ArticleJournal of chemical theory and computation2016
The Allostery Landscape: Quantifying Thermodynamic Couplings in Biomolecular Systems.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Framework for Quantifying the Efficiency of Competing Signal Transmission Modes in Proteins.Journal of the American Chemical Society · 2026Article
- The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase.Communications biology · 2022Article
- MptpA Kinetics Enhanced by Allosteric Control of an Active Conformation.Journal of molecular biology · 2022Article
- Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids.Journal of molecular biology · 2022Review
- Lipase-catalyzed esterification in water enabled by nanomicelles. Applications to 1-pot multi-step sequences.Chemical science · 2022Article
- Theory of Allosteric Regulation in Hsp70 Molecular Chaperones.QRB discovery · 2020Article
- Kinetic asymmetry allows macromolecular catalysts to drive an information ratchet.Nature communications · 2019Review
- 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
- Fluctuation Theorem of Information Exchange within an Ensemble of Paths Conditioned on Correlated-Microstates.Entropy (Basel, Switzerland) · 2019Article
- A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins.PLoS computational biology · 2018Article
- A partially-open inward-facing intermediate conformation of LeuT is associated with NaNature communications · 2018Article
- Thermodynamic Coupling Function Analysis of Allosteric Mechanisms in the Human Dopamine Transporter.Biophysical journal · 2018Article
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3 authors.
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Abstract
Allostery plays a fundamental role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two collective variables is not a single number, but instead a two-dimensional thermodynamic coupling function that is directly related to the mutual information from information theory and the copula density function from probability theory. On this basis, we demonstrate how to quantify the contribution of specific energy terms to this thermodynamic coupling function, enabling an approximate decomposition that reveals the mechanism of allostery. We illustrate the thermodynamic coupling function and its use by showing how allosteric coupling in the alanine dipeptide molecule contributes to the overall shape of the Φ/Ψ free energy surface, and by identifying the interactions that are necessary for this coupling.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.