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Repeated two-hybrid screening detects transient protein–protein interactions

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Abstract

Yeast two-hybrid (Y2H) screening is a powerful method to detect protein–protein interactions (PPI) at the genomic-scale. A recently proposed framework for binary interactome mapping recommends the repeated screening approach to improve the quality of PPI data. Such repeated screening reveals Y2H interactions ranging from highly sampled to singleton interactions. The quality and the biological significance of interactions from distinguished sampling classes remain unknown. In order to systematically characterize such interactions, we have chosen a dataset of 1,262 interactions that were screened repeatedly four-times. The interactions were classified as highly sampled, weakly sampled, and singleton interactions. We assessed the quality of interactions in different sampling classes using features such as protein structural properties, conservation in yeast and presence of known domain–domain interactions that are previously associated with false positive rates. Our analysis reveals that the quality of singleton interactions is comparable to that of highly sampled interactions. Interestingly, singletons encompass a higher fraction of known domain–domain interactions than highly sampled ones. Furthermore, we observed that the singleton interactions are transient in nature, while the highly sampled interactions are predominantly part of stable complexes. Hence, the repeated Y2H screening method is ideal for detecting transient PPIs that are crucial in cellular signaling pathways.

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Acknowledgments

We thank Sathyapriya Rajagopal for editorial support. The work was supported by the German BMBF (NGFN2 KB-P04T03/T05, 01GR0471, 01GR0475; NGFNp NeuroNet-TP1/TP3, 01GS08170, 01GS08171).

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Authors and Affiliations

  1. Max Delbrueck Center for Molecular Medicine (MDC), AG Neuroproteomics, Robert-Rössle-Str. 10, 13125, Berlin-Buch, Germany

    Arunachalam Vinayagam & Erich E. Wanker

  2. Max Planck Institute for Molecular Genetics (MPI-MG), Otto-Warburg Laboratory, Ihnestraße 63-73, 14195, Berlin, Germany

    Ulrich Stelzl

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  1. Arunachalam Vinayagam
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  2. Ulrich Stelzl
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  3. Erich E. Wanker
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Correspondence to Arunachalam Vinayagam or Erich E. Wanker.

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Dedicated to Professor Sandor Suhai on the occasion of his 65th birthday and published as part of the Suhai Festschrift Issue.

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Vinayagam, A., Stelzl, U. & Wanker, E.E. Repeated two-hybrid screening detects transient protein–protein interactions. Theor Chem Acc 125, 613–619 (2010). https://doi.org/10.1007/s00214-009-0651-8

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