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The spontaneous generation of transmembrane gradients is an important fundamental research goal for artificial nanotechnology. The active transport processes that give rise to such gradients directly mirror the famous Maxwell's Demon thought experiment, where a Demon partitions particles between two chambers to generate a nonequilibrium state. Despite these similarities, discussion of Maxwell's Demon is absent in the literature on artificial membrane transport. By contrast, the emergence of rational design principles for nonequilibrium artificial molecular motors can trace its intellectual roots directly to this famous thought experiment. This perspective highlights the links between Maxwell's Demon and nonequilibrium machines, and argues that understanding the implications of this 19th century thought experiment is crucial to the future development of transmembrane active transport processes. [ABSTRACT FROM AUTHOR]

Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here we explore the de novo construction of protein machinery from designed axle and rotor components with internal cyclic or dihedral symmetry. We find that the axle-rotor systems assemble in vitro and in vivo as designed. Using cryo-electron microscopy, we find that these systems populate conformationally variable relative orientations reflecting the symmetry of the coupled components and the computationally designed interface energy landscape. These mechanical systems with internal degrees of freedom are a step toward the design of genetically encodable nanomachines. [ABSTRACT FROM AUTHOR]

A coarse-grain method for simulations of the dynamics of active protein inclusions in lipid bilayers is described. It combines the previously proposed hybrid simulations of bilayers [M.-J. Huang, R. Kapral, A. S. Mikhailov, and H.-Y. Chen, J. Chem. Phys. 137, 055101 (2012)], based on molecular dynamics for the lipids and multi-particle collision dynamics for the solvent, with an elastic-network description of active proteins. The method is implemented for a model molecular machine which performs active conformational motions induced by ligand binding and its release after reaction. The situation characteristic for peripheral membrane proteins is considered. Statistical investigations of the effects of single active or passive inclusions on the shape of the membrane are carried out. The results show that the peripheral machine produces asymmetric perturbations of the thickness of two leaflets of the membrane. It also produces a local saddle in the midplane height of the bilayer. Analysis of the power spectrum of the fluctuations of the membrane midplane shows that the conformational motion of the machine perturbs these membrane fluctuations. The hydrodynamic lipid flows induced by cyclic conformational changes in the machine are analyzed. It is shown that such flows are long-ranged and should provide an additional important mechanism for interactions between active inclusions in biological membranes. [ABSTRACT FROM AUTHOR]

Structural biology studies performed inside cells can capture molecular machines in action within their native context. In this work, we developed an integrative in-cell structural approach using the genome-reduced human pathogen Mycoplasma pneumoniae. We combined whole-cell cross-linking mass spectrometry, cellular cryo–electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at subnanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpointed NusA at the interface between a NusG-bound elongating RNAP and the ribosome and propose that it can mediate transcription-translation coupling. Translation inhibition dissociated the expressome, whereas transcription inhibition stalled and rearranged it. Thus, the active expressome architecture requires both translation and transcription elongation within the cell. [ABSTRACT FROM AUTHOR]

Mechanically interlocked molecules are likely candidates for the design and synthesis of artificial molecular machines. Although polyrotaxanes have already found niche applications in exotic materials with specialized mechanical properties, efficient synthetic protocols to produce them with precise numbers of rings encircling their polymer dumbbells are still lacking. We report the assembly line–like emergence of poly[n]rotaxanes with increasingly higher energies by harnessing artificial molecular pumps to deliver rings in pairs by cyclical redox-driven processes. This programmable strategy leads to the precise incorporation of two, four, six, eight, and 10 rings carrying 8+, 16+, 24+, 32+, and 40+ charges, respectively, onto hexacationic polymer dumbbells. This strategy depends precisely on the number of redox cycles applied chemically or electrochemically, in both stepwise and one-pot manners. [ABSTRACT FROM AUTHOR]

Synthetic nanoscale complexes capable of mechanical movement are often studied theoretically using discrete-state models that involve instantaneous transitions between metastable states. A number of general results have been derived within this framework, including a 'no-pumping theorem' that restricts the possibility of generating directed motion by the periodic variation of external parameters. Motivated by recent experiments using time-resolved vibrational spectroscopy [Panman et al., Science 328, 1255 (2010)], we introduce a more detailed and realistic class of models in which transitions between metastable states occur by finite-time, diffusive processes rather than sudden jumps. We show that the no-pumping theorem remains valid within this framework. [ABSTRACT FROM AUTHOR]

