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The internal organization of cells is largely determined by the architecture and orientation of the microtubule network. Microtubules serve as polar tracks for the selective transport of specific molecular motors toward either their plus or minus ends. How both motors reciprocally move microtubules and organize the network's arrangement and polarity is unknown. Here, we combined experiments on reconstituted systems and theory to study the interaction of microtubules with both plus-and minus-end directed motors bound to a fluid membrane. Depending on motor concentrations, the system could lead either to the constant transport of microtubules or to their alignment, stacking, and immobilization in regular bands that separate motors into domains of opposite polarities. In bands, microtubules shared the same polarity and segregated the two opposing motors accordingly. These regular patterns resulted from the balance of forces produced by the two motors as they walked in opposite directions along microtubules. The system was maintained in a dynamic steady state in which the directional transport of microtubule-bound motors compensates for the random diffusion of lipid-bound motors. The size of motor domains depended on their respective concentrations. The constant flow of motors allowed the system to respond to variations in motor concentrations by moving microtubules to adapt to the new force balance. The polar sorting and linear arrangement of microtubules associated with the segregation of motors of opposite polarity are typical of cellular architectures, which these data may help to better understand. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) is marked by the gradual and age-related deterioration of nerve cells in the central nervous system. The histopathological features observed in the brain affected by AD are the aberrant buildup of extracellular and intracellular amyloid-β and the formation of neurofibrillary tangles consisting of hyperphosphorylated tau protein. Axonal transport is a fundamental process for cargo movement along axons and relies on molecular motors like kinesins and dyneins. Kinesin's responsibility for transporting crucial cargo within neurons implicates its dysfunction in the impaired axonal transport observed in AD. Impaired axonal transport and dysfunction of molecular motor proteins, along with dysregulated signaling pathways, contribute significantly to synaptic impairment and cognitive decline in AD. Dysregulation in tau, a microtubule-associated protein, emerges as a central player, destabilizing microtubules and disrupting the transport of kinesin-1. Kinesin-1 superfamily members, including kinesin family members 5A, 5B, and 5C, and the kinesin light chain, are intricately linked to AD pathology. However, inconsistencies in the abundance of kinesin family members in AD patients underline the necessity for further exploration into the mechanistic impact of these motor proteins on neurodegeneration and axonal transport disruptions across a spectrum of neurological conditions. This review underscores the significance of kinesin-1's anterograde transport in AD. It emphasizes the need for investigations into the underlying mechanisms of the impact of motor protein across various neurological conditions. Despite current limitations in scientific literature, our study advocates for targeting kinesin and autophagy dysfunctions as promising avenues for novel therapeutic interventions and diagnostics in AD. [ABSTRACT FROM AUTHOR]

Top‐down control of small motion is possible through top‐down controlled molecular motors in replacement of larger actuators like MEMS or NEMS (micro‐ or nano‐electromechanical systems) in the current precision technology. Improving top‐down control of molecular motors to every single step is desirable for this purpose, and also for synchronization of motor actions for amplified effects. Here we report a designed single‐stranded DNA molecular motor powered by alternated ultraviolet and visible light for processive track‐walking, with the two light colours each locking the motor in a full directional step to allow saturated driving but no overstepping. This novel nano‐optomechanical driving mechanism pushes the top‐down control of molecular motors down to every single step, thus providing a key technical capability to advance the molecular motor‐based precision technology and also motor synchronization for amplified effects. [ABSTRACT FROM AUTHOR]

Top‐down control of small motion is possible through top‐down controlled molecular motors in replacement of larger actuators like MEMS or NEMS (micro‐ or nano‐electromechanical systems) in the current precision technology. Improving top‐down control of molecular motors to every single step is desirable for this purpose, and also for synchronization of motor actions for amplified effects. Here we report a designed single‐stranded DNA molecular motor powered by alternated ultraviolet and visible light for processive track‐walking, with the two light colours each locking the motor in a full directional step to allow saturated driving but no overstepping. This novel nano‐optomechanical driving mechanism pushes the top‐down control of molecular motors down to every single step, thus providing a key technical capability to advance the molecular motor‐based precision technology and also motor synchronization for amplified effects. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Rotavirus (RV) replicates within viroplasms, membraneless electron-dense globular cytosolic inclusions with liquid–liquid phase properties. In these structures occur the virus transcription, replication, and packaging of the virus genome in newly assembled double-layered particles. The viroplasms are composed of virus proteins (NSP2, NSP5, NSP4, VP1, VP2, VP3, and VP6), single- and double-stranded virus RNAs, and host components such as microtubules, perilipin-1, and chaperonins. The formation, coalescence, maintenance, and perinuclear localization of viroplasms rely on their association with the cytoskeleton. A stabilized microtubule network involving microtubules and kinesin Eg5 and dynein molecular motors is associated with NSP5, NSP2, and VP2, facilitating dynamic processes such as viroplasm coalescence and perinuclear localization. Key post-translation modifications, particularly phosphorylation events of RV proteins NSP5 and NSP2, play pivotal roles in orchestrating these interactions. Actin filaments also contribute, triggering the formation of the viroplasms through the association of soluble cytosolic VP4 with actin and the molecular motor myosin. This review explores the evolving understanding of RV replication, emphasizing the host requirements essential for viroplasm formation and highlighting their dynamic interplay within the host cell. [ABSTRACT FROM AUTHOR]

