G3BP1 Is a Tunable Switch that Triggers Phase Separation to Assemble Stress Granules.

The mechanisms underlying ribonucleoprotein (RNP) granule assembly, including the basis for establishing and maintaining RNP granules with distinct composition, are unknown. One prominent type of RNP granule is the stress granule (SG), a dynamic and reversible cytoplasmic assembly formed in eukaryotic cells in response to stress. Here, we show that SGs assemble through liquid-liquid phase separation (LLPS) arising from interactions distributed unevenly across a core protein-RNA interaction network. The central node of this network is G3BP1, which functions as a molecular switch that triggers RNA-dependent LLPS in response to a rise in intracellular free RNA concentrations. Moreover, we show that interplay between three distinct intrinsically disordered regions (IDRs) in G3BP1 regulates its intrinsic propensity for LLPS, and this is fine-tuned by phosphorylation within the IDRs. Further regulation of SG assembly arises through positive or negative cooperativity by extrinsic G3BP1-binding factors that strengthen or weaken, respectively, the core SG network.

ParB-type DNA Segregation Proteins Are CTP-Dependent Molecular Switches.

During cell division, newly replicated DNA is actively segregated to the daughter cells. In most bacteria, this process involves the DNA-binding protein ParB, which condenses the centromeric regions of sister DNA molecules into kinetochore-like structures that recruit the DNA partition ATPase ParA and the prokaroytic SMC/condensin complex. Here, we report the crystal structure of a ParB-like protein (PadC) that emerges to tightly bind the ribonucleotide CTP. The CTP-binding pocket of PadC is conserved in ParB and composed of signature motifs known to be essential for ParB function. We find that ParB indeed interacts with CTP and requires nucleotide binding for DNA condensation in vivo. We further show that CTP-binding modulates the affinity of ParB for centromeric parS sites, whereas parS recognition stimulates its CTPase activity. ParB proteins thus emerge as a new class of CTP-dependent molecular switches that act in concert with ATPases and GTPases to control fundamental cellular functions.

The switching mechanism of the bacterial rotary motor combines tight regulation with inherent flexibility.

Regulatory switches are wide spread in many biological systems. Uniquely among them, the switch of the bacterial flagellar motor is not an on/off switch but rather controls the motor's direction of rotation in response to binding of the signaling protein CheY. Despite its extensive study, the molecular mechanism underlying this switch has remained largely unclear. Here, we resolved the functions of each of the three CheY-binding sites at the switch in E. coli, as well as their different dependencies on phosphorylation and acetylation of CheY. Based on this, we propose that CheY motor switching activity is potentiated upon binding to the first site. Binding of potentiated CheY to the second site produces unstable switching and at the same time enables CheY binding to the third site, an event that stabilizes the switched state. Thereby, this mechanism exemplifies a unique combination of tight motor regulation with inherent switching flexibility.

A Metastable Semiquinone Molecular Switch Modulated by Ascorbate/O2: a Study from a System Far-From-Equilibrium to Biological Assays in Mitochondria.

A molecular switch based on the metastable radical anion derived from a substituted heteroaryl quinone is described. Pyrrolil quinone thiocyanate (PQ 5) showed an interaction with the fluoride anion that was visible to the naked eye and quantified by UV/vis and 1H and 13C NMR. The metastable quinoid species formed by the interaction with F- ("ON" state) showed a molecular switching effect autocontrolled by the presence of ascorbate ("OFF" state) and back to the "ON" state by an autooxidation process, measured by visible and UV/vis spectroscopy. Due to its out-of-equilibrium properties and the exchange of matter and energy, a dissipative structural behaviour is proposed. Considering its similarity to the mechanism of coenzyme Q in oxidative phosphophorylation, PQ 5 was evaluated on Saccharomyces cerevisiae mitochondrial function for inhibition of complexes II, III and IV, reactive oxygen species (ROS) production, catalase activity and lipid peroxidation. The results showed that PQ 5 inhibited complex III activity as well as the activity of all electron transport chain (ETC) complexes. In addition, PQ 5 reduced ROS production and catalase activity in yeast. The results suggest that PQ 5 may have potential applications as a new microbicidal compound by inducing ETC dysfunction.

Anthraquinodimethane-Based Molecular Switches Tethered by Four-Arm Star-like Polymers.

