Microscopic reversibility as the organizing principle of molecular machines

Molecular Ratchets and Kinetic Asymmetry: Giving Chemistry Direction

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

Design of artificial molecular motor inheriting directionality and scalability

Realizing artificial molecular motors with autonomous functionality and high performance is a major challenge in biophysics. Such motors not only provide new perspectives in biotechnology but also offer a novel approach for the bottom-up elucidation of biological molecular motors. Directionality and scalability are critical factors for practical applications. However, the simultaneous realization of both remains challenging. In this study, we propose a novel design for a rotary motor that can be fabricated using a currently available technology, DNA origami, and validate its functionality through simulations with practical parameters. We demonstrate that the motor rotates unidirectionally and processively in the direction defined by structural asymmetry, which induces kinetic asymmetry in motor motion. The motor also exhibits scalability, such that increasing the number of connections between the motor and stator allows for a larger speed, run length, and stall force.

Kinetic Asymmetry and Directionality of Nonequilibrium Molecular Systems

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

Conformational Changes and ATP Hydrolysis in Zika Helicase: The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations

We computationally study the Zika NS3 helicase, a biological motor, using ATP hydrolysis energy for nucleic acid remodeling. Through molecular mechanics and hybrid quantum mechanics/molecular mechanics simulations, we explore the conformational landscape of motif V, a conserved loop connecting the active sites for ATP hydrolysis and nucleic acid binding. ATP hydrolysis, initiated by a meta-phosphate group formation, involves the nucleophilic attack of a water molecule activated by Glu286 proton abstraction. Motif V hydrogen bonds to this water via the Gly415 backbone NH group, assisting hydrolysis. Posthydrolysis, free energy is released when the inorganic phosphate moves away from the coordination shell of the magnesium ion, inducing a significant shift in the conformational landscape of motif V to establish a hydrogen bond between the Gly415 NH group and Glu285. According to our simulations, the Zika NS3 helicase acts as a ratchet biological motor with motif V transitions steered by Gly415's γ-phosphate sensing in the ATPase site.

Temporal Self-Regulation of Mechanical Properties via Catalytic Amyloid Polymers of a Short Peptide

We report a short peptide that accessed dynamic catalytic polymers to demonstrate four-stage (sol-gel-weak gel-strong gel) temporal self-regulation of its mechanical properties. The peptide exploited its intrinsic catalytic capabilities of manipulating C-C bonds (retro-aldolase-like) that resulted in a nonlinear variation in the catalytic rate. The seven-residue sequence exploited two lysines for binding and cleaving the thermodynamically activated substrate that subsequently led to the self-regulation of the mechanical strengths of the polymerized states as a function of time and reaction progress. Interestingly, the polymerization events were modulated by the different catalytic potentials of the two terminal lysines to cleave the substrate, covalently trap the electrophilic products, and subsequently control the mechanical properties of the system.

Dynamic Insights into the Self-Activation Pathway and Allosteric Regulation of the Orphan G-Protein-Coupled Receptor GPR52

Within over 800 members of G-protein-coupled receptors, there are numerous orphan receptors whose endogenous ligands are largely unknown, providing many opportunities for novel drug discovery. However, the lack of an in-depth understanding of the intrinsic working mechanism for orphan receptors severely limits the related rational drug design. The G-protein-coupled receptor 52 (GPR52) is a unique orphan receptor that constitutively increases cellular 5'-cyclic adenosine monophosphate (cAMP) levels without binding any exogenous agonists and has been identified as a promising therapeutic target for central nervous system disorders. Although recent structural biology studies have provided snapshots of both active and inactive states of GPR52, the mechanism of the conformational transition between these states remains unclear. Here, an acceptable self-activation pathway for GPR52 was proposed through 6 μs Gaussian accelerated molecular dynamics (GaMD) simulations, in which the receptor spontaneously transitions from the active state to that matching the inactive crystal structure. According to the three intermediate states of the receptor obtained by constructing a reweighted potential of mean force, how the allosteric regulation occurs between the extracellular orthosteric binding pocket and the intracellular G-protein-binding site is revealed. Combined with the independent gradient model, several important microswitch residues and the allosteric communication pathway that directly links the two regions are both identified. Transfer entropy calculations not only reveal the complex allosteric signaling within GPR52 but also confirm the unique role of ECL2 in allosteric regulation, which is mutually validated with the results of GaMD simulations. Overall, this work elucidates the allosteric mechanism of GPR52 at the atomic level, providing the most detailed information to date on the self-activation of the orphan receptor.

