Power Strokes in Molecular Motors: Predictive, Irrelevant, or Somewhere in Between? DOI
Emanuele Penocchio, Geyao Gu, Alex Albaugh

и другие.

Journal of the American Chemical Society, Год журнала: 2024, Номер unknown

Опубликована: Дек. 20, 2024

For several decades, molecular motor directionality has been rationalized in terms of the free energy conformations visited before and after takes a step, so-called power stroke mechanism with analogues macroscopic engines. Despite theoretical experimental demonstrations its flaws, language is quite ingrained, some communities still value intuition. By building catalysis-driven into simulated numerical experiments, we here systematically report on how responds when modified accordingly to We confirm that generally does not predict directionality. Nevertheless, simulations illustrate relative stability should be included as potential design element adjust directional bias. Though strokes are formally unimportant for determining directionality, show practical attempts alter have side effects can fact The change bias align what intuition would suggested, offering explanation why flawed retain apparent utility engineering specific systems.

Язык: Английский

Non-equilibrium Steady States in Catalysis, Molecular Motors, and Supramolecular Materials: Why Networks and Language Matter DOI Creative Commons
Ivan Aprahamian, Stephen M. Goldup

Journal of the American Chemical Society, Год журнала: 2023, Номер 145(26), С. 14169 - 14183

Опубликована: Июнь 21, 2023

All chemists are familiar with the idea that, at equilibrium steady state, relative concentrations of species present in a system predicted by corresponding constants, which related to free energy differences between components. There is also no net flux species, matter how complicated reaction network. Achieving and harnessing non-equilibrium states, coupling network second spontaneous chemical process, has been subject work several disciplines, including operation molecular motors, assembly supramolecular materials, strategies enantioselective catalysis. We juxtapose these linked fields highlight their common features challenges as well some misconceptions that may be serving stymie progress.

Язык: Английский

Процитировано

79
Molecular Ratchets and Kinetic Asymmetry: Giving Chemistry Direction DOI Creative Commons
Stefan Borsley, David A. Leigh, Benjamin M. W. Roberts

и другие.

Angewandte Chemie International Edition, Год журнала: 2024, Номер 63(23)

Опубликована: Апрель 3, 2024

Abstract Over the last two decades ratchet mechanisms have transformed understanding and design of stochastic molecular systems—biological, chemical physical—in a move away from mechanical macroscopic analogies that dominated thinking regarding dynamics in 1990s early 2000s (e.g. pistons, springs, etc), to more scale‐relevant concepts underpin out‐of‐equilibrium research sciences today. Ratcheting has established nanotechnology as frontier for energy transduction metabolism, enabled reverse engineering biomolecular machinery, delivering insights into how molecules ‘walk’ track‐based synthesisers operate, acceleration reactions enables be transduced by catalysts (both motor proteins synthetic catalysts), dynamic systems can driven equilibrium through catalysis. The recognition biology, their invention systems, is proving significant areas diverse supramolecular chemistry, covalent DNA nanotechnology, polymer materials science, heterogeneous catalysis, endergonic synthesis, origin life, many other branches science. Put simply, give chemistry direction. Kinetic asymmetry, key feature ratcheting, counterpart structural asymmetry (i.e. chirality). Given ubiquity processes significance behaviour function it surely just fundamentally important. This Review charts recognition, development ratchets, focussing particularly on role which they were originally envisaged elements machinery. Different kinetically asymmetric are compared, consequences discussed. These archetypal examples demonstrate inexorably equilibrium, rather than relax towards it.

Язык: Английский

Процитировано

35
Kinetic Asymmetry and Directionality of Nonequilibrium Molecular Systems DOI
R. Dean Astumian

Angewandte Chemie International Edition, Год журнала: 2024, Номер 63(9)

Опубликована: Янв. 18, 2024

Abstract Scientists have long been fascinated by the biomolecular machines in living systems that process energy and information to sustain life. The first synthetic molecular rotor capable of performing repeated 360° rotations due a combination photo‐ thermally activated processes was reported 1999. progress designing different intervening years has remarkable, with several outstanding examples appearing last few years. Despite accomplishments, there remains confusion regarding fundamental design principles which motions molecules can be controlled, significant intellectual tension between mechanical chemical ways thinking about describing machines. A thermodynamically consistent analysis kinetics rotors pumps shows while light driven operate power‐stroke mechanism, kinetic asymmetry—the relative heights barriers—is sole determinant directionality catalysis Power‐strokes—the depths wells—play no role whatsoever determining sign directionality. These results, elaborated using trajectory thermodynamics nonequilibrium pump equality, show asymmetry governs response many non‐equilibrium phenomena.

