Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes
Enzymatic reactions often involve slow conformational changes, with reaction cycles that sometimes require milliseconds or seconds to complete. The dynamics are strongly affected by fluctuations at the nanoscale. However, such enzymes often occur in small numbers in a cell; hence, the fluctuations c...
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| Format: | Article |
| Language: | English |
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IOP Publishing
2015-01-01
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| Series: | New Journal of Physics |
| Subjects: | |
| Online Access: | https://doi.org/10.1088/1367-2630/17/3/033024 |
| _version_ | 1797751165331439616 |
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| author | Yuichi Togashi Vanessa Casagrande |
| author_facet | Yuichi Togashi Vanessa Casagrande |
| author_sort | Yuichi Togashi |
| collection | DOAJ |
| description | Enzymatic reactions often involve slow conformational changes, with reaction cycles that sometimes require milliseconds or seconds to complete. The dynamics are strongly affected by fluctuations at the nanoscale. However, such enzymes often occur in small numbers in a cell; hence, the fluctuations caused by finite numbers of molecules should also be substantial. Because of these factors, the behavior of the system is likely to deviate from that of classical reaction–diffusion equations, in which immediate reaction events are assumed to occur without memory and between a huge number of molecules. In this work, we model each enzyme as a unit represented by a phase variable to investigate the effects of fluctuations in arrays of enzymes. Using an analysis based on partial differential equations and stochastic simulations, we show that fluctuations arising from internal states of enzymes (intramolecular fluctuations) and those arising from the stochastic nature of interactions between molecules (intermolecular fluctuations) have distinctive effects on spatiotemporal patterns; the former generally disturb synchronization at high frequencies, whereas the latter can enhance synchronization. The balance of the two types of fluctuations may determine the spatiotemporal behavior of biochemical processes. |
| first_indexed | 2024-03-12T16:43:30Z |
| format | Article |
| id | doaj.art-6c1f8314405e41e99492603072f81b20 |
| institution | Directory Open Access Journal |
| issn | 1367-2630 |
| language | English |
| last_indexed | 2024-03-12T16:43:30Z |
| publishDate | 2015-01-01 |
| publisher | IOP Publishing |
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| series | New Journal of Physics |
| spelling | doaj.art-6c1f8314405e41e99492603072f81b202023-08-08T14:19:22ZengIOP PublishingNew Journal of Physics1367-26302015-01-0117303302410.1088/1367-2630/17/3/033024Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymesYuichi Togashi0Vanessa Casagrande1Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan; Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan; Applied Information Systems Research Division, Cybermedia Center , Osaka University, 5-1 Mihogaoka, Ibaraki, Osaka 567-0047, JapanBernstein Center for Computational Neuroscience, Humboldt University , Philippstraße 13, D-10115 Berlin, GermanyEnzymatic reactions often involve slow conformational changes, with reaction cycles that sometimes require milliseconds or seconds to complete. The dynamics are strongly affected by fluctuations at the nanoscale. However, such enzymes often occur in small numbers in a cell; hence, the fluctuations caused by finite numbers of molecules should also be substantial. Because of these factors, the behavior of the system is likely to deviate from that of classical reaction–diffusion equations, in which immediate reaction events are assumed to occur without memory and between a huge number of molecules. In this work, we model each enzyme as a unit represented by a phase variable to investigate the effects of fluctuations in arrays of enzymes. Using an analysis based on partial differential equations and stochastic simulations, we show that fluctuations arising from internal states of enzymes (intramolecular fluctuations) and those arising from the stochastic nature of interactions between molecules (intermolecular fluctuations) have distinctive effects on spatiotemporal patterns; the former generally disturb synchronization at high frequencies, whereas the latter can enhance synchronization. The balance of the two types of fluctuations may determine the spatiotemporal behavior of biochemical processes.https://doi.org/10.1088/1367-2630/17/3/033024reaction–diffusion systemsmolecular machinesdelayed feedback controlpattern formationstochastic processesintracellular processes |
| spellingShingle | Yuichi Togashi Vanessa Casagrande Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes New Journal of Physics reaction–diffusion systems molecular machines delayed feedback control pattern formation stochastic processes intracellular processes |
| title | Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes |
| title_full | Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes |
| title_fullStr | Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes |
| title_full_unstemmed | Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes |
| title_short | Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes |
| title_sort | spatiotemporal patterns enhanced by intra and inter molecular fluctuations in arrays of allosterically regulated enzymes |
| topic | reaction–diffusion systems molecular machines delayed feedback control pattern formation stochastic processes intracellular processes |
| url | https://doi.org/10.1088/1367-2630/17/3/033024 |
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