Engineering Biological Nanopore Approaches toward Protein Sequencing

Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.

Adsorbate motors for unidirectional translation and transport

Artificial molecular motors are designed to transform external energy into useful work in the form of unidirectional motion1. They have been studied mainly in solution2-4, but also on solid surfaces5,6, which provide fixed reference points, allowing for tracking of their movement. However, these molecules require sophisticated design and synthesis, because the motor function must be imprinted into the chemical structure, and show reduced functionality on surfaces compared with in solution5-8. DNA walkers9,10, on the other hand, impart high directionality as they include the surface as part of the motor function, but they require chemical surface patterning and sequential solvent modification for motor activation. Here we show how efficient motors can operate at much smaller length scales on a homogeneous metal surface without any liquid. This is realized by combining a surface with a simple molecule, which, by itself, does not contain any motor unit. The motion, which is tracked at the single-molecule level, is triggered by intramolecular proton transfer with a corresponding modulation of the potential energy surface. Each molecule moves with 100 percent unidirectionality along an atomically defined straight line. Proof of the motor performing meaningful work is shown by controlled transport of single carbon monoxide molecules. This simplistic concept could form the basis for the controlled bottom-up assembly of nanostructures at the atomic scale.

Photoactivated Artificial Molecular Motors

Accurate control of long-range motion at the molecular scale holds great potential for the development of ground-breaking applications in energy storage and bionanotechnology. The past decade has seen tremendous development in this area, with a focus on the directional operation away from thermal equilibrium, giving rise to tailored man-made molecular motors. As light is a highly tunable, controllable, clean, and renewable source of energy, photochemical processes are appealing to activate molecular motors. Nonetheless, the successful operation of molecular motors fueled by light is a highly challenging task, which requires a judicious coupling of thermal and photoinduced reactions. In this paper, we focus on the key aspects of light-driven artificial molecular motors with the aid of recent examples. A critical assessment of the criteria for the design, operation, and technological potential of such systems is provided, along with a perspective view on future advances in this exciting research area.

A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism

The demonstration by Ivan Barnes et al. that the serpentinization of fresh Alpine-type ultramafic rocks results in the exhalation of hot alkaline fluids is foundational to the submarine alkaline vent theory (AVT) for life's emergence to its 'improbable' thermodynamic state. In AVT, such alkaline fluids ≤ 150°C, bearing H2 > CH4 > HS--generated and driven convectively by a serpentinizing exothermic mega-engine operating in the ultramafic crust-exhale into the iron-rich, CO2> > > NO3--bearing Hadean ocean to result in hydrothermal precipitate mounds comprising macromolecular ferroferric-carbonate oxyhydroxide and minor sulfide. As the nanocrystalline minerals fougerite/green rust and mackinawite (FeS), they compose the spontaneously precipitated inorganic membranes that keep the highly contrasting solutions apart, thereby maintaining redox and pH disequilibria. They do so in the form of fine chimneys and chemical gardens. The same disequilibria drive the reduction of CO2 to HCOO- or CO, and the oxidation of CH4 to a methyl group-the two products reacting to form acetate in a sequence antedating the 'energy-producing' acetyl coenzyme-A pathway. Fougerite is a 2D-layered mineral in which the hydrous interlayers themselves harbor 2D solutions, in effect constricted to ~ 1D by preferentially directed electron hopping/tunneling, and proton Gröthuss 'bucket-brigading' when subject to charge. As a redox-driven nanoengine or peristaltic pump, fougerite forces the ordered reduction of nitrate to ammonium, the amination of pyruvate and oxalate to alanine and glycine, and their condensation to short peptides. In turn, these peptides have the flexibility to sequester the founding inorganic iron oxyhydroxide, sulfide, and pyrophosphate clusters, to produce metal- and phosphate-dosed organic films and cells. As the feed to the hydrothermal mound fails, the only equivalent sustenance on offer to the first autotrophs is the still mildly serpentinizing upper crust beneath. While the conditions here are very much less bountiful, they do offer the similar feed and disequilibria the survivors are accustomed to. Sometime during this transition, a replicating non-ribosomal guidance system is discovered to provide the rules to take on the incrementally changing surroundings. The details of how these replicating apparatuses emerged are the hard problem, but by doing so the progenote archaea and bacteria could begin to colonize what would become the deep biosphere. Indeed, that the anaerobic nitrate-respiring methanotrophic archaea and the deep-branching Acetothermia presently comprise a portion of that microbiome occupying serpentinizing rocks offers circumstantial support for this notion. However, the inescapable, if jarring conclusion is drawn that, absent fougerite/green rust, there would be no structured channelway to life.

