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Protein interaction discovery using parallel analysis of translated ORFs (PLATO)

Abstract

Identifying physical interactions between proteins and other molecules is a critical aspect of biological analysis. Here we describe PLATO, an in vitro method for mapping such interactions by affinity enrichment of a library of full-length open reading frames displayed on ribosomes, followed by massively parallel analysis using DNA sequencing. We demonstrate the broad utility of the method for human proteins by identifying known and previously unidentified interacting partners of LYN kinase, patient autoantibodies, and the small-molecules gefitinib and dasatinib.

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Figure 1: Parallel analysis of translated ORFs (PLATO).
Figure 2: Identification of known and previously undescribed interactions using PLATO.

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Acknowledgements

We would like to thank K. Waraska, M. Cicero, S. Alian and A. Gagne for assistance with Illumina sequencing, and J. Laserson for statistical advice. Thanks to D. Zhu for help with synthesis of biotin-dasatinib, which was partially supported by US National Institutes of Health U54 CA156734 to the University of Massachusetts Boston–Dana-Farber Harvard Cancer Center U54 Comprehensive Partnership (Project 3, Co-PIs: N.S. Gray, W. Zhang, and P.L. Yang). We also thank N. Gray at Harvard Medical School for valuable advice, and H. Varmus at the National Cancer Institute for providing gefitinib reagents and advice. This work was supported in part by NIH grant 3P30CA023100-25S8 to S.K. S.J.E. is an investigator with the Howard Hughes Medical Institute.

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Authors

Contributions

S.J.E. and H.B.L. conceived and supervised the project. pRD human ORFeome library was constructed by J.Z., and characterized by J.Z. and H.B.L. The PLATO protocol was developed by H.B.L. and J.Z. Clinical evaluations and patient sample acquisitions were performed by S.K. Statistical analysis was performed by U.L. under the supervision of G.C. R.S. provided gefitinib-conjugated beads. PLATO candidates were confirmed by J.Z. and G.G. A.C. provided support for the validation of LYN binding candidates. N.P. provided support for the validation of PND autoantigen candidates. Z.Z. and W.Z. provided biotin-dasatinib. The manuscript was prepared by H.B.L. and J.Z., and edited by S.J.E.

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Correspondence to Stephen J Elledge.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figs. 1–6 and Supplementary Methods (PDF 3363 kb)

Supplementary Tables 1-4

ORFeome enrichment by GST-LYN, ORFeome enrichment by PND patient autoantibodies, ORFeome enrichment by dasatinib, Sequences of DNA primers used in this study (XLSX 101 kb)

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Zhu, J., Larman, H., Gao, G. et al. Protein interaction discovery using parallel analysis of translated ORFs (PLATO). Nat Biotechnol 31, 331–334 (2013). https://doi.org/10.1038/nbt.2539

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