Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems

Chemical Reviews, Journal Year: 2024, Volume and Issue: 124(5), P. 2553 - 2582

Published: March 4, 2024

The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence sustenance life. Constructing such vitro enables stepwise build up complexity introduces opportunity to control activity using physicochemical stimuli. Rational design modulation network motifs enable engineering artificial systems with emergent functionalities. Such functional are useful for variety reasons as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules synthetic cells, even enabling molecular computation. In this review, we offer insights into chemical characteristics ERNs while also delving their potential applications associated challenges.

Language: Английский

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Dissipative Systems Driven by the Decarboxylation of Activated Carboxylic Acids

Accounts of Chemical Research, Journal Year: 2023, Volume and Issue: 56(7), P. 889 - 899

Published: March 14, 2023

ConspectusThe achievement of artificial systems capable being maintained in out-of-equilibrium states featuring functional properties is a main goal current chemical research. Absorption electromagnetic radiation or consumption species (a "chemical fuel") are the two strategies typically employed to reach such states, which have persist as long one above stimuli present. For this reason often referred "dissipative systems". In simplest scheme, dissipative system initially found resting, equilibrium state. The addition fuel causes shift an When exhausted, reverts initial, Thus, from mechanistic standpoint, turns out be catalyst for consumption. It has noted that, although very simple, scheme implies chance temporally control system. principle, modulating nature and/or amount added, can full time spent by state.In 2016, we that 2-cyano-2-phenylpropanoic acid (1a), whose decarboxylation proceeds smoothly under mild basic conditions, could used drive back and forth motion catenane-based molecular switch. donates proton catenane passes neutral state A transient protonated B. Decarboxylation resulting carboxylate (1acb), generates carbanion, which, strong base, retakes consequently, returns initial A. larger added fuel, longer transient, Since then, 1a other activated carboxylic acids (ACAs) been operation large number based on acid-base reaction, machines host-guest systems, catalysts smart materials, so on. This Account illustrates with purpose show wide applicability ACAs fuels. generality due simplicity idea underlying principle ACAs, always translates into simple experimental requirements.

Language: Английский

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Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises

Angewandte Chemie International Edition, Journal Year: 2024, Volume and Issue: 63(14)

Published: Jan. 16, 2024

Abstract Feedback‐controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal environment. Currently, creating minimalistic synthetic cells is long‐term objective systems chemistry, which motivated by natural integrity. The design, kinetic optimization, analysis to exhibit functions akin those cell still pose significant challenges. Indeed, reaching homeostasis essential engineering components. However, maintaining in artificial against agitations difficult task. Several events can provide us with guidelines conceptual understanding homeostasis, be further applicable designing systems. In this regard, we organize our review driven at different length scales, including homogeneous, compartmentalized, soft material First, stretch quick overview molecular supramolecular systems, toolbox nonlinear homeostatic Moreover, existing history their advanced self‐correcting, regulating properties also emphasized.

Language: Английский

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Temporal pH waveforms generated in an enzymatic reaction network in batch and cell-sized microcompartments

Cell Reports Physical Science, Journal Year: 2025, Volume and Issue: unknown, P. 102367 - 102367

Published: Jan. 1, 2025

Highlights•The emergent properties of the urease-esterase reaction network are investigated•The antagonistic enzymatic generates pH waveforms in batch•Front propagation and sol-gel transition fueled by network•One-cycle oscillation is realized giant unilamellar vesiclesSummaryInvestigating designing networks their phenomena backbone systems chemistry. Designing chemical oscillators homogeneous utilizing reactions challenging due to consumption substrates over one cycle. Here, we show that an comprising urea-urease ester-esterase can generate temporal variations a batch. We developed coupled kinetic model elucidate mechanism accurately captures experimentally observed variation time. To demonstrate remarkable potential network, expanded on this discovery generating front presenting several applications coupling fuel pH-dependent processes (gelation pH-sensitive monomers emulsion-vesicle transformation). By employing strategy reactions, engineered single pulse cell-sized microcompartments, which could contribute developing synthetic cells with multiple functions.Graphical abstract

Language: Английский

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Fuel-Driven Enzymatic Reaction Networks to Program Autonomous Thiol/Disulfide Redox Systems

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: 146(15), P. 10281 - 10285

Published: April 3, 2024

Fuel-driven dissipative formation of disulfide bonds using competing oxidative activation and reductive deactivation presents a possibly very versatile avenue for autonomous materials design. However, this is challenging to realize because the direct annihilation oxidizing fuel deactivating reducing agent. We overcome challenge by introducing redox-based enzymatic reaction network (ERN), enabling molecularly dissolved thiols in fully manner. Moreover, ERN allows programming hydrogel lifetimes utilizing thiol-terminated star polymers (sPEG-SH). The can be customized operate with aliphatic aromatic should thus broadly applicable functional thiols.