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

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

Light-Fueled Transformations of a Dynamic Cage-Based Molecular System

In a chemical equilibrium, the formation of high-energy species-in a closed system-is inefficient due to microscopic reversibility. Here, we demonstrate how this restriction can be circumvented by coupling a dynamic equilibrium to a light-induced E/Z isomerization of an azobenzene imine cage. The stable E-cage resists intermolecular imine exchange reactions that would "open" it. Upon switching, the strained Z-cage isomers undergo imine exchange spontaneously, thus opening the cage. Subsequent isomerization of the Z-open compounds yields a high-energy, kinetically trapped E-open species, which cannot be efficiently obtained from the initial E-cage, thus shifting an imine equilibrium energetically uphill in a closed system. Upon heating, the nucleophile is displaced back into solution and an opening/closing cycle is completed by regenerating the stable all-E-cage. Using this principle, a light-induced cage-to-cage transformation is performed by the addition of a ditopic aldehyde.

Challenges in Inferring the Directionality of Active Molecular Processes from Single-Molecule Fluorescence Resonance Energy Transfer Trajectories

We discuss some of the practical challenges that one faces in using stochastic thermodynamics to infer directionality of molecular machines from experimental single-molecule trajectories. Because of the limited spatiotemporal resolution of single-molecule experiments and because both forward and backward transitions between the same pairs of states cannot always be detected, differentiating between the forward and backward directions of, e.g., an ATP-consuming molecular machine that operates periodically, turns out to be a nontrivial task. Using a simple extension of a Markov-state model that is commonly employed to analyze single-molecule transition-path measurements, we illustrate how irreversibility can be hidden from such measurements but in some cases can be uncovered when non-Markov effects in low-dimensional single-molecule trajectories are considered.

Formation of Catalytic Hotspots in ATP-Templated Assemblies

The self-assembly of surfactant-based structures that rely for their formation on the combination of a thermodynamically controlled and a dissipative pathway is described. Adenosine triphosphate (ATP) acts as a high-affinity template and triggers assembly formation at low surfactant concentrations. The presence of these assemblies creates the conditions for the activation of a dissipative self-assembly process by a weak-affinity substrate. The substrate-induced recruitment of additional surfactants leads to the spontaneous formation of catalytic hotspots in the ATP-stabilized assemblies that cleave the substrate. As a result of the two self-assembly processes, catalysis can be observed at a surfactant concentration at which low catalytic activity is observed in the absence of ATP.

Nanopore-based technologies beyond DNA sequencing

Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.

Non-Equilibrium Protein Folding and Activation by ATP-Driven Chaperones

Recent experimental studies suggest that ATP-driven molecular chaperones can stabilize protein substrates in their native structures out of thermal equilibrium. The mechanism of such non-equilibrium protein folding is an open question. Based on available structural and biochemical evidence, I propose here a unifying principle that underlies the conversion of chemical energy from ATP hydrolysis to the conformational free energy associated with protein folding and activation. I demonstrate that non-equilibrium folding requires the chaperones to break at least one of four symmetry conditions. The Hsp70 and Hsp90 chaperones each break a different subset of these symmetries and thus they use different mechanisms for non-equilibrium protein folding. I derive an upper bound on the non-equilibrium elevation of the native concentration, which implies that non-equilibrium folding only occurs in slow-folding proteins that adopt an unstable intermediate conformation in binding to ATP-driven chaperones. Contrary to the long-held view of Anfinsen’s hypothesis that proteins fold to their conformational free energy minima, my results predict that some proteins may fold into thermodynamically unstable native structures with the assistance of ATP-driven chaperones, and that the native structures of some chaperone-dependent proteins may be shaped by their chaperone-mediated folding pathways.

Dissipative DNA nanotechnology

DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines and nanostructures. A major goal in this field is to build devices with life-like properties, such as directional motion, transport, communication and adaptation. Here we provide an overview of the nascent field of dissipative DNA nanotechnology, which aims at developing life-like systems by combining programmable nucleic-acid reactions with energy-dissipating processes. We first delineate the notions, terminology and characteristic features of dissipative DNA-based systems and then we survey DNA-based circuits, devices and materials whose functions are controlled by chemical fuels. We emphasize how energy consumption enables these systems to perform work and cyclical tasks, in contrast with DNA devices that operate without dissipative processes. The ability to take advantage of chemical fuel molecules brings dissipative DNA systems closer to the active molecular devices that exist in nature.