How does a biomolecular machine achieve high speed at high efficiency? We explore optimization principles using a simple two-state dynamical model. With this model, we establish physical principles--such as the optimal way to distribute free-energy changes and barriers across the machine cycle--and connect them to biological mechanisms. We find that a machine can achieve high speed without sacrificing efficiency by varying its conformational free energy to directly link the downhill, chemical energy to the uphill, mechanical work and by splitting a large work step into more numerous, smaller substeps. Experimental evidence suggests that these mechanisms are commonly used by biomolecular machines. This model is useful for exploring questions of evolution and optimization in molecular machines. [ABSTRACT FROM AUTHOR]

The treatment of [Co(d- or l-ebp)]− with CdX2 (X = Br−, I−) gave a cyclic CoIII3CdII3 complex with a 12-membered metalloring, [Cd3X3{Co(d- or l-ebp)}3] (d3- or l3-1X). The use of a 1 : 1 mixture of [Co(d-ebp)]− and [Co(l-ebp)]−, instead of [Co(d- or l-ebp)]−, led to the creation of a cyclic CoIII6CdII6 complex with a 24-membered metalloring, [Cd6X6(H2O)6{Co(d-ebp)}3{Co(l-ebp)}3] (d3l3-2X). Compounds d3l3-2X were also produced when d3-1X and l3-1X were mixed in water in a 1 : 1 ratio, illustrating the conversion of a pair of homochiral metallorings into a double-sized heterochiral metalloring. [ABSTRACT FROM AUTHOR]

Many families of natural products are synthesized by large multidomain biological machines commonly referred to as megasynthases. While the advance of mechanism‐based tools has opened new windows into the structural features within the protein–protein interfaces guiding carrier protein dependent enzymes, there is an immediate need for tools that can be engaged to link co‐translated domains in a site‐selective manner. Now, the use of silylcyanohydrins is demonstrated in a two‐step, two‐site selective crosslinking for the trapping of carrier–protein interactions within megasynthases. This advance provides a new tool to trap intermediate states within multimodular systems, a key step toward understanding the specificities within fatty acid (FAS) and polyketide (PKS) synthases. [ABSTRACT FROM AUTHOR]

The field of synthetic molecular machines has quickly evolved in recent years, growing from a fundamental curiosity to a highly active field of chemistry. Many different applications are being explored in areas such as catalysis, self-assembled and nanostructured materials, and molecular electronics. Rotary molecular motors hold great promise for achieving dynamic control of molecular functions as well as for powering nanoscale devices. However, for these motors to reach their full potential, many challenges still need to be addressed. In this paper we focus on the design principles of rotary motors featuring a double-bond axle and discuss the major challenges that are ahead of us. Although great progress has been made, further design improvements, for example in terms of efficiency, energy input, and environmental adaptability, will be crucial to fully exploit the opportunities that these rotary motors offer. [ABSTRACT FROM AUTHOR]

The coordinated motion of many individual components underpins the operation of all machines. However, despite generations of experience in engineering, understanding the motion of three or more coupled components remains a challenge, known since the time of Newton as the "three-body problem." Here, we describe, quantify, and simulate a molecular three-body problem of threading two molecular rings onto a linear molecular thread. Specifically, we use voltage-triggered reduction of a tetrazine-based thread to capture two cyanostar macrocycles and form a [3]pseudorotaxane product. As a consequence of the noncovalent coupling between the cyanostar rings, we find the threading occurs by an unexpected and rare inchworm-like motion where one ring follows the other. The mechanism was derived from controls, analysis of cyclic voltammetry (CV) traces, and Brownian dynamics simulations. CVs from two noncovalently interacting rings match that of two covalently linked rings designed to thread via the inchworm pathway, and they deviate considerably from the CV of a macrocycle designed to thread via a stepwise pathway. Time-dependent electrochemistry provides estimates of rate constants for threading. Experimentally derived parameters (energy wells, barriers, diffusion coefficients) helped determine likely pathways of motion with rate-kinetics and Brownian dynamics simulations. Simulations verified intercomponent coupling could be separated into ring-thread interactions for kinetics, and ring-ring interactions for thermodynamics to reduce the three-body problem to a two-body one. Our findings provide a basis for high-throughput design of molecular machinery with multiple components undergoing coupled motion. [ABSTRACT FROM AUTHOR]

The article examines the effectiveness of molecular machine to keep living things alive. It states that chemist David Leigh at the University of Manchester in Great Britain has developed various nanoscale machines which perform useful tasks. Also mentioned is the fundamental application of the machines such as shuttles, walkers and elevators.

