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Structural modeling reveals the allosteric switch controlling the chitin utilization program of Vibrio cholerae
Open accessPublished version of a preprint
Abstract
Signal transduction by histidine kinases (HKs) is nearly ubiquitous in bacterial species. HKs can either sense ligands directly or indirectly via a cognate solute-binding protein (SBP). The molecular basis for SBP-dependent signal reception, however, remains poorly understood in most cases. CBP and ChiS are the SBP–HK pair that activate the chitin utilization program of Vibrio cholerae . Here, we elucidate the molecular basis for allosteric regulation of CBP–ChiS by generating structural models of this complex in the unliganded and liganded states, which we support with extensive genetic, biochemical, and cell biological analysis. Our results reveal that ligand-binding induces a large conformational interface switch that is distinct from previously described SBP–HKs. Structural modeling suggests that similar interface switches may also regulate other uncharacterized SBP–HKs. Together, these results extend our understanding of signal transduction in bacterial species and highlight an approach for uncovering the molecular basis of allostery in protein complexes.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Accurate structure prediction of biomolecular interactions with AlphaFold 3
Abramson, J., Adler, J., Dunger, J., Evans, R., Green, T., Pritzel, A., Ronneberger, O., Willmore, L., Ballard, A. J., Bambrick, J., et al. (2024) · Nature · doi:10.1038/s41586-024-07487-w · Cited by 15,861 · cited 1×
“To help define the molecular basis for CBP - dependent allosteric regulation of ChiS activity, we sought to generate structural models of CBP–ChiS using AlphaFold - Multimer v3 (AF - Mv3) (16–18) and AlphaFold3 (AF3) (19).”
Predicting multiple conformations via sequence clustering and AlphaFold2
Wayment-Steele, H. K., Ojoawo, A., Otten, R., Apitz, J. M., Pitsawong, W., Hömberger, M., Ovchinnikov, S., Colwell, L., & Kern, D. (2024) · Nature · doi:10.1038/s41586-023-06832-9 · Cited by 545
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Metadata
- Authors
- Anderson, H. S., & Dalia, A. B.
- Affiliations
- Indiana University Bloomington (US)
- Corresponding author
- Dalia, Ankur B.
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2025-12-04
- Volume
- 122
- Issue
- 49
- Pages
- e2523358122-e2523358122
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC12704726
- OpenAlex
- W4417002172
- Cited by
- 1
- References
- 3
- Citations by year
- 2025: 1
- FWCI
- 0.59
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed Central (submittedVersion)
- Funders
- HHS | NIH (R35GM128674)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Studies on Chitinases and Chitosanases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Keywords
- Vibrio cholerae, chitin utilization, solute binding protein, histidine kinase, CBP, allosteric regulation, ligand-induced conformational change, signal transduction, protein complex structure, structural modeling
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