Photoresponsive supramolecular polymers have a major potential for applications in responsive materials that are externally triggered by light with spatio‐temporal control of their polymerisation state. While changes in macroscopic properties revealed the adaptive nature of these materials, it remains challenging to capture the dynamic depolymerisation process at the molecular level, which requires fast observation techniques combined with in situ irradiation. By implementing in situ UV illumination into a High‐Speed Atomic Force Microscope (HS‐AFM) setup, we have been able to capture the disassembly of a light‐driven molecular motor‐based supramolecular polymer. The real‐time visualisation of the light‐triggered disassembly process not only reveals cooperative depolymerisation, it also shows that this process continues after illumination is halted. Combining the data with cryo‐electron microscopy and spectroscopy approaches, we obtain a molecular‐level description of the motor‐based polymer dynamics reminiscent of actin chain‐end depolymerisation. Our detailed understanding of supramolecular depolymerisation will drive the development of future responsive polymer systems. [ABSTRACT FROM AUTHOR]

Photoresponsive supramolecular polymers have a major potential for applications in responsive materials that are externally triggered by light with spatio‐temporal control of their polymerisation state. While changes in macroscopic properties revealed the adaptive nature of these materials, it remains challenging to capture the dynamic depolymerisation process at the molecular level, which requires fast observation techniques combined with in situ irradiation. By implementing in situ UV illumination into a High‐Speed Atomic Force Microscope (HS‐AFM) setup, we have been able to capture the disassembly of a light‐driven molecular motor‐based supramolecular polymer. The real‐time visualisation of the light‐triggered disassembly process not only reveals cooperative depolymerisation, it also shows that this process continues after illumination is halted. Combining the data with cryo‐electron microscopy and spectroscopy approaches, we obtain a molecular‐level description of the motor‐based polymer dynamics reminiscent of actin chain‐end depolymerisation. Our detailed understanding of supramolecular depolymerisation will drive the development of future responsive polymer systems. [ABSTRACT FROM AUTHOR]

Immobilization of stimulus‐responsive systems on solid surfaces is beneficial for controlled signal transmission and adaptive behavior while allowing the characterization of the functional interface with high sensitivity and high spatial resolution. Positioning of the stimuli‐responsive units with nanometer‐scale precision across the adaptive surface remains one of the bottlenecks in the extraction of cooperative function. Nanoscale organization, cooperativity, and amplification remain key challenges in bridging the molecular and the macroscopic worlds. Here we report on the design, synthesis, and scanning tunneling microscopy (STM) characterization of overcrowded alkene photoswitches merged in self‐assembled networks physisorbed at the solid‐liquid interface. A detailed anchoring strategy that ensures appropriate orientation of the switches with respect to the solid surface through the use of bis‐urea groups is presented. We implement a co‐assembly strategy that enables the merging of the photoswitches within physisorbed monolayers of structurally similar 'spacer' molecules. The self‐assembly of the individual components and the co‐assemblies was examined in detail using (sub)molecular resolution STM which confirms the robust immobilization and controlled orientation of the photoswitches within the spacer monolayers. The experimental STM data is supported by detailed molecular mechanics (MM) simulations. Different designs of the switches and the spacers were investigated which allowed us to formulate guidelines that enable the precise organization of the photoswitches in crystalline physisorbed self‐assembled molecular networks. [ABSTRACT FROM AUTHOR]

Dynein, an ancient microtubule-based motor protein, performs diverse cellular functions in nearly all eukaryotic cells, with the exception of land plants. It has evolved into three subfamilies—cytoplasmic dynein-1, cytoplasmic dynein-2, and axonemal dyneins—each differentiated by their cellular functions. These megadalton complexes consist of multiple subunits, with the heavy chain being the largest subunit that generates motion and force along microtubules by converting the chemical energy of ATP hydrolysis into mechanical work. Beyond this catalytic core, the functionality of dynein is significantly enhanced by numerous non-catalytic subunits. These subunits are integral to the complex, contributing to its stability, regulating its enzymatic activities, targeting it to specific cellular locations, and mediating its interactions with other cofactors. The diversity of non-catalytic subunits expands dynein's cellular roles, enabling it to perform critical tasks despite the conservation of its heavy chains. In this review, we discuss recent findings and insights regarding these non-catalytic subunits. [ABSTRACT FROM AUTHOR]

We propose a general mathematical and computational approach to study cellular transport driven by a group of kinesin motors. It is a framework for multi-scale modeling that integrates kinetic models of single kinesin motors, including detachment and reattachment events, to study group behaviors of several motors. By formulating the problem as a semi-Markov process and applying a central limit theorem, asymptotic velocity and diffusivity can be readily calculated, which offers considerable computational advantage over Monte Carlo simulations in tasks such as parameter sensitivity analysis and model selection. We demonstrate the method with some examples. The importance of incorporating the intrinsic microscopic-level dynamics of individual motors is illustrated by showing how changes at the microscopic level propagate to the motor-cargo complex at a mesoscopic level. Particularly, we showcase an example in which changes in the second moment of single-motor characteristics gives rise to different first moment characteristics of the motor group. [ABSTRACT FROM AUTHOR]