Major improvements in the synthesis of surface‐mounted rotary molecular machines based on ruthenium(II) complexes are reported. The development of a one‐pot indium(III)‐mediated “N‐deprotection/ester reductive sulfidation” sequence allowed step economy, reproducibility and high efficiency in the synthesis of the thioether‐functionalized tripodal ligand. Switching to the thallium salt of hydrotris(indazolyl)borate and to microwave heating further optimized the preparation of the common intermediate in the modular synthesis of symmetric and dissymmetric molecular motors and gears. The penta(4‐bromophenyl)cyclopentadienyl ruthenium(II) key precursor is now reproducibly synthesized in 5 steps and 31 % overall yield on the longest linear sequence. Subsequent fivefold Suzuki–Miyaura coupling with ferroceneboronic acid led to a new C5‐symmetric pentaferrocenyl molecular motor. [ABSTRACT FROM AUTHOR]

Intrigued by the potential of nanoscale machines, scientists have long attempted to control molecular motion. We monitored the individual 0.7-nanometer steps of a single molecular hopper as it moved in an electric field along a track in a nanopore controlled by a chemical ratchet. The hopper demonstrated characteristics desired in a moving molecule: defined start and end points, processivity, no chemical fuel requirement, directional motion, and external control. The hopper was readily functionalized to carry cargos. For example, a DNA molecule could be ratcheted along the track in either direction, a prerequisite for nanopore sequencing. [ABSTRACT FROM AUTHOR]

A promising application for design and deployment of molecular machines is nanoscale transport, driven by artificial cilia. In this contribution, we present several further steps toward this goal, beyond our first‐generation artificial cilium (Raeker et al., J. Phys. Chem. A 2012, 116, 11241). Promising new azobenzene‐derivatives were tested for use as cilium motors. Using a QM/MM partitioning in on‐the‐fly photodynamics, excited‐state surface‐hopping trajectories were calculated for each isomerization direction and each motor version. The methods used were reparametrized semiempirical quantum chemistry together with floating‐occupation configuration interaction as the QM part and the OPLSAA‐L forcefield as MM part. In addition, we simulated actual particle transport by a single cilium attached to a model surface, with varying attachment strengths and modes, and with transport targets ranging from single atoms to multi‐molecule arrangements. Our results provide valuable design guidelines for cilia‐driven nanoscale transport and emphasize the need to carefully select the whole setup (not just the cilium itself, but also its surface attachment and the dynamic cilium‐target interaction) to achieve true transport. © 2018 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Abstract: Artificial molecular machines can be operated using either physical or chemical inputs. Light‐powered motors display clean and autonomous operations, whereas chemically driven machines generate waste products and are intermittent in their motions. Herein, we show that controlled changes in applied electrochemical potentials can drive the operation of artificial molecular pumps in a semi‐autonomous manner—that is, without the need for consecutive additions of chemical fuel(s). The electroanalytical approach described in this Communication promotes the assembly of cyclobis(paraquat‐p‐phenylene) rings along a positively charged oligomeric chain, providing easy access to the formation of multiple mechanical bonds by means of a controlled supply of electricity. [ABSTRACT FROM AUTHOR]

Abstract: Each constitutive chain of a conducting polymer electrode acts as a reversible multi‐step electrochemical molecular motor: reversible reactions drive reversible conformational movements of the chain. The reaction‐driven cooperative actuation of those molecular machines generates, or destroys, inside the film the free volume required to lodge/expel balancing counterions and solvent: reactions drive reversible film volume variations, which basic structural components are here identified and quantified from electrochemical responses. The content of the reactive dense gel (chemical molecular machines, ions and water) mimics that of the intracellular matrix in living functional cells. Reaction‐driven properties (composition‐dependent properties) and devices replicate biological functions and organs. An emerging technological world of soft, wet, reaction‐driven, multifunctional and biomimetic devices and the concomitant zoomorphic or anthropomorphic robots is presented. [ABSTRACT FROM AUTHOR]

The paper presents a review of the state of the art and prospects for the development of rotary molecular switches based on transition metal bis(dicarbollide) complexes. [ABSTRACT FROM AUTHOR]

