Evolutionary Stability of Small Molecular Regulatory Networks That Exhibit Near-Perfect Adaptation
| dc.contributor.author | Singhania, Rajat | en |
| dc.contributor.author | Tyson, John J. | en |
| dc.date.accessioned | 2023-06-27T17:27:00Z | en |
| dc.date.available | 2023-06-27T17:27:00Z | en |
| dc.date.issued | 2023-06-09 | en |
| dc.date.updated | 2023-06-27T13:22:10Z | en |
| dc.description.abstract | Large-scale protein regulatory networks, such as signal transduction systems, contain small-scale modules (‘motifs’) that carry out specific dynamical functions. Systematic characterization of the properties of small network motifs is therefore of great interest to molecular systems biologists. We simulate a generic model of three-node motifs in search of near-perfect adaptation, the property that a system responds transiently to a change in an environmental signal and then returns near-perfectly to its pre-signal state (even in the continued presence of the signal). Using an evolutionary algorithm, we search the parameter space of these generic motifs for network topologies that score well on a pre-defined measure of near-perfect adaptation. We find many high-scoring parameter sets across a variety of three-node topologies. Of all possibilities, the highest scoring topologies contain incoherent feed-forward loops (IFFLs), and these topologies are evolutionarily stable in the sense that, under ‘macro-mutations’ that alter the topology of a network, the IFFL motif is consistently maintained. Topologies that rely on negative feedback loops with buffering (NFLBs) are also high-scoring; however, they are not evolutionarily stable in the sense that, under macro-mutations, they tend to evolve an IFFL motif and may—or may not—lose the NFLB motif. | en |
| dc.description.version | Published version | en |
| dc.format.mimetype | application/pdf | en |
| dc.identifier.citation | Singhania, R.; Tyson, J.J. Evolutionary Stability of Small Molecular Regulatory Networks That Exhibit Near-Perfect Adaptation. Biology 2023, 12, 841. | en |
| dc.identifier.doi | https://doi.org/10.3390/biology12060841 | en |
| dc.identifier.uri | http://hdl.handle.net/10919/115535 | en |
| dc.language.iso | en | en |
| dc.publisher | MDPI | en |
| dc.rights | Creative Commons Attribution 4.0 International | en |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en |
| dc.subject | perfect adaptation | en |
| dc.subject | molecular regulatory networks | en |
| dc.subject | evolutionary algorithm | en |
| dc.subject | evolutionary stability | en |
| dc.subject | incoherent feedforward loops | en |
| dc.title | Evolutionary Stability of Small Molecular Regulatory Networks That Exhibit Near-Perfect Adaptation | en |
| dc.title.serial | Biology | en |
| dc.type | Article - Refereed | en |
| dc.type.dcmitype | Text | en |