Microtubules and molecular motors are essential components of the cellular cytoskeleton, driving fundamental processes in vivo, including chromosome segregation and cargo transport. When reconstituted in vitro, these cytoskeletal proteins serve as energy-consuming building blocks to study the self-organization of active matter. Cytoskeletal active gels display rich emergent dynamics, including extensile flows, locally contractile asters, and bulk contraction. However, it is unclear how the protein–protein interaction kinetics set their contractile or extensile nature. Here, we explore the origin of the transition from extensile bundles to contractile asters in a minimal reconstituted system composed of stabilized microtubules, depletant, adenosine 5′-triphosphate (ATP), and clusters of kinesin-1 motors. We show that the microtubule-binding and unbinding kinetics of highly processive motor clusters set their ability to end-accumulate, which can drive polarity sorting of the microtubules and aster formation. We further demonstrate that the microscopic time scale of end-accumulation sets the emergent time scale of aster formation. Finally, we show that biochemical regulation is insufficient to fully explain the transition as generic aligning interactions through depletion, cross-linking, or excluded volume interactions can drive bundle formation despite end-accumulating motors. The extensile-to-contractile transition is well captured by a simple self-assembly model where nematic and polar aligning interactions compete to form either bundles or asters. Starting from a five-dimensional organization phase space, we identify a single control parameter given by the ratio of the different component concentrations that dictates the material-scale organization. Overall, this work shows that the interplay of biochemical and mechanical tuning at the microscopic level controls the robust self-organization of active cytoskeletal materials. [ABSTRACT FROM AUTHOR]

Simulations can help unravel the complicated ways in which molecular structure determines function. Here, we use molecular simulations to show how slight alterations of a molecular motor's structure can cause the motor's typical dynamical behavior to reverse directions. Inspired by autonomous synthetic catenane motors, we study the molecular dynamics of a minimal motor model, consisting of a shuttling ring that moves along a track containing interspersed binding sites and catalytic sites. The binding sites attract the shuttling ring while the catalytic sites speed up a reaction between molecular species, which can be thought of as fuel and waste. When that fuel and waste are held in nonequilibrium steady-state concentrations, the free energy from the reaction drives directed motion of the shuttling ring along the track. Using this model and nonequilibrium molecular dynamics, we show that the shuttling ring's direction can be reversed by simply adjusting the spacing between binding and catalytic sites on the track. We present a steric mechanism behind the current reversal, supported by kinetic measurements from the simulations. These results demonstrate how molecular simulation can guide future development of artificial molecular motors. [ABSTRACT FROM AUTHOR]

Molecular motors, based on overcrowded alkenes (L) serving as ligands to chelate lanthanide nitrate, afford the first lanthanide‐functionalized water‐soluble ionic compound [L2‐Ln(NO3)2(H2O)2]·NO3 (LnL2). Benefitting from the "pull–push" feature of L together with 3LMCT from L to LnIII, irradiation with visible light not only drives photochemical isomerization but also induces energy transfer from L to LnIII, decreasing their intensity of low‐energy 3LMCT (ligand‐to‐metal triplet energy transfer) absorptions and sensitizing the Ln‐based luminescence. Thus, the typical EuIII‐based luminescence of EuL2 favors tracing its movement by time‐resolved luminescence, and temperature‐dependent luminescence renders it possibly to be used as potential luminescent thermometers. Very excitingly, besides a contraction of the stator by Ln–L interactions on decreasing the steric hindrance on the "fjord region," the efficiency of intramolecular 3LMCT sensitization synergetically regulates the rotary motion of lanthanide‐complexed motors in thermal helix inversion steps. [ABSTRACT FROM AUTHOR]

The Dengue Virus (DENV) non-structural protein 3 (NS3) is a multi-functional protein critical in the viral life cycle. The DENV NS3 is comprised of a serine protease domain and a helicase domain. The helicase domain itself acts as a molecular motor, either translocating in a unidirectional manner along single-stranded RNA or unwinding double-stranded RNA, processes fueled by the hydrolysis of nucleoside triphosphates. In this brief review, we summarize our contributions and ongoing efforts to uncover the thermodynamic and mechanistic functional properties of the DENV NS3 as an NTPase and helicase. [ABSTRACT FROM AUTHOR]

Molecular motors are essential for the movement and transportation of macromolecules in living organisms. Among them, rotatory motors are particularly efficient. In this study, we investigated the long-term dynamics of the designed left-handed alpha/alpha toroid (PDB: 4YY2), the RBM2 flagellum protein ring from Salmonella (PDB: 6SD5), and the V-type Na + -ATPase rotor in Enterococcus hirae (PDB: 2BL2) using microcanonical and canonical molecular dynamics simulations with the coarse-grained UNRES force field, including a lipid-membrane model, on a millisecond laboratory time scale. Our results demonstrate that rotational motion can occur with zero total angular momentum in the microcanonical regime and that thermal motions can be converted into net rotation in the canonical regime, as previously observed in simulations of smaller cyclic molecules. For 6SD5 and 2BL2, net rotation (with a ratcheting pattern) occurring only about the pivot of the respective system was observed in canonical simulations. The extent and direction of the rotation depended on the initial conditions. This result suggests that rotatory molecular motors can convert thermal oscillations into net rotational motion. The energy from ATP hydrolysis is required probably to set the direction and extent of rotation. Our findings highlight the importance of molecular-motor structures in facilitating movement and transportation within living organisms. [ABSTRACT FROM AUTHOR]

