ArticleFASEB journal : official publication of the Federation of American Societies for Experimental Biology2012
Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics.
Article in FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Article
- Allosteric Network Analysis Toolkit for Single-Domain Phosphoproteins.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Conformational dynamics and multimodal interaction of Paxillin with the focal adhesion targeting domain.Science advances · 2025Article
- Conformational dynamics and multi-modal interaction of Paxillin with the Focal Adhesion Targeting Domain.bioRxiv : the preprint server for biology · 2025Article
- Decrypting Allostery in Membrane-Bound K-Ras4B Using ComplementaryJournal of the American Chemical Society · 2024Article
- Activation mechanism of the human Smoothened receptor.Biophysical journal · 2023Article
- Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids.Journal of molecular biology · 2022Review
- Conformational spread drives the evolution of the calcium-calmodulin protein kinase II.Scientific reports · 2022Article
- PSNtools for standalone and web-based structure network analyses of conformational ensembles.Computational and structural biotechnology journal · 2022Article
- Activation mechanism ofScience advances · 2021Article
- The PyInteraph Workflow for the Study of Interaction Networks From Protein Structural Ensembles.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Structure network-based landscape of rhodopsin misfolding by mutations and algorithmic prediction of small chaperone action.Computational and structural biotechnology journal · 2021Article
- Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain.PLoS computational biology · 2020Article
- Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM.Biophysical journal · 2020Article
- webPSN v2.0: a webserver to infer fingerprints of structural communication in biomacromolecules.Nucleic acids research · 2020Article
- The Architectural Dynamics of the Bacterial Flagellar Motor Switch.Biomolecules · 2020Review
- Surveying the Side-Chain Network Approach to Protein Structure and Dynamics: The SARS-CoV-2 Spike Protein as an Illustrative Case.Frontiers in molecular biosciences · 2020Review
- The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Article
- Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II.PLoS computational biology · 2019Article
3 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
Allostery offers a highly specific way to modulate protein function. Therefore, understanding this mechanism is of increasing interest for protein science and drug discovery. However, allosteric signal transmission is difficult to detect experimentally and to model because it is often mediated by local structural changes propagating along multiple pathways. To address this, we developed a method to identify communication pathways by an information-theoretical analysis of molecular dynamics simulations. Signal propagation was described as information exchange through a network of correlated local motions, modeled as transitions between canonical states of protein fragments. The method was used to describe allostery in two-component regulatory systems. In particular, the transmission from the allosteric site to the signaling surface of the receiver domain NtrC was shown to be mediated by a layer of hub residues. The location of hubs preferentially connected to the allosteric site was found in close agreement with key residues experimentally identified as involved in the signal transmission. The comparison with the networks of the homologues CheY and FixJ highlighted similarities in their dynamics. In particular, we showed that a preorganized network of fragment connections between the allosteric and functional sites exists already in the inactive state of all three proteins.
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