Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads
- Stanford University, United States
- University of California, San Francisco, United States
Abstract
Transient, regulated binding of globular protein domains to Short Linear Motifs (SLiMs) in disordered regions of other proteins drives cellular signaling. Mapping the energy landscapes of these interactions is essential for deciphering and perturbing signaling networks but is challenging due to their weak affinities. We present a powerful technology (MRBLE-pep) that simultaneously quantifies protein binding to a library of peptides directly synthesized on beads containing unique spectral codes. Using MRBLE-pep, we systematically probe binding of human calcineurin (CN), a conserved protein phosphatase essential for the immune response and target of immunosuppressants, to the PxIxIT SLiM. We discover that flanking residues and post-translational modifications critically contribute to PxIxIT-CN affinity and identify CN-binding peptides based on multiple scaffolds with a wide range of affinities. The quantitative biophysical data provided by this approach will improve computational modeling efforts, elucidate a broad range of weak protein-SLiM interactions, and revolutionize our understanding of signaling networks.
Data availability
All data generated or analysed during this study are included in the manuscript and supporting files. In addition, all data generated or analyzed during this study are available in an associated public OSF repository (DOI 10.17605/OSF.IO/FPVE2).
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Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beadsOpen Science Framework, DOI 10.17605/OSF.IO/FPVE2.
Article and author information
Author details
Polly Morrell Fordyce
Funding
National Institute of General Medical Sciences (DP2GM123641)
- Polly Morrell Fordyce
National Institute of General Medical Sciences (R01GM107132)
- Kurt S Thorn
National Institute of General Medical Sciences (R01GM119336)
- Martha S Cyert
National Institute of General Medical Sciences (R01GM117189)
- Tanja Kortemme
National Institute of General Medical Sciences (R01GM110089)
- Tanja Kortemme
Chan Zuckerberg Biohub
- Tanja Kortemme
Chan Zuckerberg Biohub
- Polly Morrell Fordyce
Sloan Foundation
- Polly Morrell Fordyce
Beckman Foundation
- Polly Morrell Fordyce
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Michael A Marletta, University of California, Berkeley, United States
Version history
- Received: August 8, 2018
- Accepted: July 3, 2019
- Accepted Manuscript published: July 8, 2019 (version 1)
- Version of Record published: September 5, 2019 (version 2)
Copyright
© 2019, Nguyen et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads
eLife 8:e40499.
https://doi.org/10.7554/eLife.40499
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