Active nematics represent a relatively new class of materials with liquid crystalline properties that rely on an energy source to maintain their structure and dynamics. In this paper, we focus on the well-known microtubule-kinesin-based active nematic, powered by chemical energy as ATP (Adenosine triphosphate), and report on how ATP depletion impacts active nematic defect dynamics and texture. Using fluorescence microscope video imaging, we measure the time averaged mean defect separations and root mean square velocities of the active flows as a function of time. We also characterise textural changes and the growth of void space in the network after ATP depletion using an image binarization technique. [ABSTRACT FROM AUTHOR]

In single-molecule experiments, the dynamics of molecular motors are often observed indirectly by measuring the trajectory of an attached bead in a motor–bead assay. In this work, we propose a method to extract the step size and stalling force for a molecular motor without relying on external control parameters. We discuss this method for a generic hybrid model that describes bead and motor via continuous and discrete degrees of freedom, respectively. Our deductions are solely based on the observation of waiting times and transition statistics of the observable bead trajectory. Thus, the method is non-invasive, operationally accessible in experiments and can, in principle, be applied to any model describing the dynamics of molecular motors. We briefly discuss the relation of our results to recent advances in stochastic thermodynamics on inference from observable transitions. Our results are confirmed by extensive numerical simulations for parameters values of an experimentally realized F1-ATPase assay. [ABSTRACT FROM AUTHOR]

Diabetic peripheral neuropathy (DPN) is a chronic and prevalent metabolic disease that gravely endangers human health and seriously affects the quality of life of hyperglycemic patients. More seriously, it can lead to amputation and neuropathic pain, imposing a severe financial burden on patients and the healthcare system. Even with strict glycemic control or pancreas transplantation, peripheral nerve damage is difficult to reverse. Most current treatment options for DPN can only treat the symptoms but not the underlying mechanism. Patients with long-term diabetes mellitus (DM) develop axonal transport dysfunction, which could be an important factor in causing or exacerbating DPN. This review explores the underlying mechanisms that may be related to axonal transport impairment and cytoskeletal changes caused by DM, and the relevance of the latter with the occurrence and progression of DPN, including nerve fiber loss, diminished nerve conduction velocity, and impaired nerve regeneration, and also predicts possible therapeutic strategies. Understanding the mechanisms of diabetic neuronal injury is essential to prevent the deterioration of DPN and to develop new therapeutic strategies. Timely and effective improvement of axonal transport impairment is particularly critical for the treatment of peripheral neuropathies. [ABSTRACT FROM AUTHOR]

The unidirectional rotation of chemically crosslinked light‐driven molecular motors is shown to progressively shift the swelling equilibrium of hydrogels. The concentration of molecular motors and the initial strand density of the polymer network are key parameters to modulate the macroscopic contraction of the material, and both parameters can be tuned using polymer chains of different molecular weights. These findings led to the design of optimized hydrogels revealing a half‐time contraction of approximately 5 min. Furthermore, under inhomogeneous stimulation, the local contraction event was exploited to design useful bending actuators with an energy output 400 times higher than for previously reported self‐assembled systems involving rotary motors. In the present configuration, we measure that a single molecular motor can lift up loads of 200 times its own molecular weight. [ABSTRACT FROM AUTHOR]

The unidirectional rotation of chemically crosslinked light‐driven molecular motors is shown to progressively shift the swelling equilibrium of hydrogels. The concentration of molecular motors and the initial strand density of the polymer network are key parameters to modulate the macroscopic contraction of the material, and both parameters can be tuned using polymer chains of different molecular weights. These findings led to the design of optimized hydrogels revealing a half‐time contraction of approximately 5 min. Furthermore, under inhomogeneous stimulation, the local contraction event was exploited to design useful bending actuators with an energy output 400 times higher than for previously reported self‐assembled systems involving rotary motors. In the present configuration, we measure that a single molecular motor can lift up loads of 200 times its own molecular weight. [ABSTRACT FROM AUTHOR]

Network-based biocomputation (NBC) relies on accurate guiding of biological agents through nanofabricated channels produced by lithographic patterning techniques. Here, we report on the large-scale, wafer-level fabrication of optimized microfluidic channel networks (NBC networks) using electron-beam lithography as the central method. To confirm the functionality of these NBC networks, we solve an instance of a classical non-deterministic-polynomial-time complete ("NP-complete") problem, the subset-sum problem. The propagation of cytoskeletal filaments, e.g., molecular motor-propelled microtubules or actin filaments, relies on a combination of physical and chemical guiding along the channels of an NBC network. Therefore, the nanofabricated channels have to fulfill specific requirements with respect to the biochemical treatment as well as the geometrical confienement, with walls surrounding the floors where functional molecular motors attach. We show how the material stack used for the NBC network can be optimized so that the motor-proteins attach themselves in functional form only to the floor of the channels. Further optimizations in the nanolithographic fabrication processes greatly improve the smoothness of the channel walls and floors, while optimizations in motor-protein expression and purification improve the activity of the motor proteins, and therefore, the motility of the filaments. Together, these optimizations provide us with the opportunity to increase the reliability of our NBC devices. In the future, we expect that these nanolithographic fabrication technologies will enable production of large-scale NBC networks intended to solve substantially larger combinatorial problems that are currently outside the capabilities of conventional software-based solvers. [ABSTRACT FROM AUTHOR]