Molecular switches that reversibly change their structures and physical properties are important for applications such as sensing and information processing at molecular scales. In order to avoid the intermolecular aggregation that is often detrimental to the stimuli-responses of molecular switches, previous studies of molecular switches have been often conducted in dilute solutions which are difficult for applications in solid-state devices. Here we report molecular design and synthesis that integrates anthraquinodimethane as molecular switching units into polymers with amenable processibility in solid states. Optical and electron spin resonance characterizations indicate that the four-arm polymers of poly(ϵ-caprolactone) or poly(D,L-lactide) tethered from anthraquinodimethane slow down the dynamics of the conformational switching between the folded and the twisted conformations, enhance the photoluminescence in solid states and impart materials with a small energy gap from singlet ground state to thermally accessible triplet state.

A Cyclotriveratrylene Solvent-Dependent Chiral Switch.

Chiral molecular switches are attracting attention as they could pave the way to chiral molecular machines. Herein, we report on the design and synthesis of a single molecule chiral switch based on a cyclotriveratrylene scaffold, in which the chirality inversion is controlled by the solvent. Hemicryptophanes are built around a C3 cyclotriveratrylene chiral unit, with either M or P handedness, connected to another tripod and usually displaying an "out" configuration. Here, we demonstrate that solvents are able to control the "in" and "out" configurations of the CTV unit, creating a chiral molecular switch from (M/P)"in" to (P/M)"out" handedness. The full characterization of the "in" and "out" configurations and of the chirality switch were made possible by combining NMR, HPLC, ECD, DFT and molecular dynamics. Interestingly, bulky aromatic solvents such as 2-t-butylphenol favor the "in" configuration while polar aprotic solvents such as acetone favor the "out" configuration. This chiral switch was found to be fully reversible allowing the system to oscillate between two different M and P configurations several times upon the action of solvents stimuli.

A Phosphorus-centred, Zirconocene-bridged Tetraradical: Synthesis, Structure and Application as Molecular Double Switch.

Biradicals are important intermediates in the formation and breaking of a chemical bond. Their use as molecular switches is of particular interest. Much less is known about tetraradicals, which can, for example, consist of two biradical(oid) units. Here we report the synthesis of the first persistent phosphorus-centred tetraradical bound to a transition metal fragment. Starting from a zirconocene complex, rac-(ebthi)ZrCl2 (rac-(ebthi) = 1,2-ethylene-1,10-bis(h5-tetrahydroin-denyl), two cyclo-1,3-diphospha-pentane-1,3-diyls were successfully introduced, which finally led to the isolation of a deep green zircon-cene-bridged bis(biradicaloid) complex (5) that can act as a double molecular switch. Under the influence of light (570 nm), this tetra-radical forms a transannular bond in each of the two five-membered biradical units, leading to the formation of housane 5h. Upon irradiation at 415 nm, the reverse reaction is observed, fully reco-vering tetraradical 5. Through single-crystal-to-single-crystal trans-formation, both stable species of the molecular switch could be structurally characterised using SCXRD. The switching under the influence of light and the activation of molecular hydrogen were analysed in solution using NMR and UV spectroscopy. It was found that the addition of one or two equivalents of molecular hydrogen can be switched on and off by light.

A pH-Responsive Topological Switch Based on a DNA Quadruplex-Duplex Hybrid.

A guanine-rich oligonucleotide based on a human telomeric sequence but with the first three-nucleotide intervening stretch replaced by a putative 15-nucleotide hairpin-forming sequence shows a pH-dependent folding into different quadruplex-duplex hybrids in a potassium containing buffer. At slightly acidic pH, the quadruplex domain adopts a chair-type conformation. Upon increasing the pH, a transition with a midpoint close to neutral pH to a major and minor (3+1) hybrid topology with either a coaxially stacked or orthogonally oriented duplex stem-loop occurs. NMR-derived high-resolution structures reveal that an adenine protonation is prerequisite for the formation of a non-canonical base quartet, capping the outer G-tetrad at the quadruplex-duplex interface and stabilizing the antiparallel chair conformation in an acidic environment. Being directly associated with interactions at the quadruplex-duplex interface, this unique pH-dependent topological transition is fully reversible. Coupled with a conformation-sensitive optical readout demonstrated as a proof of concept using the fluorescent dye thiazole orange, the present quadruplex-duplex hybrid architecture represents a potentially valuable pH-sensing system responsive in a physiological pH range of 7±1.