Reaction cycle of operating pump protein studied with single-molecule spectroscopy

Biological machinery relies on nonequilibrium dynamics to maintain stable directional fluxes through complex reaction cycles. For such reaction cycles, the presence of microscopically irreversible conformational transitions of the protein, and the accompanying entropy production, is of central interest. In this work, we use multidimensional single-molecule fluorescence lifetime correlation spectroscopy to measure the forward and reverse conformational transitions of bacteriorhodopsin during trans-membrane H + pumping. We quantify the flux, affinity, enthalpy and entropy production through portions of the reaction cycle as a function of temperature. We find that affinity of irreversible conformational transitions decreases with increasing temperature, resulting in diminishing flux and entropy production. We show that the temperature dependence of the transition affinity is well fit by the Gibbs-Helmholtz relation, allowing the DH trans to be experimentally extracted.

Simulating a chemically fueled molecular motor with nonequilibrium molecular dynamics

Most computer simulations of molecular dynamics take place under equilibrium conditions-in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are introduced to those simulations to probe one type of nonequilibrium response to external forces. Catalysts and molecular motors, however, function based on the nonequilibrium dynamics induced by a chemical reaction's thermodynamic driving force. In this scenario, simulations require chemostats capable of preserving the chemical concentrations of the nonequilibrium steady state. We develop such a dynamic scheme and use it to observe cycles of a particle-based classical model of a catenane-like molecular motor. Molecular motors are frequently modeled with detailed-balance-breaking Markov models, and we explicitly construct such a picture by coarse graining the microscopic dynamics of our simulations in order to extract rates. This work identifies inter-particle interactions that tune those rates to create a functional motor, thereby yielding a computational playground to investigate the interplay between directional bias, current generation, and coupling strength in molecular information ratchets.

A high-fidelity light-powered nanomotor from a chemically fueled counterpart via site-specific optomechanical fuel control

Optically powered nanomotors are advantageous for clean nanotechnology over chemically fuelled nanomotors. The two motor types are further bounded by different physical principles. Despite the gap, we show here that an optically powered DNA bipedal nanomotor is readily created from a high-performing chemically fuelled counterpart by subjecting its fuel to cyclic site-specific optomechanical control - as if the fuel is optically recharged. Optimizing azobenzene-based control of the original nucleotide fuel selects a light-responsive fuel analog that replicates the different binding affinity of the fuel and reaction products. The resultant motor largely retains high-performing features of the original chemical motor, and achieves the highest directional fidelity among reported light-driven DNA nanomotors. This study thus demonstrates a novel strategy for transforming chemical nanomotors to optical ones for clean nanotechnology. The strategy is potentially applicable to many chemical nanomotors with oligomeric fuels like nucleotides, peptides and synthetic polymers, leading to a new class of light-powered nanomotors that are akin to chemical nanomotors and benefit from their generally high efficiency mechanistically. The motor from this study also provides a rare model system for studying the subtle boundary between chemical and optical nanomotors - a topic pertinent to chemomechanical and optomechanical energy conversion at the single-molecule level.

Parallel path mechanisms lead to nonmonotonic force-velocity curves and an optimum load for molecular motor function

Molecular motors convert chemical potential energy into mechanical work and perform a great number of critical biological functions. Examples include the polymerization and manipulation of nucleic acids, the generation of cellular motility and contractility, the formation and maintenance of cell shape, and the transport of materials within cells. The mechanisms underlying these molecular machines are varied, but are almost always considered in the context of a single kinetic pathway that describes motor stepping. However, the multidimensional nature of protein energy landscapes suggests the possibility of multiple reaction pathways connecting two states. Here we investigate the properties of a hypothetical molecular motor able to utilize parallel translocation mechanisms. We explore motor velocity and force dependence as a function of the energy landscape of each path and reveal the potential for such a mechanism to result in negative differential conductance. More specifically, regimes exist where increasing opposing force leads to increased velocity and an optimum load for motor function. We explore how the presence of this optimum depends on the rates of the individual paths and show that the distribution of stepping times characterized by the randomness parameter may be used to test for parallel path mechanisms. Last, we caution that experimental data consisting solely of measurements of velocity as a function of ATP concentration and force cannot be used to eliminate the possibility of such a parallel path mechanism.

Polyrotaxanes and the pump paradigm

The year 2022 marks the 30th anniversary of the first reports of polyrotaxanes in the scientific literature.

