ArticleMolecular systems biology2006
Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES.
Article in Molecular systems biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed.
- RinPy, a Python Package for Residue Interaction Network Model to Analyze Protein Structures and Predict Ligand Binding Sites.Journal of chemical information and modeling · 2026Article
- Framework for Quantifying the Efficiency of Competing Signal Transmission Modes in Proteins.Journal of the American Chemical Society · 2026Article
- Conformational Dynamics of hAgo2 Silencing: Decoding Functional Divergence across Human Argonaute Paralogs.Journal of chemical information and modeling · 2025Article
- Single-molecule FRET probes allosteric effects on protein-translocating pore loops of a AAA+ machine.Biophysical journal · 2024Article
- Combining structural and coevolution information to unveil allosteric sites.Chemical science · 2023Article
- Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase.Nature communications · 2023Article
- Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches.Journal of chemical information and modeling · 2023Review
- State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.Progress in biophysics and molecular biology · 2021Article
- Engineering an Allosteric Control of Protein Function.The journal of physical chemistry. B · 2021Review
- Structural Communication between theInternational journal of molecular sciences · 2021Article
- Comparative Analysis of Structural and Dynamical Features of Ribosome Upon Association With mRNA Reveals Potential Role of Ribosomal Proteins.Frontiers in molecular biosciences · 2021Article
- Identification of Allosteric Effects in Proteins by Elastic Network Models.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Mapping allosteric communications within individual proteins.Nature communications · 2020Article
- Integrated Computational Approaches and Tools forAllosteric Drug Discovery.International journal of molecular sciences · 2020Review
- Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.Frontiers in molecular biosciences · 2020Review
- To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations.PPAR research · 2020Article
- Review
- Molecular dynamics simulations and linear response theories jointly describe biphasic responses of myoglobin relaxation and reveal evolutionarily conserved frequent communicators.Biophysics and physicobiology · 2019Article
- Markov models for the elucidation of allosteric regulation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- Exploring allosteric communication in multiple states of the bacterial ribosome using residue network analysis.Turkish journal of biology = Turk biyoloji dergisi · 2018Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We introduce a novel approach for elucidating the potential pathways of allosteric communication in biomolecular systems. The methodology, based on Markov propagation of 'information' across the structure, permits us to partition the network of interactions into soft clusters distinguished by their coherent stochastics. Probabilistic participation of residues in these clusters defines the communication patterns inherent to the network architecture. Application to bacterial chaperonin complex GroEL-GroES, an allostery-driven structure, identifies residues engaged in intra- and inter-subunit communication, including those acting as hubs and messengers. A number of residues are distinguished by their high potentials to transmit allosteric signals, including Pro33 and Thr90 at the nucleotide-binding site and Glu461 and Arg197 mediating inter- and intra-ring communication, respectively. We propose two most likely pathways of signal transmission, between nucleotide- and GroES-binding sites across the cis and trans rings, which involve several conserved residues. A striking observation is the opposite direction of information flow within cis and trans rings, consistent with negative inter-ring cooperativity. Comparison with collective modes deduced from normal mode analysis reveals the propensity of global hinge regions to act as messengers in the transmission of allosteric signals.
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Registered trials
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.