Catalytic transport of molecular cargo using diffusive binding along a polymer track

Hydrodynamic Fluidic Pump Empowered Sensitive Recognition and Active Transport of Hydrogen Peroxide in 1D Channels

Through synthetic chemistry, the development of molecular devices for the precise selective recognition and active transport of small molecules stands as one of the most ambitious objectives in extensive medical, environmental, and biological applications. The periodical channels of the metal-organic frameworks (MOFs) with excellent chemical affinity offer vast regulatory space for reaching this goal. Herein, by post-modifying fluorescent probes and ionic liquid molecules into the Zr-MOFs (NU-1000), a donor-acceptor (D-A) system within the periodical 1D channels is created to construct a hydrodynamic fluidic pump within the abundant 1D channels. Irradiation with light serves to initiate and direct fluid motion, expediting the transport of H2O2 molecules to the active site, thus boosting the sensor sensitivity through gas enrichment. The rapid mass transfer, characterized by a high flow rate and intensified interaction between the D-A system and H2O2 molecules, enables the detection of H2O2 at concentrations as low as 20 ppb. Besides, with the aid of incident light, the pump system exhibits active transport characteristics by transporting radicals derived from H2O2 against a concentration gradient, reaching a remarkable 10th cycle. The strategy of achieving active transport of small molecules through pore modification holds promise for advancing the development of artificial bioactive channels.

Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them

The Mycobacterium tuberculosis trifunctional enzyme (MtTFE) is an α2β2 tetrameric enzyme in which the α-chain harbors the 2E-enoyl-CoA hydratase (ECH) and 3S-hydroxyacyl-CoA dehydrogenase (HAD) active sites, and the β-chain provides the 3-ketoacyl-CoA thiolase (KAT) active site. Linear, medium-chain and long-chain 2E-enoyl-CoA molecules are the preferred substrates of MtTFE. Previous crystallographic binding and modeling studies identified binding sites for the acyl-CoA substrates at the three active sites, as well as the NAD binding pocket at the HAD active site. These studies also identified three additional CoA binding sites on the surface of MtTFE that are different from the active sites. It has been proposed that one of these additional sites could be of functional relevance for the substrate channeling (by surface crawling) of reaction intermediates between the three active sites. Here, 226 fragments were screened in a crystallographic fragment-binding study of MtTFE crystals, resulting in the structures of 16 MtTFE-fragment complexes. Analysis of the 121 fragment-binding events shows that the ECH active site is the `binding hotspot' for the tested fragments, with 41 binding events. The mode of binding of the fragments bound at the active sites provides additional insight into how the long-chain acyl moiety of the substrates can be accommodated at their proposed binding pockets. In addition, the 20 fragment-binding events between the active sites identify potential transient binding sites of reaction intermediates relevant to the possible channeling of substrates between these active sites. These results provide a basis for further studies to understand the functional relevance of the latter binding sites and to identify substrates for which channeling is crucial.

Coupling of SARS-CoV-2 to Aβ Amyloid Fibrils

The COVID-19 infection has been more problematic for individuals with certain health predispositions. Coronaviruses could also interfere with neural diseases if the viruses succeed in entering the brain. Therefore, it might be of principal interest to examine a possible coupling of coronaviruses and amyloid fibrils. Here, molecular dynamics simulations were used to investigate direct coupling of SARS-CoV-2 and Aβ fibrils, which play a central role in neural diseases. The simulations revealed several stable binding configurations and their dynamics of Aβ42 fibrils attached to spike proteins of the Omicron and Alpha variants of SARS-CoV-2.

Dual enzyme-powered chemotactic cross β amyloid based functional nanomotors

Nanomotor chassis constructed from biological precursors and powered by biocatalytic transformations can offer important applications in the future, specifically in emergent biomedical techniques. Herein, cross β amyloid peptide-based nanomotors (amylobots) were prepared from short amyloid peptides. Owing to their remarkable binding capabilities, these soft constructs are able to host dedicated enzymes to catalyze orthogonal substrates for motility and navigation. Urease helps in powering the self-diffusiophoretic motion, while cytochrome C helps in providing navigation control. Supported by the simulation model, the design principle demonstrates the utilization of two distinct transport behaviours for two different types of enzymes, firstly enhanced diffusivity of urease with increasing fuel (urea) concentration and secondly, chemotactic motility of cytochrome C towards its substrate (pyrogallol). Dual catalytic engines allow the amylobots to be utilized for enhanced catalysis in organic solvent and can thus complement the technological applications of enzymes.

