Four‐Variable Model of an Enzymatic Oscillator Based on Trypsin

Semenov, Sergey N.; Ainla, Alar; Skorb, Ekaterina V.; Postma, Sjoerd G. J.

doi:10.1002/ijch.201700146

Cited by 6 publications

(5 citation statements)

References 29 publications

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“…The points at [Maleimide] = 6.2 mM; f / V = 2.42 × 10 −4 and 2.96 × 10 −4 s −1 represent locally stable steady states. The red and blue colors denote the result of the linear stability analysis of the three-variable model with the following parameters: [ 8 ] = 56 mM; k 1 = 0.507 s −1 M −1 , k 2 = 300 s −1 M −1 , k 3 = 0.0099 s −1 , k 4 = 3.7 × 10 −5 s −1 (Supplementary Section 7 ) 60 . e The experimental observation of the locally stable steady state.…”

Section: Resultsmentioning

confidence: 99%

Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization

et al. 2021

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Autocatalytic and oscillatory networks of organic reactions are important for designing life-inspired materials and for better understanding the emergence of life on Earth; however, the diversity of the chemistries of these reactions is limited. In this work, we present the thiol-assisted formation of guanidines, which has a mechanism analogous to that of native chemical ligation. Using this reaction, we designed autocatalytic and oscillatory reaction networks that form substituted guanidines from thiouronium salts. The thiouronium salt-based oscillator show good stability of oscillations within a broad range of experimental conditions. By using nitrile-containing starting materials, we constructed an oscillator where the concentration of a bicyclic derivative of dihydropyrimidine oscillates. Moreover, the mixed thioester and thiouronium salt-based oscillator show unique responsiveness to chemical cues. The reactions developed in this work expand our toolbox for designing out-of-equilibrium chemical systems and link autocatalytic and oscillatory chemistry to the synthesis of guanidinium derivatives and the products of their transformations including analogs of nucleobases.

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Section: Resultsmentioning

confidence: 99%

Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization

et al. 2021

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“…Several oscillating chemical reactions have been discovered over the last 200 years . While classical oscillators feature electrochemical and inorganic components, − more contemporary examples are based on chemo-mechanical systems, supramolecular polymers, and there are several systems where continuous-flow stirred tank reactors (CSTRs) are used to drive oscillations. − CSTRs constantly replenish starting materials and remove products while maintaining a fixed volume and are the major experimental tool for developing out-of-equilibrium systems and rationally designed oscillators. , …”

Section: Introductionmentioning

confidence: 99%

A Chemical Reaction Network Drives Complex Population Dynamics in Oscillating Self-Reproducing Vesicles

Zhang,

Howlett,

Silvester

et al. 2024

J. Am. Chem. Soc.

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We report chemically fueled oscillations of vesicles. The population cycling of vesicles is driven by their self-reproduction and collapse within a biphasic reaction network involving the interplay of molecular and supramolecular events. We studied the oscillations on the molecular and supramolecular scales and tracked vesicle populations in time by interferometric scattering microscopy and dynamic light scattering. Complex supramolecular events were observed during oscillations�including vesicle reproduction, growth, and decomposi-tion�and differences in the number, size, and mass of aggregates can often be observed within and between pulses. This system's dynamic behavior is reminiscent of a reproductive cycle in living cells.

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“…Many, perhaps most, autocatalysis-driven relaxation oscillators and oscillatory mechanism-based models (e.g., Belousov–Zhabotinsky (BZ) reaction, , bromate–sulfite oscillatory reaction, the landmark Boissonade–De Kepper model, and trypsin oscillatory reaction , ) contain at least two inhibition processes or two inhibitors. Is the presence of a second negative feedback essential?…”

Section: Introductionmentioning

confidence: 99%

“…27 The thiol-oscillating system is robust with respect to variations in flow rate and possesses additional characteristics of interest, including entrainment, the ability of an oscillatory mixture to engender oscillations in a nonoscillatory substrate, 21 and hybridization, the capacity to oscillate when an appropriate combination of two substrates, each of which would be incapable of oscillating on its own, is employed. Many, perhaps most, autocatalysis-driven relaxation oscillators and oscillatory mechanism-based models (e.g., Belousov−Zhabotinsky (BZ) reaction, 28,29 bromate−sulfite oscillatory reaction, 15 the landmark Boissonade−De Kepper model, 30 and trypsin oscillatory reaction 31,32 ) contain at least two inhibition processes or two inhibitors. Is the presence of a second negative feedback essential?…”

Section: ■ Introductionmentioning

confidence: 99%

Role of Fast and Slow Inhibitors in Oscillatory Rhythm Design

Wang,

Cheng,

Yuan

et al. 2023

J. Am. Chem. Soc.

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In biological or abiotic systems, rhythms occur, owing to the coupling between positive and negative feedback loops in a reaction network. Using the Semenov–Whitesides oscillatory network for thioester hydrolysis as a prototype, we experimentally and theoretically analyzed the role of fast and slow inhibitors in oscillatory reaction networks. In the presence of positive feedback, a single fast inhibitor generates a time delay, resulting in two saddle-node bifurcations and bistability in a continuously stirred tank reactor. A slow inhibitor produces a node-focus bifurcation, resulting in damped oscillations. With both fast and slow inhibitors present, the node-focus bifurcation repeatedly modulates the saddle-node bifurcations, producing stable periodic oscillations. These fast and slow inhibitions result in a pair of time delays between steeply ascending and descending dynamics, which originate from the positive and negative feedbacks, respectively. This pattern can be identified in many chemical relaxation oscillators and oscillatory models, e.g., the bromate–sulfite pH oscillatory system, the Belousov–Zhabotinsky reaction, the trypsin oscillatory system, and the Boissonade–De Kepper model. This study provides a novel understanding of chemical and biochemical rhythms and suggests an approach to designing such behavior.

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Four‐Variable Model of an Enzymatic Oscillator Based on Trypsin

Cited by 6 publications

References 29 publications

Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization

Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization

A Chemical Reaction Network Drives Complex Population Dynamics in Oscillating Self-Reproducing Vesicles

Role of Fast and Slow Inhibitors in Oscillatory Rhythm Design

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