scholarly journals The Dynamics of an Oscillating Enzymatic Reaction Network is Crucially Determined by Side Reactions

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Aleksandr A. Pogodaev ◽  
Tijs T. Lap ◽  
Wilhelm T. S. Huck
2019 ◽  
Author(s):  
Jie Deng ◽  
Andreas Walther

We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization system. The systems are based on a monomeric species pool that is fueled by ATP and orchestrated by an enzymatic reaction network (ERN) of ATP-powered ligation and concurrent cleavage. Such systems display autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomer of dimers to ultimately randomized polymer structure before being ultimately degraded back to monomers once the fuel is consumed. The enabling key principle is to design monomer species having kinetically selected molecular recognition with respect to the structure-forming step (ATP-powered ligation) by encoding different sticky-end overhangs into the ligation area. However, all formed structures are equally degraded, and the orthogonal molecular recognition of the different starting species are harmonized during the constantly occurring restriction process, leading in consequence to a reconfiguration of the driven dynamic nanostructures on a higher hierarchical level. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.


Catalysts ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1374
Author(s):  
Andreas Brune ◽  
Andreas Seidel-Morgenstern ◽  
Christof Hamel

This study intends to provide insights into various aspects related to the reaction kinetics of the VOx catalyzed propane dehydrogenation including main and side reactions and, in particular, catalyst deactivation and regeneration, which can be hardly found in combination in current literature. To kinetically describe the complex reaction network, a reduced model was fitted to lab scale experiments performed in a fixed bed reactor. Additionally, thermogravimetric analysis (TGA) was applied to investigate the coking behavior of the catalyst under defined conditions considering propane and propene as precursors for coke formation. Propene was identified to be the main coke precursor, which agrees with results of experiments using a segmented fixed bed reactor (FBR). A mechanistic multilayer-monolayer coke growth model was developed to mathematically describe the catalyst coking. Samples from long-term deactivation experiments in an FBR were used for regeneration experiments with oxygen to gasify the coke deposits in a TGA. A power law approach was able to describe the regeneration behavior well. Finally, the results of periodic experiments consisting of several deactivation and regeneration cycles verified the long-term stability of the catalyst and confirmed the validity of the derived and parametrized kinetic models for deactivation and regeneration, which will allow model-based process development and optimization.


2019 ◽  
Author(s):  
Jie Deng ◽  
Andreas Walther

We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization system. The systems are based on a monomeric species pool that is fueled by ATP and orchestrated by an enzymatic reaction network (ERN) of ATP-powered ligation and concurrent cleavage. Such systems display autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomer of dimers to ultimately randomized polymer structure before being ultimately degraded back to monomers once the fuel is consumed. The enabling key principle is to design monomer species having kinetically selected molecular recognition with respect to the structure-forming step (ATP-powered ligation) by encoding different sticky-end overhangs into the ligation area. However, all formed structures are equally degraded, and the orthogonal molecular recognition of the different starting species are harmonized during the constantly occurring restriction process, leading in consequence to a reconfiguration of the driven dynamic nanostructures on a higher hierarchical level. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.


2018 ◽  
Vol 57 (43) ◽  
pp. 14065-14069 ◽  
Author(s):  
Britta Helwig ◽  
Bob van Sluijs ◽  
Aleksandr A. Pogodaev ◽  
Sjoerd G. J. Postma ◽  
Wilhelm T. S. Huck

2019 ◽  
Author(s):  
Laura Heinen ◽  
Andreas Walther

<div><div><div><p>Inspired by the dynamics of the dissipative self-assembly of microtubules, chemically fueled synthetic systems with transient lifetimes are emerging for non-equilibrium materials design. However, realizing programmable or even adaptive structural dynamics has proven challenging because it requires synchronization of energy uptake and dissipation events within true steady states, which remains difficult to orthogonally control in supramolecular systems. Here, we demonstrate full synchronization of both events by ATP-fueled activation and dynamization of covalent DNA bonds via an enzymatic reaction network of concurrent ligation and cleavage. Critically, the average bond ratio and the frequency of bond exchange are imprinted into the energy dissipation kinetics of the network and tunable through its constituents. We introduce temporally and structurally programmable dynamics by polymerization of transient, dynamic covalent DNA polymers with adaptive steady-state properties in dependence of ATP fuel and enzyme concentrations. This approach enables generic access to non-equilibrium soft matter systems with adaptive and programmable dynamics.</p></div></div></div>


