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Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):9213-8. doi: 10.1073/pnas.1204952109. Epub 2012 May 21.

Multiplex assay for condition-dependent changes in protein-protein interactions.

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1
Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, CA 94304, USA.

Abstract

Changes in protein-protein interactions that occur in response to environmental cues are difficult to uncover and have been poorly characterized to date. Here we describe a yeast-based assay that allows many binary protein interactions to be assessed in parallel and under various conditions. This method combines molecular bar-coding and tag array technology with the murine dihydrofolate reductase-based protein-fragment complementation assay. A total of 238 protein-fragment complementation assay strains, each representing a unique binary protein complex, were tagged with molecular barcodes, pooled, and then interrogated against a panel of 80 diverse small molecules. Our method successfully identified specific disruption of the Hom3:Fpr1 interaction by the immunosuppressant FK506, illustrating the assay's capacity to identify chemical inhibitors of protein-protein interactions. Among the additional findings was specific cellular depletion of the Dst1:Rbp9 complex by the anthracycline drug doxorubicin, but not by the related drug idarubicin. The assay also revealed chemical-induced accumulation of several binary multidrug transporter complexes that largely paralleled increases in transcript levels. Further assessment of two such interactions (Tpo1:Pdr5 and Snq2:Pdr5) in the presence of 1,246 unique chemical compounds revealed a positive correlation between drug lipophilicity and the drug response in yeast.

PMID:
22615397
PMCID:
PMC3384208
DOI:
10.1073/pnas.1204952109
[Indexed for MEDLINE]
Free PMC Article
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