Molecular Synchronization Waves in Arrays of Allosterically Regulated Enzymes

Casagrande, Vanessa; Togashi, Yuichi; Mikhailov, Alexander S.

doi:10.1103/physrevlett.99.048301

Cited by 13 publications

(19 citation statements)

References 21 publications

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“…We modeled each enzyme as shown in figure 1, using similar methods to those described in our previous studies [6,7] (see also [13][14][15][16]). The state of enzyme i at time t is represented by a single phase coordinate ϕ t ( )…”

Section: Methodsmentioning

confidence: 99%

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Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes

Togashi

Casagrande

2015

New J. Phys.

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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.

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Section: Methodsmentioning

confidence: 99%

“…We previously reported the synchronization of enzymes in systems such as these, where interactions manifest via diffusive product molecules [6,7]. Spatiotemporal patterns of product concentrations such as traveling waves, standing waves, and spirals were observed.…”

Section: Introductionmentioning

confidence: 99%

Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes

Togashi

Casagrande

2015

New J. Phys.

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“…Note that the machines are still sufficiently well separated one from another and possible synchronization effects of their cycles (cf. [11]) are therefore neglected.…”

Section: Formulation Of the Modelmentioning

confidence: 99%

Towards active microfluidics: Interface turbulence in thin liquid films with floating molecular machines

Alonso

Mikhailov

2009

Phys. Rev. E

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Thin liquid films with floating active protein machines are considered. Cyclic mechanical motions within the machines, representing microscopic swimmers, lead to molecular propulsion forces applied to the air-liquid interface. We show that, when the rate of energy supply to the machines exceeds a threshold, the flat interface becomes linearly unstable. As the result of this instability, the regime of interface turbulence, characterized by irregular traveling waves and propagating machine clusters, is established. Numerical investigations of this nonlinear regime are performed. Conditions for the experimental observation of the instability are discussed.

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“…Complex dynamical synchronization patterns and travelling waves have been seen in numerical simulations. [69]…”

Section: Related Systemsmentioning

confidence: 99%

Nonequilibrium Microstructures in Reactive Monolayers as Soft Matter Systems

Mikhailov

Ertl

2009

ChemPhysChem

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Chemical systems provide classical examples of nonequilibrium pattern formation. Reactions in weak aqueous solutions, such as the extensively investigated Belousov-Zhabotinsky reaction, demonstrate a rich variety of patterns, ranging from travelling fronts to rotating spiral waves and chemical turbulence. Pattern formation in such systems is based on interplay between the reactions and diffusion. Intrinsically, this puts a restriction on the minimum length scale of the developing structures, which cannot be shorter than the diffusion length of the reactants. However, much smaller nonequilibrium structures, with characteristic lengths reaching down to nanoscales, are also possible. They are found in reactive soft matter, where energetic interactions between molecules are present as well. In these systems, chemical reactions and diffusion interfere with phase transitions, yielding active, stationary or dynamic microstructures. Nonequilibrium soft-matter microstructures are of fundamental importance for biological cells and may have interesting engineering applications. In this Minireview, we focus on the microstructures found in reactive soft-matter monolayers at solid surfaces or liquid-air interfaces.

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Molecular Synchronization Waves in Arrays of Allosterically Regulated Enzymes

Cited by 13 publications

References 21 publications

Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes

Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes

Towards active microfluidics: Interface turbulence in thin liquid films with floating molecular machines

Nonequilibrium Microstructures in Reactive Monolayers as Soft Matter Systems

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