Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution
Open accessPublished version of a preprint
Abstract
The utility of genetically encoded biosensors for sensing the activity of signaling proteins has been hampered by a lack of strategies for matching sensor sensitivity to the physiological concentration range of the target. Here we used computational protein design to generate intracellular sensors of Ras activity (LOCKR-based Sensor for Ras activity (Ras-LOCKR-S)) and proximity labelers of the Ras signaling environment (LOCKR-based, Ras activity-dependent Proximity Labeler (Ras-LOCKR-PL)). These tools allow the detection of endogenous Ras activity and labeling of the surrounding environment at subcellular resolution. Using these sensors in human cancer cell lines, we identified Ras-interacting proteins in oncogenic EML4-Alk granules and found that Src-Associated in Mitosis 68-kDa (SAM68) protein specifically enhances Ras activity in the granules. The ability to subcellularly localize endogenous Ras activity should deepen our understanding of Ras function in health and disease and may suggest potential therapeutic strategies.
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Cites
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- Authors
- Zhang, J. Z., Nguyen, W. H., Greenwood, N., Rose, J. C., Ong, S.-E., Maly, D. J., & Baker, D.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of Washington (US)
- Stanford Medicine (US)
- Corresponding author
- Zhang, Jason Z.
- Maly, Dustin J.
- Baker, David
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2024-01-25
- Volume
- 42
- Issue
- 12
- Pages
- 1888-1898
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC11631767
- OpenAlex
- W4391223677
- Cited by
- 37
- References
- 8
- Citations by year
- 2026: 13 · 2025: 19 · 2024: 4 · 2023: 1
- FWCI
- 4.90
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Biotechnology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Helen Hay Whitney Foundation
- Howard Hughes Medical Institute
- Audacious Project
- U.S. Department of Health & Human Services | National Institutes of Health (S10OD021502, R01GM145011, R01GM086858)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Biotin and Related Studies
- Keywords
- genetically encoded biosensors, computational protein design, proximity labeling, subcellular localization, Sam68, oncogenic signaling, cancer cell lines
- MeSH terms
- Humans, Biosensing Techniques, Signal Transduction, ras Proteins, Cell Line, Tumor, Adaptor Proteins, Signal Transducing
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