The 3‐satisfiability Problem (3‐SAT) is a demanding combinatorial problem that is of central importance among the nondeterministic polynomial (NP) complete problems, with applications in circuit design, artificial intelligence, and logistics. Even with optimized algorithms, the solution space that needs to be explored grows exponentially with the increasing size of 3‐SAT instances. Thus, large 3‐SAT instances require excessive amounts of energy to solve with serial electronic computers. Network‐based biocomputation (NBC) is a parallel computation approach with drastically reduced energy consumption. NBC uses biomolecular motors to propel cytoskeletal filaments through nanofabricated networks that encode mathematical problems. By stochastically exploring possible paths through the networks, the cytoskeletal filaments find possible solutions. However, to date, no NBC algorithm for 3‐SAT has been available. Herein, an algorithm that converts 3‐SAT into an NBC‐compatible network format is reported and four small 3‐SAT instances (with up to three variables and five clauses) using the actin–myosin biomolecular motor system are experimentally solved. Because practical polynomial conversions to 3‐SAT exist for many important NP complete problems, the result opens the door to enable NBC to solve small instances of a wide range of problems. [ABSTRACT FROM AUTHOR]

V-ATPases are rotary motor proteins that convert the chemical energy of ATP into the electrochemical potential of ions across cell membranes. V-ATPases consist of two rotary motors, Vo and V1, and Enterococcus hirae V-ATPase (EhVoV1) actively transports Na+ in Vo (EhVo) by using torque generated by ATP hydrolysis in V1 (EhV1). Here, we observed ATP-driven stepping rotation of detergent-solubilized EhVoV1 wildtype, aE634A, and BR350K mutants under various Na+ and ATP concentrations ([Na+] and [ATP], respectively) by using a 40-nm gold nanoparticle as a low-load probe. When [Na+] was low and [ATP] was high, under the condition that only Na+ binding to EhVo is rate limiting, wild-type and aE634A exhibited 10 pausing positions reflecting 10-fold symmetry of the EhVo rotor and almost no backward steps. Duration time before the forward steps was inversely proportional to [Na+], confirming that Na+ binding triggers the steps. When both [ATP] and [Na+] were low, under the condition that both Na+ and ATP bindings are rate limiting, aE634A exhibited 13 pausing positions reflecting 10- and 3-fold symmetries of EhVo and EhV1, respectively. The distribution of duration time before the forward step was fitted well by the sum of two exponential decay functions with distinct time constants. Furthermore, occasional backward steps smaller than 36° were observed. Small backward steps were also observed during three long ATP cleavage pauses of BR350K. These results indicate that EhVo and EhV1 do not share pausing positions, Na+ and ATP bindings occur at different angles, and the coupling between EhVo and EhV1 has a rigid component. [ABSTRACT FROM AUTHOR]

Circular polarized light is utilized in communication and display technologies and a major challenge is to develop systems that can be switched between left and right circular polarized luminescence with high degrees of polarization and enable multiple addressable stable states. Luminescent dyes in Liquid Crystal (LC) cholesteric phases are attractive systems to generate, amplify and modulate circularly polarized luminescence (CPL). In the present study, we employ light‐driven molecular motors as photo‐controlled chiral dopants in LCs to switch the handedness of the LC and the circular polarization of luminescence from an achiral dye embedded in the mesogenic material. Tuning of the color of the CPL and the retention time of the photoprogrammed helicity is demonstrated making use of a variety of motors and dyes. The flexibility offered by the design based on inherently chiral unidirectional rotary motors provides full control over CPL non‐invasively by light, opening possibilities for pixilated displays with externally addressable polarization. [ABSTRACT FROM AUTHOR]

Circular polarized light is utilized in communication and display technologies and a major challenge is to develop systems that can be switched between left and right circular polarized luminescence with high degrees of polarization and enable multiple addressable stable states. Luminescent dyes in Liquid Crystal (LC) cholesteric phases are attractive systems to generate, amplify and modulate circularly polarized luminescence (CPL). In the present study, we employ light‐driven molecular motors as photo‐controlled chiral dopants in LCs to switch the handedness of the LC and the circular polarization of luminescence from an achiral dye embedded in the mesogenic material. Tuning of the color of the CPL and the retention time of the photoprogrammed helicity is demonstrated making use of a variety of motors and dyes. The flexibility offered by the design based on inherently chiral unidirectional rotary motors provides full control over CPL non‐invasively by light, opening possibilities for pixilated displays with externally addressable polarization. [ABSTRACT FROM AUTHOR]

Molecular machines are at the frontier of biology and chemistry. The ability to control molecular motion and emulating the movement of biological systems are major steps towards the development of responsive and adaptive materials. Amazing progress has been seen for the design of molecular machines including light‐induced unidirectional rotation of overcrowded alkenes. However, the feasibility of inducing unidirectional rotation about a single bond as a result of chemical conversion has been a challenging task. In this Review, an overview of approaches towards the design, synthesis, and dynamic properties of different classes of atropisomers which can undergo controlled switching or rotation under the influence of a chemical stimulus is presented. They are categorized as molecular switches, rotors, motors, and autonomous motors according to their type of response. Furthermore, we provide a future perspective and challenges focusing on building sophisticated molecular machines. [ABSTRACT FROM AUTHOR]

