ArticlePLoS computational biology2019
Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed.
- Artificial Intelligence and Protein Design: A retrospective study on 20-year emerging trends and core research areas from bibliometric perspectives.Probiotics and antimicrobial proteins · 2026Article
- Enhancing the performance of Magnets photosensors.Nature communications · 2026Article
- Conserved structural motifs in PAS, LOV, and CRY proteins regulate circadian rhythms and are therapeutic targets.FEBS letters · 2026Review
- Molecular insights into the elevator-type mechanism of the cyanobacterial bicarbonate transporter BicA.Biophysical journal · 2025Article
- From Deep Mutational Mapping of Allosteric Protein Landscapes to Deep Learning of Allostery and Hidden Allosteric Sites: Zooming in on "Allosteric Intersection" of Biochemical and Big Data Approaches.International journal of molecular sciences · 2023Review
- Machine learning and protein allostery.Trends in biochemical sciences · 2023Review
- 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
- Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor.Computational and structural biotechnology journal · 2022Article
- Dynamics of hydrogen bonds in the secondary structures of allosteric proteinComputational and structural biotechnology journal · 2022Article
- Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE.PLoS computational biology · 2021Article
- UMAP as a Dimensionality Reduction Tool for Molecular Dynamics Simulations of Biomacromolecules: A Comparison Study.The journal of physical chemistry. B · 2021Article
- ivis Dimensionality Reduction Framework for Biomacromolecular Simulations.Journal of chemical information and modeling · 2020Article
- Deciphering the Allosteric Process of theThe journal of physical chemistry. B · 2020Article
- Unraveling the energetic significance of chemical events in enzyme catalysis via machine-learning based regression approach.Communications chemistry · 2020Article
- Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.Frontiers in molecular biosciences · 2020Review
- Directed kinetic transition network model.The Journal of chemical physics · 2019Article
- Machine Learning Classification Model for Functional Binding Modes of TEM-1 β-Lactamase.Frontiers in molecular biosciences · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an atomistic allosteric mechanism leading to the discovery of the unexpected importance of A'α/Aβ and previously overlooked Eα/Fα loops in the conformational change. This approach could be applicable to other allosteric proteins in general to provide interpretable atomistic representations of their otherwise elusive allosteric mechanisms.
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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.