Hydrogel Rivet with Unidirectional Shape Morphing for Flexible Mechanical Assembly.

Integrating diverse materials and functions into highly additive produce has piqued global interest due to the increasing demands of intelligent soft robotics. Nevertheless, existing assembly techniques, especially supramolecular assembly which heavily rely on precise chemical design and specific recognition, may prove inadequate when confronted with diverse external demands. Inspired by the traditional mechanical assembly, rivet connection, herein, a thermo-responsive hydrogel with unidirectional shape-morphing is fabricated and a stable mechanical assembly is constructed by emulating the rivet connection mechanism. This system employed poly(acrylamide-co-acrylic acid) [P(AAm-co-AAc)] to induce continuous swelling and hexylamine-modified polyvinyl alcohol (PVA-C6) as a molecular switch to control the swelling process. The hydrogel rivet, initially threaded through pre-fabricated hollows in two components. Subsequently, upon the disassociation of alkane chains the molecular switch would activate, inducing swelling and stable mechanical assembly via anchor structures. Moreover, to enhance the assembly strength, knots are introduced to enhance assembly strength, guiding localized stress release for programmed deformations. Additionally, the system can be remotely controlled using near-infrared light (NIR) by incorporating photo-thermal nanoparticles. This work presents a universal and efficient strategy for constructing stable mechanical assemblies without compromising overall softness, offering significant potential for the fabrication of integrated soft robots.

Emerging functions of pseudoenzymes.

As sequence and structural databases grow along with powerful analysis tools, the prevalence and diversity of pseudoenzymes have become increasingly evident. Pseudoenzymes are present across the tree of life in a large number of enzyme families. Pseudoenzymes are defined as proteins that lack conserved catalytic motifs based on sequence analysis. However, some pseudoenzymes may have migrated amino acids necessary for catalysis, allowing them to catalyze enzymatic reactions. Furthermore, pseudoenzymes retain several non-enzymatic functions such as allosteric regulation, signal integration, scaffolding, and competitive inhibition. In this review, we provide examples of each mode of action using the pseudokinase, pseudophosphatase, and pseudo ADP-ribosyltransferase families. We highlight the methodologies that facilitate the biochemical and functional characterization of pseudoenzymes to encourage further investigation in this burgeoning field.

Probing Spin-Dependent Ballistic Charge Transport at Single-Nanometer Length Scales.

The coherent transport of charge and spin is a key requirement of future devices for quantum computing and communication. Scattering at defects or impurities may significantly reduce the coherence of quantum-mechanical states, thereby affecting the device functionality. While numerous methods exist to experimentally assess charge transport, the real-space detection of a material's ballistic spin transport properties with nanometer resolution remains a challenge. Here we report on a novel approach that utilizes a combination of spin-polarized scanning tunneling microscopy (SP-STM) and the recently introduced molecular nanoprobe (MONA) technique. It relies on the local injection of spin-polarized charge carriers from a magnetic STM tip and their detection by a single surface-deposited phthalocyanine molecule via reversible electron-induced tautomerization events. Based on the particular electronic structure of the Rashba alloy BiAg2, which is governed by a spin-momentum-locked surface state, we prove that the current direction inverses upon tip magnetization reversal.

Fluorescent Materials Based on Spiropyran for Advanced Anti-Counterfeiting and Information Encryption.

In daily life, counterfeit and substandard products, particularly currency, medicine, food, and confidential documents, are capable of bringing about very serious consequences. The development of anti-counterfeiting and authentication technologies with multilevel securities is a powerful means to overcome this challenge. Among various anti-counterfeiting technologies, fluorescent anti-counterfeiting technology is well-known and commonly used to fight counterfeiters due to its wide material source, low cost, simple usage, good concealment, and simple response mechanism. Spiropyran is favored by scientists in the fields of anti-counterfeiting and information encryption due to its reversible photochromic property. Here, we summarize the current available spiropyran-based fluorescent materials from design to anti-counterfeiting applications. This review will be help scientists to design and develop fluorescent anti-counterfeiting materials with high security, high performance, quick response, and high anti-counterfeiting level.