Molecular machines are at the frontier of biology and chemistry. The ability to control molecular motion and emulating the movement of biological systems are major steps towards the development of responsive and adaptive materials. Amazing progress has been seen for the design of molecular machines including light‐induced unidirectional rotation of overcrowded alkenes. However, the feasibility of inducing unidirectional rotation about a single bond as a result of chemical conversion has been a challenging task. In this Review, an overview of approaches towards the design, synthesis, and dynamic properties of different classes of atropisomers which can undergo controlled switching or rotation under the influence of a chemical stimulus is presented. They are categorized as molecular switches, rotors, motors, and autonomous motors according to their type of response. Furthermore, we provide a future perspective and challenges focusing on building sophisticated molecular machines. [ABSTRACT FROM AUTHOR]

A possibility of utilization of molecular motors for creation of unidirectional rotation of tiny disks floating on a surface is considered theoretically. The bottom side of the disk is covered with grafted motors combined with flat blades submerges into a viscous liquid for torque generation. When exposes to UV‐light, the motors start to rotate all in the same direction, and they transfer their rotation to the blades creating a mechanical torque that turns the disk. The disk angular velocity scales as ω ∼ Ω L/R where Ω is motor angular velocity, L is the length of the oars, R is the micro‐disk size. A competition between directional ballistic‐type rotation and rotative diffusion is considered. The setup can be used for evaluation of the primary motor parameters: the motor rotation speed Ω = 2πf, and the maximum motor torque load Mmax. [ABSTRACT FROM AUTHOR]

We describe azophenylindane based molecular motors (aphin-switches) which have two different rotamers of trans-configuration and four different rotamers of cis-configuration. The behaviors of these motors were investigated both experimentally and computationally. The conversion of aphin-switch does not yield single isomer but a mixture of these. Although the trans to cis conversion leads to the increase of the system entropy some of the cis-rotamers can directly convert to each other while others should convert via trans-configuration. The motion of aphin-switches resembles the work of a mixing machine with indane group serving as a base and phenol group serving as a beater. The aphin-switches presented herein may provide a basis for promising applications in advanced biological systems or particularly in cases where on demand disordering of molecular packing has value, such as lipid bilayers. [ABSTRACT FROM AUTHOR]

Mechanisms coupling the chemical reactions of oxidation and ATP synthesis in cellular metabolism by the fundamental biological process of oxidative phosphorylation (OX PHOS) in mitochondria provide > 90% of the energy requirements in living organisms. Mathematical graph theory methods have been extensively used to characterize various metabolic, regulatory, and disease networks in biology. However, networks of energy coupling mechanisms in OX PHOS have not been represented and analyzed previously by these approaches. Here, the problem of biological energy coupling is translated into a graph-theoretical framework, and all possible coupling schemes between oxidation and ATP synthesis are represented as graphs connecting these processes by various intermediates or states. The problem is shown to be transformed into the hard problem of finding a Hamiltonian tour in the networks of possible constituent mechanisms, given the constraints of a cyclical nature of operation of enzymes and biological molecular machines. Accessible mathematical proofs of three theorems that guarantee sufficient conditions for the existence of a Hamiltonian cycle in simple graphs are provided. The results of the general theorems are applied to the set of possible coupling mechanisms in OX PHOS and shown to (1) unequivocally differentiate between the major theories and mechanisms of energy coupling, (2) greatly reduce the possibilities for detailed consideration, and (3) deduce the biologically selected mechanism using additional constraints from the cumulative experimental record. Finally, an algorithm is constructed to implement the graph-theoretical procedure. In summary, the enormous power and generality of mathematical theorems and approaches in graph theory are shown to help solve a fundamental problem in biology. [ABSTRACT FROM AUTHOR]

In artificial small‐molecule machines, molecular motors can be used to perform work on coupled systems by applying a mechanical load—such as strain—that allows for energy transduction. Here, we report how ring strain influences the rotation of a rotary molecular motor. Bridging the two halves of the motor with alkyl tethers of varying sizes yields macrocycles that constrain the motor's movement. Increasing the ring size by two methylene increments increases the mobility of the motor stepwise and allows for fine‐tuning of strain in the system. Small macrocycles (8–14 methylene units) only undergo a photochemical E/Z isomerization. Larger macrocycles (16–22 methylene units) can perform a full rotational cycle, but thermal helix inversion is strongly dependent on the ring size. This study provides systematic and quantitative insight into the behavior of molecular motors under a mechanical load, paving the way for the development of complex coupled nanomachinery. [ABSTRACT FROM AUTHOR]