Язык: Английский

Процитировано

23
The role of kinetic asymmetry and power strokes in an information ratchet DOI Creative Commons

Lorna Binks,

Stefan Borsley, Todd R. Gingrich

и другие.

Chem, Год журнала: 2023, Номер 9(10), С. 2902 - 2917

Опубликована: Июнь 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

Язык: Английский

Процитировано

37
Artificial Molecular Ratchets: Tools Enabling Endergonic Processes DOI Creative Commons
Thitiporn Sangchai, Shaymaa Al Shehimy, Emanuele Penocchio

и другие.

Angewandte Chemie International Edition, Год журнала: 2023, Номер 62(47)

Опубликована: Авг. 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.

Язык: Английский

Процитировано

32
Ratcheting synthesis DOI
Stefan Borsley, James Gallagher, David A. Leigh

и другие.

Nature Reviews Chemistry, Год журнала: 2023, Номер 8(1), С. 8 - 29

Опубликована: Дек. 15, 2023

Язык: Английский

Процитировано

30
A Minimalistic Covalent Bond‐Forming Chemical Reaction Cycle that Consumes Adenosine Diphosphate DOI Creative Commons
Tommaso Marchetti, Benjamin M. W. Roberts, Diego Frezzato

и другие.

Angewandte Chemie International Edition, Год журнала: 2024, Номер 63(22)

Опубликована: Март 27, 2024

Abstract The development of synthetic active matter requires the ability to design materials capable harnessing energy from a source carry out work. Nature achieves this using chemical reaction cycles in which released an exergonic is used drive biochemical processes. Although many chemically fuelled that control transient responses, such as self‐assembly, have been reported, generally high complexity reported systems hampers full understanding how available actually exploited by these systems. This lack limiting factor matter. Here, we report minimalistic responsive cycle adenosine diphosphate (ADP) triggers formation catalyst for its own hydrolysis. establishes interdependence between concentrations network components resulting catalyst. sufficiently simple all kinetic and thermodynamic parameters governing behaviour can be characterised, allowing models built simulate progress reactions within network. While current does not enable ADP‐hydrolysis populate non‐equilibrium composition, provide insight into way dissipates energy. Furthermore, essential principles are revealed constructing driven systems, composition away equilibrium through consumption

Язык: Английский

Процитировано

7
Analysis of kinetic asymmetry in a multi-cycle reaction network establishes the principles for autonomous compartmentalized molecular ratchets DOI Creative Commons
Emanuele Penocchio,

Ahmad Bachir,

Alberto Credi

и другие.

Chem, Год журнала: 2024, Номер 10(12), С. 3644 - 3655

Опубликована: Сен. 13, 2024

Язык: Английский

Процитировано

7
ATP Drives the Formation of a Catalytic Hydrazone through an Energy Ratchet Mechanism DOI Creative Commons
Tommaso Marchetti, Diego Frezzato, Luca Gabrielli

и другие.

Angewandte Chemie International Edition, Год журнала: 2023, Номер 62(33)

Опубликована: Июнь 27, 2023

Abstract An energy ratchet mechanism is exploited for the synthesis of a molecule. In presence adenosine triphosphate (ATP), hydrazone‐bond formation between an aldehyde and hydrazide accelerated composition at thermodynamic equilibrium shifted towards hydrazone. Enzymatic hydrolysis ATP installs kinetically stable state, which hydrazone present higher concentration compared to in degradation products ATP. It shown that kinetic state has enhanced catalytic activity RNA‐model compound.

Язык: Английский

Процитировано

14
A molecular origin of non-reciprocal interactions between interacting active catalysts DOI
Niladri Sekhar Mandal, Ayusman Sen, R. Dean Astumian

и другие.

Chem, Год журнала: 2023, Номер 10(4), С. 1147 - 1159

Опубликована: Дек. 29, 2023

Язык: Английский

Процитировано

12