Spontaneous Reorganization of DNA-Based Polymers in Higher Ordered Structures Fueled by RNA

We demonstrate a strategy that allows for the spontaneous reconfiguration of self-assembled DNA polymers exploiting RNA as chemical fuel. To do this, we have rationally designed orthogonally addressable DNA building blocks that can be transiently deactivated by RNA fuels and subtracted temporarily from participation in the self-assembly process. Through a fine modulation of the rate at which the building blocks are reactivated we can carefully control the final composition of the polymer and convert a disordered polymer in a higher order polymer, which is disfavored from a thermodynamic point of view. We measure the dynamic reconfiguration via fluorescent signals and confocal microscopy, and we derive a kinetic model that captures the experimental results. Our approach suggests a novel route toward the development of biomolecular materials in which engineered chemical reactions support the autonomous spatial reorganization of multiple components.

Nonequilibrium thermodynamics of light-induced reactions

Current formulations of nonequilibrium thermodynamics of open chemical reaction networks only consider chemostats as free-energy sources sustaining nonequilibrium behaviors. Here, we extend the theory to include incoherent light as a source of free energy. We do so by relying on a local equilibrium assumption to derive the chemical potential of photons relative to the system they interact with. This allows us to identify the thermodynamic potential and the thermodynamic forces driving light-reacting chemical systems out-of-equilibrium. We use this framework to treat two paradigmatic photochemical mechanisms describing light-induced unimolecular reactions-namely, the adiabatic and diabatic mechanisms-and highlight the different thermodynamics they lead to. Furthermore, using a thermodynamic coarse-graining procedure, we express our findings in terms of commonly measured experimental quantities, such as quantum yields.

Chemically Fueled Self-Assembly in Biology and Chemistry

Life is a non-equilibrium state of matter maintained at the expense of energy. Nature uses predominantly chemical energy stored in thermodynamically activated, but kinetically stable, molecules. These high-energy molecules are exploited for the synthesis of other biomolecules, for the activation of biological machinery such as pumps and motors, and for the maintenance of structural order. Knowledge of how chemical energy is transferred to biochemical processes is essential for the development of artificial systems with life-like processes. Here, we discuss how chemical energy can be used to control the structural organization of organic molecules. Four different strategies have been identified according to a distinguishable physical-organic basis. For each class, one example from biology and one from chemistry are discussed in detail to illustrate the practical implementation of each concept and the distinct opportunities they offer. Specific attention is paid to the discussion of chemically fueled non-equilibrium self-assembly. We discuss the meaning of non-equilibrium self-assembly, its kinetic origin, and strategies to develop synthetic non-equilibrium systems.

Radical-pairing-induced molecular assembly and motion

Radical-pairing interactions between conjugated organic π-radicals are relative newcomers to the inventory of molecular recognition motifs explored in supramolecular chemistry. The unique electronic, magnetic, optical and redox-responsive properties of the conjugated π-radicals render molecules designed with radical-pairing interactions useful for applications in various areas of chemistry and materials science. In particular, the ability to control formation of radical cationic or anionic species, by redox stimulation, provides a flexible trigger for directed assembly and controlled molecular motions, as well as a convenient means of inputting energy to fuel non-equilibrium processes. In this Review, we provide an overview of different examples of radical-pairing-based recognition processes and of their emerging use in (1) supramolecular assembly, (2) templation of mechanically interlocked molecules, (3) stimuli-controlled molecular switches and, by incorporation of kinetic asymmetry in the design, (4) the creation of unidirectional molecular transporters based on pumping cassettes powered by fuelled switching of radical-pairing interactions. We conclude the discussion with an outlook on future directions for the field.

Chemically-powered swimming and diffusion in the microscopic world

The past decade has seen intriguing reports and heated debates concerning the chemically-driven enhanced motion of objects ranging from small molecules to millimetre-size synthetic robots. These objects, in solutions in which chemical reactions were occurring, were observed to diffuse (spread non-directionally) or swim (move directionally) at rates exceeding those expected from Brownian motion alone. The debates have focused on whether observed enhancement is an experimental artefact or a real phenomenon. If the latter were true, then we would also need to explain how the chemical energy is converted into mechanical work. In this Perspective, we summarize and discuss recent observations and theories of active diffusion and swimming. Notably, the chemomechanical coupling and magnitude of diffusion enhancement are strongly size-dependent and should vanish as the size of the swimmers approaches the molecular scale. We evaluate the reliability of common techniques to measure diffusion coefficients and finish by considering the potential applications and chemical to mechanical energy conversion efficiencies of typical nanoswimmers and microswimmers.