Language: Английский

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DNA-Based Signaling Networks for Transient Colloidal Co-Assemblies

Journal of the American Chemical Society, Journal Year: 2023, Volume and Issue: 145(32), P. 17819 - 17830

Published: Aug. 6, 2023

Programmable chemical circuits inspired by signaling networks in living cells are a promising approach for the development of adaptive and autonomous self-assembling molecular systems material functions. Progress has been made at level, but connecting control to larger elements such as colloids that enable real-space studies access functional materials is sparse can suffer from kinetic traps, flocculation, or difficult system integration protocols. Herein, we report toehold-mediated DNA strand displacement reaction network capable autonomously directing two different microgels into transient self-regulating co-assemblies. The functionalized with become elemental components network. flexibility circuit design allows installation delay phases accelerators chaining additional modules upstream downstream core circuit. provides an adaptable robust route regulate other building blocks advanced biomimetic

Language: Английский

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Spatially Controlled Self‐Assembly of Supramolecular Hydrogels Enabled by Light‐Triggered Catalysis

Macromolecular Rapid Communications, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

Spatial control over supramolecular self-assembly prevails in living system, yet remains difficult to replicate synthetic scenarios. Here, on the basis of a hydrazone formation-mediated hydrogelation access patterning hydrogels is demonstrated via light-triggered catalysis strategy. A photoacid generator that can produce protons aqueous solutions upon irradiation employed. The generated lead drop pH around three units (initial 7.0), effectively accelerating formation and gelators. Because catalysis, samples presence show lower critical gelation concentration, higher stiffness, denser networks. Importantly, by performing selective using differently shaped masks, various spatially resolved following shapes masks are fabricated. concept realize spatial provides an alternative approach toward bottom-up fabrication structured soft materials for applications such as tissue engineering, single cell manipulation, biosensing.

Language: Английский

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Transient colloidal crystals fueled by electrochemical reaction products

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 28, 2025

Conventional electric field directed colloidal assembly enables fabricating ordered structures but lacks temporal control over state. Chemical reaction networks have been discovered that transiently assemble colloids; however, they slow dynamics (hrs – days) and poor tunability, utilize complex reagents, produce kinetically trapped states. Here we demonstrate transient crystals autonomously form, breakup, reconstitute in response to an electrochemical network driven by a time invariant electrical stimulus. Aqueous mixtures of micron sized colloids para-benzoquinone (BQ) were subjected superimposed oscillatory steady potentials, i.e., multimode induce electrokinetic flows around proton-coupled BQ redox reactions. Transient states coincided with electrochemically generated pH spikes near the cathode. We wide tunability state lifetimes two orders magnitude modifying potential electrode separation. An transport model showed interaction advancing acidic alkaline fronts from anodic oxidation cathodic reduction caused transients. present theoretical experimental evidence indicates mediated competition between opposing scale electrohydrodynamic electroosmotic flows, latter which is dependent. methods for struggle This study demonstrates disassemble, reassemble network, achieving using potentials.

Language: Английский

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Imine-Based Transient Supramolecular Polymers

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: March 19, 2025

Systems that change properties upon exposure to chemical stimuli offer the interesting prospect of (partially) mimicking functions living systems. Over past decade, numerous supramolecular systems whose composition and are regulated by dissipation fuels have been reported. These typically based on transient transformation a "dormant" species into an active, self-assembling monomer. The process is powered fuel consumption terminates depletion, restoring initial dormant state. Previously reported out-of-equilibrium polymerizations relied activation adding or removing small structural units enable polymerization. Here, we present approach combines reversibility dynamic covalent chemistry trigger "recycling" components combinatorial library (DCL). Treatment equilibrated DCL aliphatic imines aromatic amines with activated carboxylic acid (ACA) generates dissipative protonated amines. acidic conditions creation polymer held together interactions between crown ether moieties embedded in scaffold imines. Thus, reshuffles connectivity enables temporary purely (polymeric) system polymer. We demonstrate strategy using two different feedstocks consisting diimine macrocycle involving calix[4]arene distribution imine (cyclo)oligomers derived from isophthalaldehyde skeleton.

Language: Английский

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Nonequilibrium Self-Assembly Control by the Stochastic Landscape Method

Journal of Chemical Information and Modeling, Journal Year: 2025, Volume and Issue: unknown

Published: April 8, 2025

Self-assembly of building blocks is a fundamental process in nanotechnology, materials science, and biological systems, offering pathways to the formation complex functional structures through local interactions. However, lack effective error correction mechanisms often limits efficiency precision assembly, particularly systems with strong binding energies. Inspired by cellular processes stochastic resetting, we present closed-loop feedback control method that employs transient modulations interaction energies, mimicking, for instance, global effect pH changes as nonequilibrium drives optimize assembly outcomes real time. By leveraging landscape method, framework using energy trend-based segmentation predict self-assembly behavior, our approach dynamically analyzes system's state trends guide actions. We show modulation during kinetic trapping conditions substantially enhances yields reduces times across diverse scenarios. This strategy provides broadly applicable, data-driven optimizing processes, potential implications manufacturing responsive design, while also advancing understanding controlled molecular synthetic contexts.

Language: Английский

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