2016 ◽  
Vol 2 (11) ◽  
pp. 843-849 ◽  
Author(s):  
Marlies Nijemeisland ◽  
Loai K. E. A. Abdelmohsen ◽  
Wilhelm T. S. Huck ◽  
Daniela A. Wilson ◽  
Jan C. M. van Hest

2019 ◽  
Author(s):  
Jie Deng ◽  
Andreas Walther

We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization system. The systems are based on a monomeric species pool that is fueled by ATP and orchestrated by an enzymatic reaction network (ERN) of ATP-powered ligation and concurrent cleavage. Such systems display autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomer of dimers to ultimately randomized polymer structure before being ultimately degraded back to monomers once the fuel is consumed. The enabling key principle is to design monomer species having kinetically selected molecular recognition with respect to the structure-forming step (ATP-powered ligation) by encoding different sticky-end overhangs into the ligation area. However, all formed structures are equally degraded, and the orthogonal molecular recognition of the different starting species are harmonized during the constantly occurring restriction process, leading in consequence to a reconfiguration of the driven dynamic nanostructures on a higher hierarchical level. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.


2018 ◽  
Vol 130 (43) ◽  
pp. 14261-14265 ◽  
Author(s):  
Britta Helwig ◽  
Bob van Sluijs ◽  
Aleksandr A. Pogodaev ◽  
Sjoerd G. J. Postma ◽  
Wilhelm T. S. Huck

2019 ◽  
Vol 5 (7) ◽  
pp. eaaw0590 ◽  
Author(s):  
Laura Heinen ◽  
Andreas Walther

Inspired by the dynamics of the dissipative self-assembly of microtubules, chemically fueled synthetic systems with transient lifetimes are emerging for nonequilibrium materials design. However, realizing programmable or even adaptive structural dynamics has proven challenging because it requires synchronization of energy uptake and dissipation events within true steady states, which remains difficult to orthogonally control in supramolecular systems. Here, we demonstrate full synchronization of both events by ATP-fueled activation and dynamization of covalent DNA bonds via an enzymatic reaction network of concurrent ligation and cleavage. Critically, the average bond ratio and the frequency of bond exchange are imprinted into the energy dissipation kinetics of the network and tunable through its constituents. We introduce temporally and structurally programmable dynamics by polymerization of transient, dynamic covalent DNA polymers with adaptive steady-state properties in dependence of ATP fuel and enzyme concentrations. This approach enables generic access to nonequilibrium soft matter systems with adaptive and programmable dynamics.


2013 ◽  
Vol 10 (87) ◽  
pp. 20130489 ◽  
Author(s):  
Ganhui Lan ◽  
Yuhai Tu

The incoherent type-1 feed-forward loop (I1-FFL) is ubiquitous in biological regulatory circuits. Although much is known about the functions of the I1-FFL motif, the energy cost incurred in the network and how it affects the performance of the network have not been investigated. Here, we study a generic I1-FFL enzymatic reaction network modelled after the GEF–GAP–Ras pathway responsible for chemosensory adaptation in eukaryotic cells. Our analysis shows that the I1-FFL network always operates out of equilibrium. Continuous energy dissipation is necessary to drive an internal phosphorylation–dephosphorylation cycle that is crucial in achieving strong short-time response and accurate long-time adaptation. In particular, we show quantitatively that the energy dissipated in the I1-FFL network is used (i) to increase the system's initial response to the input signals; (ii) to enhance the adaptation accuracy at steady state; and (iii) to expand the range of such accurate adaptation. Moreover, we find that the energy dissipation rate, the catalytic speed and the maximum adaptation accuracy in the I1-FFL network satisfy the same energy–speed–accuracy relationship as in the negative-feedback-loop (NFL) networks. Because the I1-FFL and NFL are the only two basic network motifs that enable accurate adaptation, our results suggest that a universal cost–performance trade-off principle may underlie all cellular adaptation processes independent of the detailed biochemical circuit architecture.


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