Meta-Substituted Asymmetric Azobenzenes: Insights into Structure-Property Relationship.

This article presents a comprehensive investigation into the functionalization of methoxyphenylazobenzene using electron-directing groups located at the meta position relative to the azo group. Spectroscopic analysis of meta-functionalized azobenzenes reveals that the incorporation of electron-withdrawing units significantly influences the absorption spectra of both E and Z isomers, while electron-donating functionalities lead to more subtle changes. The thermal relaxation process from Z to E result in almost twice as prolonged for electron-withdrawing functionalized azobenzenes compared to their electron-rich counterparts. Computational analysis contributes a theoretical understanding of the electronic structure and properties of meta-substituted azobenzenes. This combined approach, integrating experimental and computational techniques, yields significant insights into the structure-property relationship of meta-substituted asymmetrical phenolazobenzenes.

Orthogonal Photoswitching in a Porous Organic Framework.

The development of photoresponsive systems with non-invasive orthogonal control by distinct wavelengths of light is still in its infancy. In particular, the design of photochemically triggered-orthogonal systems integrated into solid materials that enable multiple dynamic control over their properties remains a longstanding challenge. Here, we report the orthogonal and reversible control of two types of photoswitches in an integrated solid porous framework, that is, visible-light responsive o-fluoroazobenzene and nitro-spiropyran motifs. The properties of the constructed material can be selectively controlled by different wavelengths of light thus generating four distinct states providing a basis for dynamic multifunctional materials. Solid-state NMR spectroscopy demonstrated the selective transformation of the azobenzene switch in the bulk, which in turn modulates N2 and CO2 adsorption.

A novel TF molecular switch-mechanism found in two contrasting ecotypes of a psammophyte, Agriophyllum squarrosum, in regulating transcriptional drought memory.

BACKGROUND: Prior drought stress may change plants response patterns and subsequently increase their tolerance to the same condition, which can be referred to as "drought memory" and proved essential for plants well-being. However, the mechanism of transcriptional drought memory in psammophytes remains unclear. Agriophyllum squarrosum, a pioneer species on mobile dunes, is widely spread in Northern China's vast desert areas with outstanding ability of water use efficiency. Here we conducted dehydration-rehydration treatment on A. squarrosum semi-arid land ecotype AEX and arid land ecotype WW to dissect the drought memory mechanism of A. squarrosum, and to determine the discrepancy in drought memory of two contrasting ecotypes that had long adapted to water heterogeneity. RESULT: Physiological traits monitoring unveiled the stronger ability and longer duration in drought memory of WW than that of AEX. A total of 1,642 and 1,339 drought memory genes (DMGs) were identified in ecotype AEX and WW, respectively. Furthermore, shared DMGs among A. squarrosum and the previously studied species depicted that drought memory commonalities in higher plants embraced pathways like primary and secondary metabolisms; while drought memory characteristics in A. squarrosum were mainly related to response to heat, high light intensity, hydrogen peroxide, and dehydration, which might be due to local adaptation to desert circumstances. Heat shock proteins (HSPs) occupied the center of the protein-protein interaction (PPI) network in drought memory transcription factors (TF), thus playing a key regulatory role in A. squarrosum drought memory. Co-expression analysis of drought memory TFs and DMGs uncovered a novel regulating module, whereby pairs of TFs might function as molecular switches in regulating DMG transforming between high and low expression levels, thus promoting drought memory reset. CONCLUSION: Based on the co-expression analysis, protein-protein interaction prediction, and drought memory metabolic network construction, a novel regulatory module of transcriptional drought memory in A. squarrosum was hypothesized here, whereby recurrent drought signal is activated by primary TF switches, then amplified by secondary amplifiers, and thus regulates downstream complicated metabolic networks. The present research provided valuable molecular resources on plants' stress-resistance basis and shed light on drought memory in A. squarrosum.

Gated Photochromism of Dithienylethene-Embedded Expanded Calixphyrins.