Fast and slow walking driven by chemical fuel

We demonstrate the fast forward and slow backward motion of a biped on a tetrahedral track using chemical fuel, cooperative binding and kinetic selectivity. Walking of the biped is based on its dibenzyl amine feet that bind to zinc porphyrin units and, upon protonation, to dibenzo 24-crown-8 sites affording pseudorotaxane linkages.

Advancement of Electrochemical Thermoelectric Conversion with Molecular Technology

Thermocells are a thermoelectric conversion technology that utilizes the shift in an electrochemical equilibrium arising from a temperature difference. This technology has a long history; however, its low conversion efficiency impedes its practical usage. Recently, an increasing number of reports have shown drastic improvements in thermoelectric conversion efficiency, and thermocells could arguably represent an alternative to solid thermoelectric devices. In this Minireview, we regard thermocells as molecular systems consisting of successive molecular processes responding to a temperature change to achieve energy generation. Various molecular technologies have been applied to thermocells in recent years, and could stimulate diverse research fields, including supramolecular chemistry, physical chemistry, electrochemistry, and solid-state ionics. These research approaches will also provide novel methods for achieving a sustainable society in the future.

Effective screening of Coulomb repulsions in water accelerates reactions of like-charged compounds by orders of magnitude

The reaction kinetics between like-charged compounds in water is extremely slow due to Coulomb repulsions. Here, we demonstrate that by screening these interactions and, in consequence, increasing the local concentration of reactants, we boost the reactions by many orders of magnitude. The reaction between negatively charged Coenzyme A molecules accelerates ~5 million-fold using cationic micelles. That is ~10⁴ faster kinetics than in 0.5 M NaCl, although the salt is ~10⁶ more concentrated. Rate enhancements are not limited to micelles, as evidenced by significant catalytic effects (10⁴-10⁵-fold) of other highly charged species such as oligomers and polymers. We generalize the observed phenomenon by analogously speeding up a non-covalent complex formation-DNA hybridization. A theoretical analysis shows that the acceleration is correlated to the catalysts' surface charge density in both experimental systems and enables predicting and controlling reaction rates of like-charged compounds with counter-charged species.

Single-Molecule Unidirectional Processive Movement along a Helical Polymer Chain in Non-aqueous Medium

In this work, a molecule "walking" along a single chain of a synthetic helical polymer, which is used as a rail on a substrate in an organic solvent at room temperature, is observed. The walking comprises the unidirectional processive movement of a short-chain molecule along a chiral helical chain in 3 nm steps, driven by Brownian motion and a tapping effect of the atomic force microscopy tip based on a flash ratchet mechanism. Furthermore, the rail consists of a long-chain substituted phenylacetylene polymer with pendant cholesteryl groups, along which the short-chain molecule can walk as a result of van der Waals interactions. The macromolecular motion is videoed using a fast-scanning atomic force microscope, and additionally, this phenomenon is also simulated by all-atom molecular dynamics calculations. On the basis of these results, we propose the principle of a polymer molecular motor. This is the first report of a synthetic walking machine of a chiral helical polymer driven by thermal fluctuation as an artificial life function.

Accelerating supramolecular aggregation by molecular sliding

Diffusion-based translocation along DNA or RNA molecules is essential for genome regulatory proteins to execute their biological functions. The reduced dimensionality of the searching process makes the proteins bind specific target sites at a "faster-than-diffusion-controlled rate". We herein report a photoresponsive slider-track diffusion system capable of self-assembly rate acceleration, which consists of (-)-camphorsulfonic acid, 4-(4'-n-octoxylphenylazo)benzenesulfonic acid, and isotactic poly(2-vinylpyridine). The protonated pyridine rings act as the footholds for anionic azo sliders to diffusively bind and slide along polycationic tracks via electrostatic interactions. Ultraviolet light triggers the trans to cis isomerization and aggregation of azo sliders, which can be monitored by multiple spectroscopic methods without labeling. The presence of vinyl polymer track increases the aggregation rate of cis azobenzene up to ∼20 times, depending on the stereoregularity of the polymer chain, the acid/base ratio and the addition of salt. This system has a feature of simplicity, monitorability, controllability, and could find applications in designing molecular machines with desired functionalities.

