The role of kinetic asymmetry and power strokes in an information ratchet

Chem, Journal Year: 2023, Volume and Issue: 9(10), P. 2902 - 2917

Published: June 19, 2023

Biomolecular machines are driven by information ratchet mechanisms, where kinetic asymmetry in the machine's chemomechanical cycle of fuel-to-waste catalysis induces net directional dynamics. A large-scale energetically downhill conformational change, termed a "power stroke," has often been erroneously implicated as mechanistic driving feature such machines. We investigated roles and power strokes series rotaxane-based ratchets found that alone determines directionality all use same amount fuel to reach normalized steady state. However, can nonetheless influence performance, how fast state is reached. Moreover, nonequilibrium thermodynamic analysis revealed alter form (information [Shannon entropy] versus intercomponent binding energy) free energy stored ratchets. These findings have implications for both understanding biological design principles artificial (supra)molecular

Language: Английский

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Artificial Molecular Ratchets: Tools Enabling Endergonic Processes

Angewandte Chemie International Edition, Journal Year: 2023, Volume and Issue: 62(47)

Published: Aug. 7, 2023

Abstract Non‐equilibrium chemical systems underpin multiple domains of contemporary interest, including supramolecular chemistry, molecular machines, prebiotic and energy transduction. Experimental chemists are now pioneering the realization artificial that can harvest away from equilibrium. In this tutorial Review, we provide an overview ratchets: mechanisms enabling absorption environment. By focusing on mechanism type—rather than application domain or source—we offer a unifying picture seemingly disparate phenomena, which hope will foster progress in fascinating science.

Language: Английский

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Kinetic Asymmetry versus Dissipation in the Evolution of Chemical Systems as Exemplified by Single Enzyme Chemotaxis

Journal of the American Chemical Society, Journal Year: 2023, Volume and Issue: 145(10), P. 5730 - 5738

Published: March 3, 2023

Single enzyme chemotaxis is a phenomenon by which nonequilibrium spatial distribution of an created and maintained concentration gradients the substrate product catalyzed reaction. These can arise either naturally through metabolism or experimentally, e.g., flow materials microfluidic channels use diffusion chambers with semipermeable membranes. Numerous hypotheses regarding mechanism this have been proposed. Here, we discuss based solely on chemical reaction show that kinetic asymmetry, difference in transition state energies for dissociation/association product, diffusivities bound free forms enzyme, are determinates direction result positive negative chemotaxis, both demonstrated experimentally. Exploration these fundamental symmetries govern behavior helps to distinguish between possible mechanisms evolution system from initial steady whether principle determines shifts when exposed external energy source thermodynamics kinetics latter being supported results present paper. Our that, while dissipation ineluctably accompanies phenomena, including systems do not evolve maximize minimize but rather attain greater stability accumulate regions where their effective coefficient as small possible. The chemotactic response formed other enzymes participating catalytic cascade provides forming loose associations known metabolons. Significantly, force due depends asymmetry so be nonreciprocal, one attracted another repelled one, seeming contradiction Newtons third law. This nonreciprocity important ingredient active matter.

Language: Английский

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Kinetic Barrier Diagrams to Visualize and Engineer Molecular Nonequilibrium Systems

Small, Journal Year: 2023, Volume and Issue: 19(14)

Published: Jan. 26, 2023

Molecular nonequilibrium systems hold great promises for the nanotechnology of future. Yet, their development is slowed by absence an informative representation. Indeed, while potential energy surfaces comprise in principle all information, they hide dynamic interplay multiple reaction pathways underlying systems, i.e., degree kinetic asymmetry. To offer insightful visual representation asymmetry, we extended approach pertaining to catalytic networks, span model, focusing on system dynamics - rather than thermodynamics. Our encompasses both chemically and photochemically driven ranging from unimolecular motors simple self-assembly schemes. The obtained diagrams give immediate access information needed guide experiments, such as states' population, rate machine operation, maximum work output, effects design changes. proposed barrier a unifying graphical tool disparate phenomena.

Language: Английский

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Elucidation of collagen amino acid interactions with metals (B, Ni) encapsulated graphene/PEDOT material: Insight from DFT calculations and MD simulation

Journal of Molecular Liquids, Journal Year: 2023, Volume and Issue: 390, P. 122950 - 122950

Published: Aug. 31, 2023

Language: Английский

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