Abstract: Rotaxane‐based molecular shuttles are often operated using low‐symmetry axles and changing the states of the binding stations. A molecular shuttle capable of directional shuttling of an acid‐responsive cone‐like macrocycle on a single‐state symmetric dumbbell axle is now presented. The axle contains three binding stations: one symmetric di(quaternary ammonium) station and two nonsymmetric phenyl triazole stations arranged in opposite orientations. Upon addition of an acid, the protonated macrocycle shuttles from the di(quaternary ammonium) station to the phenyl triazole binding station closer to its butyl groups. This directional shuttling presumably originates from charge repulsion and an orientational binding preference between the cone‐like cavity and the nonsymmetric phenyl triazole station. This mechanism for achieving directional shuttling by manipulating only the wheels instead of the tracks is new for artificial molecular machines. [ABSTRACT FROM AUTHOR]

In situ structural information on molecular machines can be invaluable in understanding their assembly, mechanism and evolution. Here, the use of electron cryotomography (ECT) to obtain significant insights into how an archetypal molecular machine, the bacterial flagellar motor, functions and how it has evolved is described. Over the last decade, studies using a high‐throughput, medium‐resolution ECT approach combined with genetics, phylogenetic reconstruction and phenotypic analysis have revealed surprising structural diversity in flagellar motors. Variations in the size and the number of torque‐generating proteins in the motor visualized for the first time using ECT has shown that these variations have enabled bacteria to adapt their swimming torque to the environment. Much of the structural diversity can be explained in terms of scaffold structures that facilitate the incorporation of additional motor proteins, and more recent studies have begun to infer evolutionary pathways to higher torque‐producing motors. This review seeks to highlight how the emerging power of ECT has enabled the inference of ancestral states from various bacterial species towards understanding how, and `why', flagellar motors have evolved from an ancestral motor to a diversity of variants with adapted or modified functions. [ABSTRACT FROM AUTHOR]

In 2016, the Nobel Prize in Chemistry was awarded for pioneering work on molecular machines. Half a year later, in Toulouse, the first molecular car race, a "nanocar race", was held by using the tip of a scanning tunneling microscope as an electrical remote control. In this Focus Review, we discuss the current state-of-the-art in research on molecular machines at interfaces. In the first section, we briefly explain the science behind the nanocar race, followed by a selection of recent examples of controlling molecules on surfaces. Finally, motion synchronization and the functions of molecular machines at liquid interfaces are discussed. This new concept of molecular tuning at interfaces is also introduced as a method for the continuous modification and optimization of molecular structure for target functions. [ABSTRACT FROM AUTHOR]

The movement of three pairs of different non-photoresponsive rotaxanes can be efficiently controlled by visible light through a photo-induced proton-transfer (PIPT) strategy in the presence of the photoacid 1-MEH. Moreover, the PIPT strategy also provides systems with a good fatigue resistance after more than 50 cycles. [ABSTRACT FROM AUTHOR]

A fluorescent bistable pseudorotaxane was devised and shown to display pH-gated photoresponsive ring shuttling. At pH ＞ 7.5 shuttling does not take place after light stimulation while at pH ≈ 5 the macrocycle is quantitatively translocated. [ABSTRACT FROM AUTHOR]

Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics are often modeled by transitions between a set of discrete metastable conformational states. In general, the free-energy change associated with each transition can increase the forward rate constant, decrease the reverse rate constant, or both. In contrast to previous optimizations, we find that in general flux is maximized neither by devoting all free-energy changes to increasing forward rate constants nor by solely decreasing reverse rate constants. Instead, the optimal free-energy splitting depends on the detailed dynamics. Extending our analysis to machines with vulnerable states (from which they can break down), in the strong driving corresponding to in vivo cellular conditions, processivity is maximized by reducing the occupation of the vulnerable state. [ABSTRACT FROM AUTHOR]

A mini-review: As the top-down approach for miniaturisation of technology reaches its inherent limitations, robust strategies to build nanoscale machinery components, which have the ability to convert an input energy into motion, from the molecular level up, become increasingly important. Nature is certainly the most proficient in the control of molecular level motion; nevertheless, many successes have been enjoyed in the pursuit of mimicking key aspects of nature’s molecular machines, including two state switches, ion pumps, unidirectional rotary motors and molecular robots that can move molecular cargo. This mini-review outlines of some of the most impressive recent examples towards this end. [ABSTRACT FROM AUTHOR]