In artificial small‐molecule machines, molecular motors can be used to perform work on coupled systems by applying a mechanical load—such as strain—that allows for energy transduction. Here, we report how ring strain influences the rotation of a rotary molecular motor. Bridging the two halves of the motor with alkyl tethers of varying sizes yields macrocycles that constrain the motor's movement. Increasing the ring size by two methylene increments increases the mobility of the motor stepwise and allows for fine‐tuning of strain in the system. Small macrocycles (8–14 methylene units) only undergo a photochemical E/Z isomerization. Larger macrocycles (16–22 methylene units) can perform a full rotational cycle, but thermal helix inversion is strongly dependent on the ring size. This study provides systematic and quantitative insight into the behavior of molecular motors under a mechanical load, paving the way for the development of complex coupled nanomachinery. [ABSTRACT FROM AUTHOR]

Motor proteins, also known as biological molecular motors, play important roles in various intracellular processes. Experimental investigations suggest that molecular motors interact with each other during the cellular transport, but the nature of such interactions remains not well understood. Stimulated by these observations, we present a theoretical study aimed to understand the effect of the range of interactions on dynamics of interacting molecular motors. For this purpose, we develop a new version of the totally asymmetric simple exclusion processes in which nearest-neighbor as well as the next nearest-neighbor interactions are taken into account in a thermodynamically consistent way. A theoretical framework based on a cluster mean-field approximation, which partially takes correlations into account, is developed to evaluate the stationary properties of the system. It is found that fundamental currentâ€"density relations in the system strongly depend on the strength and the sign of interactions, as well as on the range of interactions. For repulsive interactions stronger than some critical value, a mean-field theoretical approach predicts that increasing the range of interactions might lead to a change from unimodal to trimodal dependence in the flux-density fundamental diagram. However, it is not fully supported by extensive Monte Carlo computer simulations that test theoretical predictions. Although in most ranges of parameters a reasonable agreement between theoretical calculations and computer simulations is observed, there are situations when the cluster mean-field approach fails to describe properly the dynamics in the system. Theoretical arguments to explain these observations are presented. Our theoretical analysis clarifies the microscopic picture of how the range of interactions influences the dynamics of interacting molecular motors. [ABSTRACT FROM AUTHOR]

Optical switches in lipid membranes are an emerging tool to tune the properties of the bilayer or membrane protein integrated therein. Here, we use simple geometry and physics considerations to deduce structural criteria to design efficient photoactivated switches for lipid membranes. We compare how the area of projection on the bilayer of various classes of photoswitches changes upon the trans/cis or open/closed transition and show that azobenzene and stilbene should distort the bilayer structure the most. We also conclude that planar-elongated molecules, in which atoms of isomerizable double bond have no additional substituents, while substituents of the fragments adjacent to the double bond prevent formation of the planar molecule in cis configuration, are to be the best photoswitches for lipid membranes. [ABSTRACT FROM AUTHOR]

Molecular motors transform external energy input into directional motions and offer exquisite precision for nano‐scale manipulations. To make full use of molecular motor capacities, their directional motions need to be transmitted and used for powering downstream molecular events. Here we present a macrocyclic molecular motor structure able to perform repetitive molecular threading of a flexible tetraethylene glycol chain through the macrocycle. This mechanical threading event is actively powered by the motor and leads to a direct translation of the unidirectional motor rotation into unidirectional translation motion (chain versus ring). The mechanism of the active mechanical threading is elucidated and the actual threading step is identified as a combined helix inversion and threading event. The established molecular machine function resembles the crucial step of macroscopic weaving or sewing processes and therefore offers a first entry point to a "molecular knitting" counterpart. [ABSTRACT FROM AUTHOR]

Molecular motors transform external energy input into directional motions and offer exquisite precision for nano‐scale manipulations. To make full use of molecular motor capacities, their directional motions need to be transmitted and used for powering downstream molecular events. Here we present a macrocyclic molecular motor structure able to perform repetitive molecular threading of a flexible tetraethylene glycol chain through the macrocycle. This mechanical threading event is actively powered by the motor and leads to a direct translation of the unidirectional motor rotation into unidirectional translation motion (chain versus ring). The mechanism of the active mechanical threading is elucidated and the actual threading step is identified as a combined helix inversion and threading event. The established molecular machine function resembles the crucial step of macroscopic weaving or sewing processes and therefore offers a first entry point to a "molecular knitting" counterpart. [ABSTRACT FROM AUTHOR]

The Ton complex is a molecular motor at the inner membrane of Gram-negative bacteria that uses a proton gradient to apply forces on outer membrane (OM) proteins to permit active transport of nutrients into the periplasmic space. Recently, the structure of the ExbB–ExbD subcomplex was determined in several bacterial species, but the complete structure and stoichiometry of TonB have yet to be determined. The C-terminal end of TonB is known to cross the periplasm and interact with TonB-dependent outer membrane transport proteins with high affinity. Yet despite having significant knowledge of these transport proteins, it is not clear how the Ton motor opens a pathway across the outer membrane for nutrient import. Additionally, the mechanism by which energy is harnessed from the inner membrane subcomplex and transduced to the outer membrane via TonB is not well understood. In this review, we will discuss the gaps in the knowledge about the complete structure of the Ton motor complex and the relationship between ion flow used to generate mechanical work at the outer membrane and the nutrient transport process. [ABSTRACT FROM AUTHOR]