Fluorescent Microswimmers Based on Cross-β Amyloid Nanotubes and Divergent Cascade Networks

Shaped through millions of years of evolution, the spatial localization of multiple enzymes in living cells employs extensive cascade reactions to enable highly coordinated multimodal functions. Herein, by utilizing a complex divergent cascade, we exploit the catalytic potential as well as templating abilities of streamlined cross-β amyloid nanotubes to yield two orthogonal roles simultaneously. The short peptide based paracrystalline nanotube surfaces demonstrated the generation of fluorescence signals within entangled networks loaded with alcohol dehydrogenase (ADH). The nanotubular morphologies were further used to generate cascade-driven microscopic motility through surface entrapment of sarcosine oxidase (SOX) and catalase (Cat). Moreover, a divergent cascade network was initiated by upstream catalysis of the substrate molecules through the surface mutation of catalytic moieties. Notably, the resultant downstream products led to the generation of motile fluorescent microswimmers by utilizing the two sets of orthogonal properties and, thus, mimicked the complex cascade-mediated functionalities of extant biology.

Through the Eyes of Creators: Observing Artificial Molecular Motors

Inspired by molecular motors in biology, there has been significant progress in building artificial molecular motors, using a number of quite distinct approaches. As the constructs become more sophisticated, there is also an increasing need to directly observe the motion of artificial motors at the nanoscale and to characterize their performance. Here, we review the most used methods that tackle those tasks. We aim to help experimentalists with an overview of the available tools used for different types of synthetic motors and to choose the method most suited for the size of a motor and the desired measurements, such as the generated force or distances in the moving system. Furthermore, for many envisioned applications of synthetic motors, it will be a requirement to guide and control directed motions. We therefore also provide a perspective on how motors can be observed on structures that allow for directional guidance, such as nanowires and microchannels. Thus, this Review facilitates the future research on synthetic molecular motors, where observations at a single-motor level and a detailed characterization of motion will promote applications.

Antimicrobial Properties and the Effect of Temperature on the Formation of Secondary Metabolites in Psychrophilic Micromycetes

Abstract

The ability of representatives of psychrotolerant micromycetes to produce antimicrobial compounds was studied. A promising producer of antibiotics, Penicillium vulpinum KPB F-290, was selected (from 98 cultures) as a result of the screening. The producer was active against opportunistic fungi and bacteria. The isolated active fractions can be attributed to the group of antimicrobial compounds, including ß-lactam antibiotics and peptides.

Light-controlled micron-scale molecular motion

The micron-scale movement of biomolecules along supramolecular pathways, mastered by nature, is a remarkable system requiring strong yet reversible interactions between components under the action of a suitable stimulus. Responsive microscopic systems using a variety of stimuli have demonstrated impressive relative molecular motion. However, locating the position of a movable object that travels along self-assembled fibres under an irresistible force has yet to be achieved. Here, we describe a purely supramolecular system where a molecular 'traveller' moves along a 'path' over several microns when irradiated with visible light. Real-time imaging of the motion in the solvated state using total internal reflection fluorescence microscopy shows that anionic porphyrin molecules move along the fibres of a bis-imidazolium gel upon irradiation. Slight solvent changes mean movement and restructuring of the fibres giving microtoroids, indicating control of motion by fibre mechanics with solvent composition. The insight provided here may lead to the development of artificial travellers that can perform catalytic and other functions.

Size-selective Catalytic Polymer Acylation with a Molecular Tetrahedron

Selective catalysis at the molecular level represents a cornerstone of chemical synthesis. However, it still remains an open question how to elevate tunable catalysis to larger length scales to functionalize whole polymer chains in a selective manner. We now report a hydrazone-linked tetrahedron with wide openings, which acts as a catalyst to size-selectively functionalize polydisperse polymer mixtures. Our experimental and computational evidence supports a dual role of the hydrazone-linked tetrahedron. To accelerate functionalization of the polymer substrates, the tetrahedron (i) unfolds the polymer substrates and/or breaks the polymer aggregates as well as (ii) enables target sites (amino groups) on the polymers to coordinate with catalytic units (triglyme) attached to the tetrahedron. With the tetrahedron as the catalyst, we find that the reactivity of the shorter polymers increases selectively. Our findings enable the possibility to engineer hydrolytically stable molecular polyhedra as organocatalysts for size-selective polymer modification.