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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Modern chemical graph theory

Wiley Interdisciplinary Reviews Computational Molecular Science, Journal Year: 2024, Volume and Issue: 14(5)

Published: Sept. 1, 2024

Abstract Graph theory has a long history in chemistry. Yet as the breadth and variety of chemical data is rapidly changing, so too do graph encoding methods analyses that yield qualitative quantitative insights. Using illustrative cases within basic mathematical framework, we showcase modern theory's utility Chemists' analysis model development toolkit. The both experimental simulation discussed at various levels granularity information. This followed by discussion two major classes theoretical analyses: identifying connectivity patterns partitioning methods. Measures, metrics, descriptors, topological indices are then introduced with an emphasis upon enhancing interpretability incorporation into physical models. Challenging described include strategies for studying time dependence. Throughout, incorporate recent advancements computer science applied mathematics propelling new domains study. article categorized under: Molecular Statistical Mechanics > Dynamics Monte‐Carlo Methods Structure Mechanism Computational Materials Science Structures

Language: Английский

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Spatiotemporal generation of alternating disparate pH domains via audible sound controlled opposing enzymatic reactions

Chemical Communications, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Spatiotemporal control of acid- and base-producing enzymatic reactions using audible sound enables the creation alternating disparate pH domains in a solution.

Language: Английский

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Cofactor-independent, photoenzymatic, reductions with water mediated by rGQDs

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 17, 2025

Enzymatic reductions catalyzed by reductases, such as aldo/ketoreductases (AKRs), imine and ene reductases generally depend on the regeneration of nicotinamide cofactors for industrial viability. This usually involves addition a cosubstrate second enzyme, dehydrogenase, e.g. glucose / dehydrogenase. For commercial viability it would be more interesting to use water sacrificial supply necessary hydrogen atoms. is possible using photocatalytic methods involving precious metal, Rh Ru, complexes electron mediators. A problem associated with photobiocatalysis in general weak penetration ultraviolet or visible light biological systems. Here we report unprecedented near infrared (NIR) combination hybrid photoenzyme based IR responsive reductive graphene quantum dots (rGQDs) that are non-toxic AKRs. We envisaged immobilization AKR close proximity rGQDs could enable direct transfer atoms from prochiral ketone substrate without requiring cofactor. To test this hypothesis, immobilized surface cross-linked AKR. The resulting rGQD/AKR photobiocatalyst mediated synthesis pharmaceutical intermediate, (R)-1-[3,5-bis(trifluoromethyl)-phenyl] ethanol ((R)-3,5-BTPE) corresponding ketone, 82% yield > 99.99% ee under 50 mW·cm^{− 2} illumination. work opens new avenues create artificial photoenzymes simplify in vitro biocatalysis coupling renewable solar energy sustainable chemical production. Since accounts about half entire spectrum its efficient utilization crucial applications sunlight. have demonstrated our can effectively utilize catalyze enzymatic reduction ketone. these photobiocatalysts insoluble solids they readily recovered, recycled potentially employed continuous flow operation.

Language: Английский

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A metabolomic approach of AI-driven enzymatic digestion of pumpkin seed flour for producing umami metabolites

International Journal of Gastronomy and Food Science, Journal Year: 2025, Volume and Issue: unknown, P. 101117 - 101117

Published: Jan. 1, 2025

Language: Английский

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Extending protein-film electrochemistry across enzymology and biological inorganic chemistry to investigate, track and control the reactions of non-redox enzymes and spectroscopically silent metals

JBIC Journal of Biological Inorganic Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Abstract Protein film electrochemistry has helped to unravel many complex reactivities of electron-transferring proteins and enzymes. A versatile descendant, the ‘Electrochemical Leaf’, offers new opportunities extend electrochemical control myriad enzymes that neither transfer electrons nor catalyse any redox reaction, including those dependent on spectroscopically limited, labile or other challenging metal ions. By embedding a cascade comprised several enzymes—one which electrochemically recycles NAD(P)(H), second being dehydrogenase—within porous electrode formed from fused nanoparticles, interconnected reactions are tightly channeled transmit energy information, rapidly interactively. Under nanoconfinement, nicotinamide cofactors intermediates serve as specific current carriers, far beyond electron itself. Graphical abstract

Language: Английский

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Integrating protein contact networks for the engineering of thermostable lipase a

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: unknown, P. 141725 - 141725

Published: March 1, 2025

Language: Английский

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Membrane Transport Modulates the pH-Regulated Feedback of an Enzyme Reaction Confined within Lipid Vesicles

ACS Nano, Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

Understanding ion transport dynamics in reactive vesicles is pivotal for exploring biological and chemical processes essential designing synthetic cells. In this work, we investigate how proton membrane potential regulate pH an autocatalytic enzyme reaction within lipid vesicles. Combining experimental numerical methods, demonstrate that compartmentalization membranes accelerates internal reactions, attributed to protection from the external acidic environment. experiments, explored movement significantly impacts reactions by changing bilayer thickness, adding transporters, varying buffers. Numerical investigations incorporated electrical capacitance into a kinetic model of process, elucidating mechanisms dictate control time observed experiment, driven both gradients. These findings establish framework controlling clock via changes targeted manipulation movement, which could aid design cells with precise, controlled functionalities.

Language: Английский

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Timed batch inputs unlock significantly higher yields for enzymatic cascades

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 7, 2025

The dynamic properties of enzymatic reaction networks (ERNs) are difficult to predict due the emergence allosteric interactions, product inhibitions and competition for resources, that all only materialize once have been assembled. In batch systems, optimization starting concentrations is challenging, as composition mixture changes continuously, prohibiting optimal conditions full duration reaction. Allowing reagents be added over time would circumvent this limitation, but route has never explored yield complex sequences. Here, we use an active learning workflow construct maximally informative datasets train predictive kinetic models account possible interactions in system. We subsequently show first time, these can used significantly (> 5-fold) improve yields a model cascade (the pentose phosphate pathway) by designing recipe time-dependent inputs each component within network such favors production target metabolite. This work represents generally applicable strategy optimizing networks.

Language: Английский

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Coacervates as enzymatic microreactors

Chemical Society Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

We review advances in coacervate-based microreactors, covering enzyme selection, recruitment strategies, microreactor compositions, and their impact on reaction kinetics.

Language: Английский

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