Umami is an important element affecting food taste, and the development of umami peptides is a topic of interest in food‐flavoring research. The existing technology used for traditional screening of umami peptides is time‐consuming and labor‐intensive, making it difficult to meet the requirements of high‐throughput screening, which limits the rapid development of umami peptides. The difficulty in performing a standard measurement of umami intensity is another problem that restricts the development of umami peptides. The existing methods are not sensitive and specific, making it difficult to achieve a standard evaluation of umami taste. This review summarizes the umami receptors and umami peptides, focusing on the problems restricting the development of umami peptides, high‐throughput screening, and establishment of evaluation standards. The rapid screening of umami peptides was realized based on molecular docking technology and a machine learning method, and the standard evaluation of umami could be realized with a bionic taste sensor. The progress of rapid screening and evaluation methods significantly promotes the study of umami peptides and increases its application in the seasoning industry. [ABSTRACT FROM AUTHOR]

Coupling of mechanical forces and chemical transformations is central to the biophysics of molecular machines, polymer chemistry, fracture mechanics, tribology, and other disciplines. As a consequence, the same physical principles and theoretical models should be applicable in all of those fields; in fact, similar models have been invoked (and often repeatedly reinvented) to describe, for example, cell adhesion, dry and wet friction, propagation of cracks, and action of molecular motors. This perspective offers a unified view of these phenomena, described in terms of chemical kinetics with rates of elementary steps that are force dependent. The central question is then to describe how the rate of a chemical transformation (and its other measurable properties such as the transition path) depends on the applied force. I will describe physical models used to answer this question and compare them with experimental measurements, which employ single-molecule force spectroscopy and which become increasingly common. Multidimensionality of the underlying molecular energy landscapes and the ensuing frequent misalignment between chemical and mechanical coordinates result in a number of distinct scenarios, each showing a nontrivial force dependence of the reaction rate. I will discuss these scenarios, their commonness (or its lack), and the prospects for their experimental validation. Finally, I will discuss open issues in the field. [ABSTRACT FROM AUTHOR]

The reversible oxidation/reduction of polypyrrole films coating a platinum electrode is studied here in NaCl aqueous solution by cyclic voltammetry at different scan rates. Reacting polypyrrole films are dense gels constituted by molecular (polymeric) electrochemical machines, ions and water, mimicking the intracellular matrix of living cells. Both, the extension of the reaction (the consumed charge) and the electrical energy consumed by the oxidation and reduction reactions change as a function of the scan rate or of the imposed frequency. That means that the reaction involving conformational, or allosteric, movements of the reacting polymeric chains senses the imposed working energetic conditions. A theoretical description of the attained empirical results is presented getting the sensing equations. An important energetic asymmetry exists for those reactions between oxidation and reduction consumed energies. Technological outlooks related to the efficiency of electrochemical energy transducers are presented. Results are translated to biological organs as muscles constituted by chemical molecular machines working under demand of higher energies by brain suggesting how the back signal informing the brain about the working energetic conditions can be generated. [ABSTRACT FROM AUTHOR]

High-pressure microscopy is one of the powerful techniques to visualize the effects of hydrostatic pressures on research targets. It could be used for monitoring the pressure-induced changes in the structure and function of molecular machines in vitro and in vivo . This review focuses on the dynamic properties of the assemblies and machines, analyzed by means of high-pressure microscopy measurement. We developed a high-pressure microscope that is optimized both for the best image formation and for the stability to hydrostatic pressure up to 150 MPa. Application of pressure could change polymerization and depolymerization processes of the microtubule cytoskeleton, suggesting a modulation of the intermolecular interaction between tubulin molecules. A novel motility assay demonstrated that high hydrostatic pressure induces counterclockwise (CCW) to clockwise (CW) reversals of the Escherichia coli flagellar motor. The present techniques could be extended to study how molecular machines in complicated systems respond to mechanical stimuli. [ABSTRACT FROM AUTHOR]

The review considers main advances achieved in recent years in a fairly old and simultaneously modern field of research, controlled motion at the molecular level and its practical transformation in the form of synthetic molecular machines and devices. The basic principles of the design and controlled linear and rotational motion in such molecular systems and various useful functions potentially inherent in synthetic molecular machines have been discussed. Examples of already implemented molecular rotors, shuttles, switches, transporters, and muscles are given. Finally, immediate and more distant prospects for the development of this fascinating and very important field of nanotechnology are presented. [ABSTRACT FROM AUTHOR]

