ArticleProtein science : a publication of the Protein Society2024
AlphaFold2 captures the conformational landscape of the HAMP signaling domain.
Article in Protein science : a publication of the Protein Society, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 19 citations in OpenAlex.
- ThemBio · 2026Article
- Conformational diversity in poly-HAMP arrays and its implications for signal transduction.Protein science : a publication of the Protein Society · 2026Article
- Learnable protein representations in computational biology for predicting drug-target affinity.Journal of cheminformatics · 2026Review
- Sequence Prediction, Structural Modelling and the Challenges of Plasticity in Coiled Coils.Sub-cellular biochemistry · 2026Review
- Generation of protein dynamics by machine learning.Current opinion in structural biology · 2025Review
- CCfrag: scanning folding potential of coiled-coil fragments with AlphaFold.Bioinformatics advances · 2025Article
- Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains.Protein science : a publication of the Protein Society · 2025Article
- Atomic insights into the signaling landscape of E. coli PhoQ histidine kinase from molecular dynamics simulations.Scientific reports · 2024Article
- AlphaFold2 captures the conformational landscape of the HAMP signaling domain.Protein science : a publication of the Protein Society · 2024Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
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Abstract
In this study, we present a conformational landscape of 5000 AlphaFold2 models of the Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases (HAMP) domain, a short helical bundle that transduces signals from sensors to effectors in two-component signaling proteins such as sensory histidine kinases and chemoreceptors. The landscape reveals the conformational variability of the HAMP domain, including rotations, shifts, displacements, and tilts of helices, many combinations of which have not been observed in experimental structures. HAMP domains belonging to a single family tend to occupy a defined region of the landscape, even when their sequence similarity is low, suggesting that individual HAMP families have evolved to operate in a specific conformational range. The functional importance of this structural conservation is illustrated by poly-HAMP arrays, in which HAMP domains from families with opposite conformational preferences alternate, consistent with the rotational model of signal transduction. The only poly-HAMP arrays that violate this rule are predicted to be of recent evolutionary origin and structurally unstable. Finally, we identify a family of HAMP domains that are likely to be dynamic due to the presence of a conserved pi-helical bulge. All code associated with this work, including a tool for rapid sequence-based prediction of the rotational state in HAMP domains, is deposited at https://github.com/labstructbioinf/HAMPpred.
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