Molecular Pumps and Motors

Pumps and motors are essential components of the world as we know it. From the complex proteins that sustain our cells, to the mechanical marvels that power industries, much we take for granted is only possible because of pumps and motors. Although molecular pumps and motors have supported life for eons, it is only recently that chemists have made progress toward designing and building artificial forms of the microscopic machinery present in nature. The advent of artificial molecular machines has granted scientists an unprecedented level of control over the relative motion of components of molecules through the development of kinetically controlled, away-from-thermodynamic equilibrium chemistry. We outline the history of pumps and motors, focusing specifically on the innovations that enable the design and synthesis of the artificial molecular machines central to this Perspective. A key insight connecting biomolecular and artificial molecular machines is that the physical motions by which these machines carry out their function are unambiguously in mechanical equilibrium at every instant. The operation of molecular motors and pumps can be described by trajectory thermodynamics, a theory based on the work of Onsager, which is grounded on the firm foundation of the principle of microscopic reversibility. Free energy derived from thermodynamically non-equilibrium reactions kinetically favors some reaction pathways over others. By designing molecules with kinetic asymmetry, one can engineer potential landscapes to harness external energy to drive the formation and maintenance of geometries of component parts of molecules away-from-equilibrium, that would be impossible to achieve by standard synthetic approaches.

Barrier Crossing Dynamics from Single-Molecule Measurements

Chemists visualize chemical reactions as motion along one-dimensional "reaction coordinates" over free energy barriers. Various rate theories, such as transition state theory and the Kramers theory of diffusive barrier crossing, differ in their assumptions regarding the mathematical specifics of this motion. Direct experimental observation of the motion along reaction coordinates requires single-molecule experiments performed with unprecedented time resolution. Toward this goal, recent single-molecule studies achieved time resolution sufficient to catch biomolecules in the act of crossing free energy barriers as they fold, bind to their targets, or undergo other large structural changes, offering a window into the elusive reaction "mechanisms". This Perspective describes what we can learn (and what we have already learned) about barrier crossing dynamics through synergy of single-molecule experiments, theory, and molecular simulations. In particular, I will discuss how emerging experimental data can be used to answer several questions of principle. For example, is motion along the reaction coordinate diffusive, is there conformational memory, and is reduction to just one degree of freedom to represent the reaction mechanism justified? It turns out that these questions can be formulated as experimentally testable mathematical inequalities, and their application to experimental and simulated data has already led to a number of insights. I will also discuss open issues and current challenges in this fast evolving field of research.

An All-Photonic Molecular Amplifier and Binary Flip-flop

A chemical system is proposed that is capable of amplifying small optical inputs into large changes in internal composition, based on a feedback interaction between switchable fluorescence and visible-light photoswitching. This system would demonstrate bifurcating reaction kinetics under irradiation and reach one of two stable photostationary states depending on the initial composition of the system. This behavior would allow the system to act as a chemical realization of the flip-flop circuit, the fundamental element in sequential logic and binary memory storage. We use detailed numerical modeling to demonstrate the feasibility of the proposed behavior based on known molecular phenomena and comment on some of the conditions required to realize this system.

Enhanced catalytic activity under non-equilibrium conditions

The development of non-equilibrium synthetic systems provides access to innovative materials with life-like properties. Non-equilibrium systems require a continuous input of energy to retain their functional state, which makes for a fundamental difference to systems that operate at thermodynamic equilibrium. Kinetic asymmetry in the energy consumption pathway is required to drive systems out of equilibrium. This understanding has permitted chemists to design dissipative synthetic molecular machines and high-energy materials. Here we show that kinetic asymmetry also emerges at the macroscopic level by demonstrating that local energy delivery in the form of light to a hydrogel containing gold nanoparticles installs a non-equilibrium steady state. The instalment and maintenance of the macroscopic non-equilibrium state is facilitated by the gel matrix in which motion is governed by diffusion rather than convection. The non-equilibrium state is characterized by a persistent gradient in the surface composition of the nanoparticles embedded in the gel, which affects the fluorescent and catalytic properties of the system. We show that the overall catalytic performance of the system is enhanced under these non-equilibrium conditions. In perspective it will be possible to develop out-of-equilibrium matrices in which functional properties emerge as a result of spatially controlled energy delivery and spatially controlled chemistries.

Real-time tracking of protein unfolding with time-resolved x-ray solution scattering

The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.

