ArticleProceedings of the National Academy of Sciences of the United States of America2017
Time-resolved observation of protein allosteric communication.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- A Bayesian Approach to Interpret Time-Resolved Experiments Using Molecular Simulations.ACS physical chemistry Au · 2026Article
- Contact Cluster Modeling of Allosteric Communication in PDZ Domains.The journal of physical chemistry. B · 2026Review
- Framework for Quantifying the Efficiency of Competing Signal Transmission Modes in Proteins.Journal of the American Chemical Society · 2026Article
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches.Journal of chemical information and modeling · 2023Review
- Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids.Journal of molecular biology · 2022Review
- Energy Transport alongMaterials (Basel, Switzerland) · 2022Article
- Using azobenzene photocontrol to set proteins in motion.Nature reviews. Chemistry · 2022Review
- GCAT: A network model of mutational influences between amino acid positions in PSD95Frontiers in molecular biosciences · 2022Article
- Allosteric regulation of substrate channeling:Frontiers in molecular biosciences · 2022Review
- Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE.PLoS computational biology · 2021Article
- Hierarchical dynamics in allostery following ATP hydrolysis monitored by single molecule FRET measurements and MD simulations.Chemical science · 2021Article
- Mapping Function from Dynamics: Future Challenges for Network-Based Models of Protein Structures.Frontiers in molecular biosciences · 2021Article
- Sensing the allosteric force.Nature communications · 2020Article
- Real-time observation of ligand-induced allosteric transitions in a PDZ domain.Proceedings of the National Academy of Sciences of the United States of America · 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
- Energy flow and intersubunit signalling in GSAM: A non-equilibrium molecular dynamics study.Computational and structural biotechnology journal · 2020Article
- Topology, landscapes, and biomolecular energy transport.Nature communications · 2019Article
- Networked Communication between Polymerase and Exonuclease Active Sites in Human Mitochondrial DNA Polymerase.Journal of the American Chemical Society · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Allostery represents a fundamental mechanism of biological regulation that is mediated via long-range communication between distant protein sites. Although little is known about the underlying dynamical process, recent time-resolved infrared spectroscopy experiments on a photoswitchable PDZ domain (PDZ2S) have indicated that the allosteric transition occurs on multiple timescales. Here, using extensive nonequilibrium molecular dynamics simulations, a time-dependent picture of the allosteric communication in PDZ2S is developed. The simulations reveal that allostery amounts to the propagation of structural and dynamical changes that are genuinely nonlinear and can occur in a nonlocal fashion. A dynamic network model is constructed that illustrates the hierarchy and exceeding structural heterogeneity of the process. In compelling agreement with experiment, three physically distinct phases of the time evolution are identified, describing elastic response ([Formula: see text] ns), inelastic reorganization ([Formula: see text] ns), and structural relaxation ([Formula: see text]s). Issues such as the similarity to downhill folding as well as the interpretation of allosteric pathways are discussed.
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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.