The implementation of molecular machines in polymer science is of high interest to transfer mechanical motions from nanoscale to macroscale in order to access new kinds of active devices and materials. Toward this objective, thermodynamic and topological aspects need to be explored for reaching efficient systems capable of producing a useful work. In this paper we describe the branched polymerization of pH-sensitive bistable [c2] daisy chain rotaxanes by using copper(I)- catalyzed Huisgen 1,3-dipolar cycloaddition ("click chemistry"). With this cross-linked topology, the corresponding materials in the form of chemical gels can be contracted and expanded over a large variation of volume (∼50%) by changing the protonation state of the system. HR-MAS 1H NMR and neutron scattering experiments reveal that this macroscopic response of the gels results from the synchronized actuation of the mechanical bonds at the molecular level. [ABSTRACT FROM AUTHOR]

Biomolecular machines consume free energy to break symmetry and make directed progress. Nonequilibrium ATP concentrations are the typical free energy source, with one cycle of a molecular machine consuming a certain number of ATP, providing a fixed free energy budget. Since evolution is expected to favor rapidturnover machines that operate efficiently, we investigate how this free energy budget can be allocated to maximize flux. Unconstrained optimization eliminates intermediate metastable states, indicating that flux is enhanced in molecular machines with fewer states. When maintaining a set number of states, we show that- in contrast to previous findings-the flux-maximizing allocation of dissipation is not even. This result is consistent with the coexistence of both "irreversible" and reversible transitions in molecular machine models that successfully describe experimental data, which suggests that, in evolved machines, different transitions differ significantly in their dissipation. [ABSTRACT FROM AUTHOR]

The spliceosome is an intricate molecular machine which catalyses the removal of introns from eukaryotic mRNA precursors by two trans-esterification reactions (branching and exon ligation) to produce mature mRNA with uninterrupted protein coding sequences. The structures of the spliceosome in several key states determined by electron cryo-microscopy have greatly advanced our understanding of its molecular mechanism. The catalytic RNA core is formed during the activation of the fully assembled B to Bact complex and remains largely unchanged throughout the splicing cycle. RNA helicases and step specific factors regulate docking and undocking of the substrates (branch site and 3′ splice site) to the single RNA-based active site to catalyse the two trans-esterification reactions. [ABSTRACT FROM AUTHOR]

To a large extent, the field of 'molecular machines' started after several groups were able to prepare, reasonably easily, interlocking ring compounds (named catenanes for compounds consisting of interlocking rings and rotaxanes for rings threaded by molecular filaments or axes). Important families of molecular machines not belonging to the interlocking world were also designed, prepared, and studied but, for most of them, their elaboration was more recent than that of catenanes or rotaxanes. Since the creation of interlocking ring molecules is so important in relation to the molecular machinery area, we will start with this aspect of our work. The second part will naturally be devoted to the dynamic properties of such systems and to the compounds for which motions can be directed in a controlled manner from the outside, that is, molecular machines. We will restrict our discussion to a very limited number of examples which we consider as particularly representative of the field. [ABSTRACT FROM AUTHOR]

Vibrio cholerae is a diverse species that inhabits a wide range of environments from copepods in brackish water to the intestines of humans. In order to remain competitive, V. cholerae uses the versatile type-VI secretion system (T6SS) to secrete anti-prokaryotic and anti-eukaryotic effectors. In addition to competing with other bacterial species, V. cholerae strains also compete with one another. Some strains are able to coexist, and are referred to as belonging to the same compatibility group. Challenged by diverse competitors in various environments, different V. choleare strains secrete different combination of effectors - presumably to best suit their niche. Interestingly, all pandemic V. cholerae strains encode the same three effectors. In addition to the diversity displayed in the encoded effectors, the regulation of V. cholerae also differs between strains. Two main layers of regulation appear to exist. One strategy connects T6SS activity with behavior that is suited to fighting eukaryotic cells, while the other is linked with natural competence - the ability of the bacterium to acquire and incorporate extracellular DNA. This relationship between bacterial killing and natural competence is potentially a source of diversification for V. cholerae as it has been shown to incorporate the DNA of cells recently killed through T6SS activity. It is through this process that we hypothesize the transfer of virulence factors, including T6SS effector modules, to happen. Switching of T6SS effectors has the potential to change the range of competitors V. cholerae can kill and to newly define which strains V. cholerae can co-exist with, two important parameters for survival in diverse environments. [ABSTRACT FROM AUTHOR]