From Nonequilibrium Single-Molecule Trajectories to Underlying Dynamics

Single-molecule observations of biomolecular dynamics and folding are commonly rationalized using the model of diffusive dynamics on a free-energy landscape, which is inferred via the Boltzmann inversion of the equilibrium distribution of the experimental observable. Can the same model be applied to high-resolution single-molecule trajectories of molecular machines that lack thermal equilibrium so that the Boltzmann inversion method is inapplicable? In this Letter, we discuss two approaches to reconstructing the underlying free-energy landscape in such nonequilibrium systems and explore the performance of this model in application to trajectories with complex underlying dynamics.

Selection from a pool of self-assembling lipid replicators

Replication and compartmentalization are fundamental to living systems and may have played important roles in life’s origins. Selection in compartmentalized autocatalytic systems might provide a way for evolution to occur and for life to arise from non-living systems. Herein we report selection in a system of self-reproducing lipids where a predominant species can emerge from a pool of competitors. The lipid replicators are metastable and their out-of-equilibrium population can be sustained by feeding the system with starting materials. Phase separation is crucial for selective surfactant formation as well as autocatalytic kinetics; indeed, no selection is observed when all reacting species are dissolved in the same phase. Selectivity is attributed to a kinetically controlled process where the rate of monomer formation determines which replicator building blocks are the fittest. This work reveals how kinetics of a phase-separated autocatalytic reaction may be used to control the population of out-of-equilibrium replicators in time.

Selection in compartmentalized self-replicating systems might provide a way for life to arise from abiotic environments. Here, the authors explore selection in a system of transient autocatalytic lipids and find that autocatalytic kinetics and phase separation are the key selection factors.

On the beneficent thickness of water

In the 1930s, Lars Onsager published his famous 'reciprocal relations' describing free energy conversion processes. Importantly, these relations were derived on the assumption that the fluxes of the processes involved in the conversion were proportional to the forces (free energy gradients) driving them. For chemical reactions, however, this condition holds only for systems operating close to equilibrium-indeed very close; nominally requiring driving forces to be smaller than k B T. Fairly soon thereafter, however, it was quite inexplicably observed that in at least some biological conversions both the reciprocal relations and linear flux-force dependency appeared to be obeyed no matter how far from equilibrium the system was being driven. No successful explanation of how this 'paradoxical' behaviour could occur has emerged and it has remained a mystery. We here argue, however, that this anomalous behaviour is simply a gift of water, of its viscosity in particular; a gift, moreover, without which life almost certainly could not have emerged. And a gift whose appreciation we primarily owe to recent work by Prof. R. Dean Astumian who, as providence has kindly seen to it, was led to the relevant insights by the later work of Onsager himself.

A Molecular Dual Pump

Artificial molecular machines (AMMs) built from mechanically interlocked molecules (MIMs) can use energy ratchets to control the unidirectional motion of their component parts. These energy ratchets are operated by the alteration of kinetic barriers and thermodynamic wells, which are, in turn, determined by the switching on and off of noncovalent interactions. Previously, we have developed artificial molecular pumps (AMPs) capable of pumping rings consecutively onto a collecting chain as part of a molecular dumbbell, leading to the formation of rotaxanes. Here, we report a molecular dual pump (MDP) consisting of two individual AMPs linked in a head-to-tail fashion, wherein a single ring is pumped, in a linear manner, on and off a dumbbell involving a [2]rotaxane intermediate by exploiting the redox properties of the two pumps. This MDP, defined by the finely tuned noncovalent interactions and fueled by either chemicals or electricity, utilizes an energy ratchet mechanism to capture a ring and subsequently release it back into solution. The unidirectional motion and the resulting controlled capture and release of the ring were followed by 1D and 2D ¹H NMR spectroscopy and supported by control experiments. This molecular dual pump may be considered to be a forerunner of AMMs that are capable of pumping rings across a membrane in a way similar to how bacteriorhodopsin transports protons from one side of a membrane to the other under the influence of light. Such extensive multicomponent AMMs can lead potentially to molecular transporting platforms with positional and directional control of cargo uptake and release when, and only when, instructed.

Building machines with DNA molecules

In nature, DNA molecules carry the hereditary information. But DNA has physical and chemical properties that make it attractive for uses beyond heredity. In this Review, we discuss the potential of DNA for creating machines that are both encoded by and built from DNA molecules. We review the main methods of DNA nanostructure assembly, describe recent advances in building increasingly complex molecular structures and discuss strategies for creating machine-like nanostructures that can be actuated and move. We highlight opportunities for applications of custom DNA nanostructures as scientific tools to address challenges across biology, chemistry and engineering.

