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Ghosh S, Baltussen MG, Ivanov NM, Haije R, Jakštaitė M, Zhou T, Huck WTS. Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems. Chem Rev 2024; 124:2553-2582. [PMID: 38476077 PMCID: PMC10941194 DOI: 10.1021/acs.chemrev.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.
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Affiliation(s)
- Souvik Ghosh
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Nikita M. Ivanov
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Rianne Haije
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Miglė Jakštaitė
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tao Zhou
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Dúzs B, Holló G, Kitahata H, Ginder E, Suematsu NJ, Lagzi I, Szalai I. Appearance and suppression of Turing patterns under a periodically forced feed. Commun Chem 2023; 6:3. [PMID: 36697882 PMCID: PMC9814632 DOI: 10.1038/s42004-022-00800-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
Turing instability is a general and straightforward mechanism of pattern formation in reaction-diffusion systems, and its relevance has been demonstrated in different biological phenomena. Still, there are many open questions, especially on the robustness of the Turing mechanism. Robust patterns must survive some variation in the environmental conditions. Experiments on pattern formation using chemical systems have shown many reaction-diffusion patterns and serve as relatively simple test tools to study general aspects of these phenomena. Here, we present a study of sinusoidal variation of the input feed concentrations on chemical Turing patterns. Our experimental, numerical and theoretical analysis demonstrates that patterns may appear even at significant amplitude variation of the input feed concentrations. Furthermore, using time-dependent feeding opens a way to control pattern formation. The patterns settled at constant feed may disappear, or new patterns may appear from a homogeneous steady state due to the periodic forcing.
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Affiliation(s)
- Brigitta Dúzs
- grid.5591.80000 0001 2294 6276Laboratory of Nonlinear Chemical Dynamics, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary ,grid.5802.f0000 0001 1941 7111Present Address: University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gábor Holló
- ELKH-BME Condensed Matter Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Hiroyuki Kitahata
- grid.136304.30000 0004 0370 1101Graduate School of Science, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522 Japan
| | - Elliott Ginder
- grid.411764.10000 0001 2106 7990School of Interdisciplinary Mathematical Sciences, Graduate School of Advanced Mathematical Sciences, and Meiji Institute for Advanced Study of Mathematical Sciences (MIMS), Meiji University, 4-21-1, Nakano Tokyo, 164-8525 Japan
| | - Nobuhiko J. Suematsu
- grid.411764.10000 0001 2106 7990School of Interdisciplinary Mathematical Sciences, Graduate School of Advanced Mathematical Sciences, and Meiji Institute for Advanced Study of Mathematical Sciences (MIMS), Meiji University, 4-21-1, Nakano Tokyo, 164-8525 Japan
| | - István Lagzi
- ELKH-BME Condensed Matter Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary ,grid.6759.d0000 0001 2180 0451Department of Physics, Institute of Physics, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - István Szalai
- grid.5591.80000 0001 2294 6276Laboratory of Nonlinear Chemical Dynamics, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary
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