Motile archaea swim by means of a molecular machine called the archaellum. This structure consists of a filament attached to a membrane-embedded motor. The archaellum is found exclusively in members of the archaeal domain, but the core of its motor shares homology with the motor of type IV pili (T4P). Here, we provide an overview of the different components of the archaellum machinery and hypothetical models to explain how rotary motion of the filament is powered by the archaellum motor. [ABSTRACT FROM AUTHOR]

Endocytosis is indispensable for multiple cellular processes, including signalling, cell adhesion, migration, as well as the turnover of plasma membrane lipids and proteins. The dynamic interplay and regulation of different endocytic entry routes requires multiple cytoskeletal elements, especially motor proteins that bind to membranes and transport vesicles along the actin and microtubule cytoskeletons. Dynein and kinesin motor proteins transport vesicles along microtubules, whereas myosins drive vesicles along actin filaments. Here, we present a brief overview of multiple endocytic pathways and our current understanding of the involvement of these motor proteins in the regulation of the different cellular entry routes. We particularly focus on structural and mechanistic details of the retrograde motor proteins dynein and myosin VI (also known as MYO6), along with their adaptors, which have important roles in the early events of endocytosis. We conclude by highlighting the key challenges in elucidating the involvement of motor proteins in endocytosis and intracellular membrane trafficking. [ABSTRACT FROM AUTHOR]

Molecular motors are nanometer scale proteins involved in various intracellular processes such as cargo transport, muscle contraction and cell division. The steps in the chemo-mechanical cycle that use ATP hydrolysis to generate motion along the cytoskeletal tracks can be characterized by stepping rates depending only on the current state, permitting modeling of the cycle as a Markov process. To learn more about the nature of motor motion, cell researchers have conducted in vitro experiments in which molecular motors pull beads along filaments attached to glass slides and their velocity and run length until detachment from the microtubule are recorded. A formula is derived for distance traveled until detachment. Four molecular motors for which there are run length and velocity measurements in the literature are considered. In each case the derived formulas for run length and velocity have a generalized Michaelis–Menten form as functions of ATP concentration. The degrees of the numerator and denominator polynomials increase with the complexity of chemo-mechanical cycle. The degrees of the Michaelis–Menten form determine the maximum number of reaction rates that can be determined from experimental data on run length and velocity, however consistency conditions may reduce this number and restrict which rates can be determined. [ABSTRACT FROM AUTHOR]

Modern synthetic methods can be highly complex and proceed via multiple sequential processes. The intricate concepts can rarely be checked in all necessary detail due to the lack of suitable analysis methods. For photoinitiated reactions the starting point can be chosen to any desired precision by short or ultrafast light pulses. However, the optical analysis is blind to many aspects. Pairing the illumination of the reaction mixture with other online detection schemes proves extremely valuable. Herein we present a combination of variable temperature NMR spectroscopy with in‐situ illumination and photon‐counting to monitor the short‐lived intermediates and gain a comprehensive and quantitative picture of the working of a hemithioindigo‐based molecular motor. Application of the scheme is not limited to the field of molecular machines, we rather think that it will be of great use for any detailed identification and characterization of chemical intermediates in photochemistry, photoredox catalysis, photoswitching, or photoresponsive materials. [ABSTRACT FROM AUTHOR]

A chiral‐switchable device for circularly polarized luminescence (CPL) is fabricated based on dynamic superstructure of cholesteric liquid crystals (N*‐LC) doped with light‐driven molecular motor (MM), which achieves simultaneous modulation of chirality and intensity of CPL. Functional MM, designed with the modification of alkyl chains on the rotor, allows for advanced chemical isomerization to be driven with light. The selective reflection band due to the N*‐LC is shifted upon UV irradiation so that the reflection band moves toward the emissive band of the luminescence dyes, yielding CPL with opposite handedness and high dissymmetry factor values. The geometric changes of the motor during the rotary steps finally cause a remarkable reversible handedness inversion of the N*‐LC, which also leads switchable chirality of CPL. The dynamic N*‐LC cell bearing the light‐controlled selective reflection is useful for generating CPL from fluorescent materials and for allowing light chirality‐switching in CPL signals, which presents new possibilities for optoelectronic and photonics applications. [ABSTRACT FROM AUTHOR]

The advent of single-molecule force spectroscopy represents the introduction of forces, torques, and displacements as controlled variables in biochemistry. These methods afford the direct manipulation of individual molecules to interrogate the forces that hold together their structure, the forces and torques that these molecules generate in the course of their biochemical reactions, and the use of force, torque, and displacement as tools to investigate the mechanisms of these reactions. Because of their microscopic nature, the signals detected in these experiments are often dominated by fluctuations, which, in turn, play an important role in the mechanisms that underlie the operation of the molecular machines of the cell. Their direct observation and quantification in single-molecule experiments provide a unique window to investigate those mechanisms, as well as a convenient way to investigate fundamental new fluctuation theorems of statistical mechanics that bridge the equilibrium and non-equilibrium realms of this discipline. In this review we have concentrated on the developments that occurred in our laboratory on the characterization of biopolymers and of molecular machines of the central dogma. Accordingly, some important areas like the study of cytoskeletal motors have not been included. While we adopt at times an anecdotal perspective with the hope of conveying the personal circumstances in which these developments took place, we have made every effort, nonetheless, to include the most important developments that were taking place at the same time in other laboratories. [ABSTRACT FROM AUTHOR]