Probing complexity: thermodynamics and computational mechanics approaches to origins studies

This paper proposes new avenues for origins research that apply modern concepts from stochastic thermodynamics, information thermodynamics and complexity science. Most approaches to the emergence of life prioritize certain compounds, reaction pathways, environments or phenomena. What they all have in common is the objective of reaching a state that is recognizably alive, usually positing the need for an evolutionary process. As with life itself, this correlates with a growth in the complexity of the system over time. Complexity often takes the form of an intuition or a proxy for a phenomenon that defies complete understanding. However, recent progress in several theoretical fields allows the rigorous computation of complexity. We thus propose that measurement and control of the complexity and information content of origins-relevant systems can provide novel insights that are absent in other approaches. Since we have no guarantee that the earliest forms of life (or alien life) used the same materials and processes as extant life, an appeal to complexity and information processing provides a more objective and agnostic approach to the search for life's beginnings. This paper gives an accessible overview of the three relevant branches of modern thermodynamics. These frameworks are not commonly applied in origins studies, but are ideally suited to the analysis of such non-equilibrium systems. We present proposals for the application of these concepts in both theoretical and experimental origins settings.

Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins

Two mechanisms have been proposed for the function of motor proteins: The power stroke and the Brownian ratchet. The former refers to generation of a large downhill free energy gradient over which the motor protein moves nearly irreversibly in making a step, whereas the latter refers to biasing or rectifying the diffusive motion of the motor. Both mechanisms require input of free energy, which generally involves the processing of an ATP (adenosine 5'-triphosphate) molecule. Recent advances in experiments that reveal the details of the stepping motion of motor proteins, together with computer simulations of atomistic structures, have provided greater insights into the mechanisms. Here, we compare the various models of the power stroke and the Brownian ratchet that have been proposed. The 2 mechanisms are not mutually exclusive, and various motor proteins employ them to different extents to perform their biological function. As examples, we discuss linear motor proteins Kinesin-1 and myosin-V, and the rotary motor F₁-ATPase, all of which involve a power stroke as the essential element of their stepping mechanism.

Fatty acid based transient nanostructures for temporal regulation of artificial peroxidase activity

Natural systems access transient high energy self-assembled structures for temporal regulation of different biological functions through dissipative processes. Compartmentalization within self-assembled structures is used by living systems to organize vital biochemical reactions that define cellular metabolism. Herein, we demonstrate a simple fatty acid based system where a redox active base (dimethylaminomethyl ferrocene, Fc-NMe2 ) acts as a countercation to access unique hexagonal compartments resulting in the formation of a self-supporting gel. An oxidizing environment helps in the dissipation of energy by converting Fc-NMe2 to oxidized waste and the gel autonomously undergoes transition to a sol. Hence, the system requires the addition of the fuel Fc-NMe2 to access the temporal gel state. Notably, these transient compartments were able to temporally upregulate and downregulate hemin-catalyzed oxidation reactions mimicking peroxidase, a ubiquitous enzyme in extant biology. An order of magnitude variation in k cat values was observed with time and the chemical reaction persists as long as the gel state was present.

Kinetic asymmetry allows macromolecular catalysts to drive an information ratchet

Molecular machines carry out their function by equilibrium mechanical motions in environments that are far from thermodynamic equilibrium. The mechanically equilibrated character of the trajectories of the macromolecule has allowed development of a powerful theoretical description, reminiscent of Onsager’s trajectory thermodynamics, that is based on the principle of microscopic reversibility. Unlike the situation at thermodynamic equilibrium, kinetic parameters play a dominant role in determining steady-state concentrations away from thermodynamic equilibrium, and kinetic asymmetry provides a mechanism by which chemical free-energy released by catalysis can drive directed motion, molecular adaptation, and self-assembly. Several examples drawn from the recent literature, including a catenane-based chemically driven molecular rotor and a synthetic molecular assembler or pump, are discussed.

The mechanism by which macromolecular catalysts use energy from exergonic reactions to move, adapt, and assemble has been unclear. In this Perspective article, R. Dean Astumian shows that in addition to disequilibrium of the catalyzed reaction, kinetic asymmetry is the essential feature required to drive non-equilibrium response by an information ratchet mechanism.

Theory of Nonequilibrium Free Energy Transduction by Molecular Machines

Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they face a distinct set of challenges compared with more familiar human-engineered macroscopic machines. Here we review central questions in their performance as free energy transducers, outline theoretical and modeling approaches to understand these questions, identify both physical limits on their operational characteristics and design principles for improving performance, and discuss emerging areas of research.