ReviewPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2018
Markov models for the elucidation of allosteric regulation.
Review in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches.Journal of chemical information and modeling · 2023Review
- Domain motions, dimerization, and membrane interactions of the murine guanylate binding protein 2.Scientific reports · 2023Article
- Deep learning to decompose macromolecules into independent Markovian domains.Nature communications · 2022Article
- Allosteric control of ACE2 peptidase domain dynamics.Organic & biomolecular chemistry · 2022Article
- Using azobenzene photocontrol to set proteins in motion.Nature reviews. Chemistry · 2022Review
- Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE.PLoS computational biology · 2021Article
- Allosteric conformational ensembles have unlimited capacity for integrating information.eLife · 2021Article
- 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
- Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations.PLoS computational biology · 2019Article
- Review
- Allostery and molecular machines.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
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Authors and funding
2 authors.
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Abstract
Allosteric regulation refers to the process where the effect of binding of a ligand at one site of a protein is transmitted to another, often distant, functional site. In recent years, it has been demonstrated that allosteric mechanisms can be understood by the conformational ensembles of a protein. Molecular dynamics (MD) simulations are often used for the study of protein allostery as they provide an atomistic view of the dynamics of a protein. However, given the wealth of detailed information hidden in MD data, one has to apply a method that allows extraction of the conformational ensembles underlying allosteric regulation from these data. Markov state models are one of the most promising methods for this purpose. We provide a short introduction to the theory of Markov state models and review their application to various examples of protein allostery studied by MD simulations. We also include a discussion of studies where Markov modelling has been employed to analyse experimental data on allosteric regulation. We conclude our review by advertising the wider application of Markov state models to elucidate allosteric mechanisms, especially since in recent years it has become straightforward to construct such models thanks to software programs like PyEMMA and MSMBuilder.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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