study. We describe a protocol that covalently conserves protein interactions through time-controlled transcardiac perfusion cross-linking (tcTPC) before disruption of tissue integrity. To validate tcTPC for identifying protein-protein interactions, we established that tcTPC allowed stringent immunoaffinity purification of the bold gamma-secretase complex in high salt concentrations and detergents and was compatible with mass spectrometric identification of cross-linked aph-1, presenilin-1 and nicastrin. We then applied tcTPC to identify more than 20 proteins residing in the vicinity of the cellular prion protein (PrPC), suggesting that PrP is embedded in specialized membrane regions with a subset of molecules that, like PrP, use a glycosylphosphatidylinositol anchor for membrane attachment. Many of these proteins have been implicated in cell adhesion/neuritic outgrowth, and harbor immunoglobulin C2 and fibronectin type III−like motifs.

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Nature Biotechnology
ISSN: 1087-0156
EISSN: 1546-1696
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