Despite the fact that artificial molecular machines are on the rise, there is a long way to go to eventually fill the yawning gap that exists between biological and man-made machines in terms of both their mechanisms of action and efficiencies of operation. Herein, we describe our recent efforts directed towards the development of a second-generation (more efficient) artificial molecular pump – a wholly synthetic compound, which operates to compartmentalise highly charged rings in a high-energy state on an oligomethylene chain. The optimized artificial molecular pump operates rapidly, thanks to well-tuned noncovalent bonding interactions, paving the way to address enthalpically and entropically demanding polymers that would be difficult to obtain with the available repertoire of synthetic methods. [ABSTRACT FROM AUTHOR]

In our search for light powered molecular devices, a novel fac-[Re(CO)3(ph2phen)(trans-stpyCN)]+ complex was synthesized to show switchable trans–cis configurations of the coordinated stpyCN ligand through efficient and reversible photoassisted isomerizations. Controlled photolyses of acetonitrile solutions led to spectral changes ascribed to reversible trans⇌cis photoisomerization processes. A remarkable quantum yield for the back cis-to-trans isomerization was obtained, with the same magnitude of the trans-to-cis photoprocess, and curiously, both trans- and cis-isomers are emissive at room temperature. Photochemical and photophysical characterization studies for fac-[Re(CO)3(ph2phen)(stpyCN)]+ provided insights into the isomerization and emissive light-driven pathways that are resulted from the interactions between the close-lying intraligand and charge transfer states. The reversible cis–trans photoisomerization has potential to be exploited as light-powered molecular motors and geometry regulators in molecular machines. [ABSTRACT FROM AUTHOR]

We report on the synthesis and operation of a three-barrier, rotaxane-based, artificial molecular machine capable of sequence-specific β-homo (β³) peptide synthesis. The machine utilizes nonproteinogenic β³-amino acids, a class of amino acids not generally accepted by the ribosome, particularly consecutively. Successful operation of the machine via native chemical ligation (NCL) demonstrates that even challenging 15- and 19-membered ligation transition states are suitable for information translation using this artificial molecular machine. The peptide-bond-forming catalyst region can be removed from the transcribed peptide by peptidases, artificial and biomachines working in concert to generate a product that cannot be made by either machine alone. [ABSTRACT FROM AUTHOR]

The spliceosome is an extraordinarily dynamic molecular machine in which significant changes in composition as well as protein and RNA conformation are required for carrying out pre-mRNA splicing. Single-molecule fluorescence resonance energy transfer (smFRET) can be used to elucidate these dynamics both in well-characterized model systems and in entire spliceosomes. These types of single-molecule data provide novel information about spliceosome components and can be used to identify sub-populations of molecules with unique behaviors. When smFRET is combined with single-molecule fluorescence colocalization, conformational dynamics can be further linked to the presence or absence of a given spliceosome component. Here, we provide a description of experimental considerations, approaches, and workflows for smFRET with an emphasis on applications for the splicing machinery. [ABSTRACT FROM AUTHOR]

The J([11]B,[11]B) coupling constants of various salts of the electron-precise hexacyanodiborane(6) dianion, [B[sub 2](CN)[sub 6]][2-], were obtained using [11]B double-quantum-filtered (DQF) J-resolved solid-state nuclear magnetic resonance (SSNMR) spectroscopy. Our results show that the magnitude of the DQF J splitting is influenced by both the crystallographic symmetry of the system and the presence of dynamics. The splittings are amplified by a factor of 3 as compared to the corresponding theoretical J coupling constants for cases where (1) there is an absence of dynamics but the boron pairs are crystallographically equivalent or (2) the boron pairs are crystallographically inequivalent but are rendered magnetically equivalent on the time scale of the experiment due to dynamic disorder, which was identified by [11]B and [13]C SSNMR experiments. Consequently, molecular motions need to be taken into consideration when interpreting the results of DQF J-resolved experiments, and conversely, these experiments may be used to identify dynamic disorder. Variable-temperature NMR data support the notion of three different motional processes with correlation times ranging from 10[2] to 10[6] s[-1] over the temperature range of 248-306 K. When molecular motion and crystallographic symmetry are both accounted for, the J([11]B,[11]B) coupling constants for various [B[sub 2](CN)[sub 6]][2-] salts were measured to range from 29.4 to 35.8 Hz, and their electronic origins were determined using natural localized molecular orbital and natural bond orbital analyses. The coupling constants were found to strongly correlate to the hybridization states of the boron orbitals that form the B -- B bonds and to the strength of the B -- B bonds. This study provides a novel tool to study dynamics in ordered and disordered solids and provides new perspectives on electron-precise dianionic diboranes featuring two-center -- two-electron bonds in the context of related compounds featuring multiply and singly bonded boron spin pairs. [ABSTRACT FROM AUTHOR]

