ArticleJournal of chemical theory and computation2017
Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 78 citations in OpenAlex.
- A programmable lipid-triggered allosteric site modulates LC3 LIR receptor binding activity.Nature communications · 2026Article
- Mapping Allosteric Communication in the Nucleosome with Conditional Activity.Journal of chemical information and modeling · 2026Article
- Decrypting cryptic pockets with physics-based simulations and artificial intelligence.Current opinion in structural biology · 2026Review
- Comparing cryo-EM methods and molecular dynamics simulation to investigate heterogeneity in ligand-bound TRPV1.Nature communications · 2025Article
- Quantified Dynamics-Property Relationships: Data-Efficient Protein Engineering with Machine Learning of Protein Dynamics.Journal of chemical information and modeling · 2025Article
- MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- The G Protein Inhibitor YM-254890 is an Allosteric Glue.Journal of molecular biology · 2025Article
- Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses.Journal of molecular biology · 2025Review
- Discrete protein dynamics enable long-range communication.bioRxiv : the preprint server for biology · 2025Article
- Sparse networks of conformational fluctuations communicate signals within proteins.bioRxiv : the preprint server for biology · 2025Article
- Mapping Allosteric Communication in the Nucleosome with Conditional Activity.bioRxiv : the preprint server for biology · 2025Article
- Opening and closing of a cryptic pocket in VP35 toggles it between two different RNA-binding modes.eLife · 2025Article
- PathogenicThe journal of physical chemistry. B · 2025Article
- Regulation of the ordinal DNA translocation cycle in bacteriophage Φ29 through trans-subunit interactions.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- SARS-CoV-2 Mpro Dihedral Angles Reveal Allosteric Signaling.Proteins · 2025Article
- Mapping allosteric rewiring in related protein structures from collections of crystallographic multiconformer models.bioRxiv : the preprint server for biology · 2025Article
- Regulating IL-2 Immune Signaling Function Via A Core Allosteric Structural Network.Journal of molecular biology · 2025Article
- AlloViz: A tool for the calculation and visualisation of protein allosteric communication networks.Computational and structural biotechnology journal · 2024Article
- The G protein inhibitor YM-254890 is an allosteric glue.bioRxiv : the preprint server for biology · 2024Article
- SARS-CoV-2 3CLPro Dihedral Angles Reveal Allosteric Signaling.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Allosteric (i.e., long-range) communication within proteins is crucial for many biological processes, such as the activation of signaling cascades in response to specific stimuli. However, the physical basis for this communication remains unclear. Existing computational methods for identifying allostery focus on the role of concerted structural changes, but recent experimental work demonstrates that disorder is also an important factor. Here, we introduce the Correlation of All Rotameric and Dynamical States (CARDS) framework for quantifying correlations between both the structure and disorder of different regions of a protein. To quantify disorder, we draw inspiration from methods for quantifying "dynamic heterogeneity" from chemical physics to classify segments of a dihedral's time evolution as being in either ordered or disordered regimes. To demonstrate the utility of this approach, we apply CARDS to the Catabolite Activator Protein (CAP), a transcriptional activator that is regulated by Cyclic Adenosine MonoPhosphate (cAMP) binding. We find that CARDS captures allosteric communication between the two cAMP-Binding Domains (CBDs). Importantly, CARDS reveals that this coupling is dominated by disorder-mediated correlations, consistent with NMR experiments that establish allosteric coupling between the CBDs occurs without a concerted structural change. CARDS also recapitulates an enhanced role for disorder in the communication between the DNA-Binding Domains (DBDs) and CBDs in the S62F variant of CAP. Finally, we demonstrate that using CARDS to find communication hotspots identifies regions of CAP that are in allosteric communication without foreknowledge of their identities. Therefore, we expect CARDS to be of great utility for both understanding and predicting allostery.
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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.