ArticlePLoS computational biology2008
Memory switches in chemical reaction space.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
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- Information encoded in volumes and areas of dendritic spines is nearly maximal across mammalian brains.Scientific reports · 2023Article
- Dynamic Biophysical Cues Near the Tip Cell Microenvironment Provide Distinct Guidance Signals to Angiogenic Neovessels.Annals of biomedical engineering · 2023Article
- Using sensitivity analyses to understand bistable system behavior.BMC bioinformatics · 2023Article
- The partition representation of enzymatic reaction networks and its application for searching bi-stable reaction systems.PloS one · 2022Article
- HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks.PLoS computational biology · 2021Article
- Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex.Neuroscience · 2016Article
- Formation and Maintenance of Robust Long-Term Information Storage in the Presence of Synaptic Turnover.PLoS computational biology · 2015Article
- Emergent chemical behavior in variable-volume protocells.Life (Basel, Switzerland) · 2015Article
- The formation of multi-synaptic connections by the interaction of synaptic and structural plasticity and their functional consequences.PLoS computational biology · 2015Article
- Elements of the cellular metabolic structure.Frontiers in molecular biosciences · 2015Article
- Catalytic constants enable the emergence of bistability in dual phosphorylation.Journal of the Royal Society, Interface · 2014Article
- Network representations and methods for the analysis of chemical and biochemical pathways.Molecular bioSystems · 2013Review
- Bottom-up construction of in vitro switchable memories.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Article
- Is life unique?Life (Basel, Switzerland) · 2011Review
- Automated refinement and inference of analytical models for metabolic networks.Physical biology · 2011Article
- Trafficking motifs as the basis for two-compartment signaling systems to form multiple stable states.Biophysical journal · 2011Article
- Robust network topologies for generating switch-like cellular responses.PLoS computational biology · 2011Article
- Emergence of switch-like behavior in a large family of simple biochemical networks.PLoS computational biology · 2011Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Just as complex electronic circuits are built from simple Boolean gates, diverse biological functions, including signal transduction, differentiation, and stress response, frequently use biochemical switches as a functional module. A relatively small number of such switches have been described in the literature, and these exhibit considerable diversity in chemical topology. We asked if biochemical switches are indeed rare and if there are common chemical motifs and family relationships among such switches. We performed a systematic exploration of chemical reaction space by generating all possible stoichiometrically valid chemical configurations up to 3 molecules and 6 reactions and up to 4 molecules and 3 reactions. We used Monte Carlo sampling of parameter space for each such configuration to generate specific models and checked each model for switching properties. We found nearly 4,500 reaction topologies, or about 10% of our tested configurations, that demonstrate switching behavior. Commonly accepted topological features such as feedback were poor predictors of bistability, and we identified new reaction motifs that were likely to be found in switches. Furthermore, the discovered switches were related in that most of the larger configurations were derived from smaller ones by addition of one or more reactions. To explore even larger configurations, we developed two tools: the "bistabilizer," which converts almost-bistable systems into bistable ones, and frequent motif mining, which helps rank untested configurations. Both of these tools increased the coverage of our library of bistable systems. Thus, our systematic exploration of chemical reaction space has produced a valuable resource for investigating the key signaling motif of bistability.
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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.