A new strategy for the construction of crystalline molecular rotors is presented. The combination of a conformation-modifiable macrocyclic host and two cooperative guests affords one supramolecular gyroscope-like compound, (t-BuNH3)(18-crown-6)[ZnCl3(H2O)], in which the coordinated water molecule functions as an ultrasmall polar rotator, revealed by its significant dielectric relaxation and the molecular dynamics simulations. In addition, such a compound can reversibly undergo a polar-to- polar phase transition triggered by the changed conformation of the 18-crown-6 host, leading to a switchable on/off rotation of water molecule, well controlled by strength and direction of charge-assisted hydrogen bonds. [ABSTRACT FROM AUTHOR]

Rotaxanes, formed by an axis through the cavity of a macrocycle, are promising systems for the construction of molecular machines. A very limited number of experimental techniques are available for mechanistic studies since only mechanical bonds are formed, being NMR one of the most widely used. The major inconvenience derived from NMR use is the time-scale for threading/dethreading processes lasting a few minutes in the case of faster processes. In the present manuscript, we report the application of a new kinetic methodology based on a displacement assay for cyclodextrin-based pseudorotaxane formation. By coupling a very fast (microseconds time-scale) binding/dissociation of nitrophenol to α-CD with a dicationic axle threading/dethreading process, we have been able to study kinetic processes taking place in the millisecond time-scale. [ABSTRACT FROM AUTHOR]

Motor proteins are nature's solution for directing movement at the molecular level. The field of artificial molecular motors takes inspiration from these tiny but powerful machines. Although directional motion on the nanoscale performed by synthetic molecular machines is a relatively new development, significant advances have been made. In this review an overview is given of the principal designs of artificial molecular motors and their modes of operation. Although synthetic molecular motors have also found widespread application as (multistate) switches, we focus on the control of directional movement, both at the molecular scale and at larger magnitudes. We identify some key challenges remaining in the field. [ABSTRACT FROM AUTHOR]

Bacterial cells are critically dependent on their ability to divide. The process of division is carried out by a large and highly dynamic molecular machine, known as the divisome. An understanding of the divisomes' architecture is highly sought after, as it is essential for understanding molecular mechanisms and potentially designing antibiotic molecules that curb bacterial growth. Our current view, which is mainly based on high-resolution imaging of Escherichia coli, is that it is a patchy ring or toroid structure. However, recent super-resolution imaging has shown that the toroid structure contains at least three concentric rings, each containing a different set of proteins. Thus, the emerging picture is that the divisome has different functional modules that are spatially separated in concentric rings. [ABSTRACT FROM AUTHOR]

Highly sensitive detection of K-ras gene is of great significance in biomedical research and clinical diagnosis. Here, we developed a colorimetric biosensing system for the detection of proto-oncogene K-ras based on enhanced amplification effect of DNA molecular machine, where dual isothermal circular strand-displacement amplification ( D -SDA) occurs on two arms in one-to-one correspondence. Specifically, we designed a primer-locked hairpin probe (HP) and a primer-contained linear polymerization template (PPT). In the presence of target gene, HP can hybridize with PPT, forming a DNA molecular machine with dual functional arms (called DFA-machine). Each of the two probes in this machine is able to be extended by polymerase on its counterpart species. Moreover, with the help of nicking endonuclease, the dual isothermal polymerization is converted into dual circular strand-displacement amplification, generating a large amount of anti-hemin aptamer-contained products. After binding to hemins, the aptamer/hemin duplex, horseradish peroxidase (HRP)-mimicking DNAzyme, was formed and catalyzed the oxidation of colorless ABTS by H 2 O 2 , producing a visible green color. The proposed colorimetric assay exhibits a wide linear range from 0.01 to 150 nM with a low detection limit of 10 pM. More interestingly, the mutations existing in target gene are easily observed by the naked eye. It should be noted that this colorimetric system was proved by the analysis of K-ras gene of SW620 cell lines. The simple and powerful DFA-machine is expected to provide promising potential in the sensitive detection of biomarkers for cancer diagnosis, prognosis and therapy. [ABSTRACT FROM AUTHOR]