Dithienylethene (DTE)-embedded expanded porphyrins were synthesized and confirmed to be photochemically inactive due to the lowest excited state of the expanded porphyrins. On the other hand, DTE-embedded expanded calixphyrins exhibited reversible photochromism upon UV-irradiation to form colored closed forms, which reverted to colorless open forms upon red-light irradiation. The closed forms were oxidized with DDQ or the air to lock the recorded information by converting to photochemically inactive expanded porphyrins. This was unlocked by reduction with NaBH4 to restore expanded calixphyrins with photochromism activity. These gated photochromic behaviors were demonstrated in PMMA (polymethyl methacrylate) film.

Influence of Triptycene Annulation on the Photochromism of Diphenylnaphthopyrans: Entropic Control of Thermal Reversion.

Regioisomeric naphthopyrans annulated with triptycene, i. e., Prox-NP and Dist-NP, display divergent photochromic behaviors. While steady-state photolysis of Dist-NP led to a very labile colored intermediate that is not observable at room temperature, Prox-NP yielded a remarkably stable species characterized by X-ray crystallography as the TT isomer of o-quinonoid intermediate (Prox-NPQ) with t1/2 ca. 0.18 years at 298 K. The kinetic analysis of thermal reversion reveals that the bleaching of Prox-NPQ is entropically controlled; the steric effect due to the rigid triptycene scaffold renders Prox-NP a highly constrained system such that the photogenerated colored o-quinonoid form is more entropically relaxed. This constitutes the first instance of an entropically-controlled thermal reversion for the celebrated class of photochromic naphthopyrans. Based on the response of Prox-NP and its colored intermediate Prox-NPQ to different stimuli, namely, light, heat, and acid, the molecular system can be likened to a logic gate with the 'INHIBIT' function.

Photoisomerisation of Exo-Imine Complexes and the Role of MECP in the Reverse Thermal Equilibrium: An Experimental and DFT Computational Investigation.

Complexes [MCl2 Cp*]2 (M=Ir, Rh), [RuCl2 (p-cymene)]2 and [Ir(C^N)2 Cl]2 (HC^N=a, phenylpyridine ; b, phenylpyrazole,) react with imine ligands derived from ο-aminophenol to yield complexes with an exocyclic C=N bond which has a cis or trans configuration. The trans isomer is favoured except for sterically crowded complexes Cp*M (M=Ir, Rh) when the imine has a mesityl substituent, for which the cis isomer is favoured. The complexes undergo photoisomerisation in visible light but revert back to the original isomer over time or when heated. The rate of the thermal reverse isomerisation depends on the imine substituent and the metal fragment. DFT calculations correctly reproduce the favoured isomer and suggest that the reverse isomerisation occurs by a rehybridisation at the N atom as found in organic imines. In addition, a triplet state, thermally accessible by a Minimum Energy Crossing Point (MECP) provides a low energy pathway for reverse isomerisation in the case of the half-sandwich complexes.

The Versatile Photo-Thermal Behaviour of a 2-Hydroxyazobenzene.

Photochromic compounds are employed in implementing neuron surrogates. They will boost the development of neuromorphic engineering in wetware. In this work, the photochromic behaviours of (E)-3,4,6-trichloro-2-(p-diazenil)-phenol (t-DZH) and its conjugated phenoxide base (t-DZ) have been investigated experimentally in three different media: (1) pure acetonitrile, (2) in water and acetonitrile mixed in a 1/1 volume ratio, and (3) in an aqueous micellar solution of 3-(N,N-Dimethylmyristylammonio)propanesulfonate (SB3-14). The analysis of the spectral and kinetic features of t-DZH and t-DZ has been supported by quantum-mechanical DFT calculations, the maximum entropy method, and the determination of their colourability (C). The versatility of t-DZH and t-DZ makes them promising molecular probes of micro-environments and potential ingredients of photochemical oscillators required for implementing pacemaker neurons capable of communicating through optical signals in wetware.

A Novel Fluorescent Aptasensor for Arsenic(III) Detection Based on a Triple-Helix Molecular Switch.

A novel aptamer-based fluorescent-sensing platform with a triple-helix molecular switch (THMS) was proposed as a switch for detecting the arsenic(III) ion. The triple helix structure was prepared by binding a signal transduction probe and arsenic aptamer. Additionally, the signal transduction probe labeled with fluorophore (FAM) and quencher (BHQ1) was employed as a signal indicator. The proposed aptasensor is rapid, simple and sensitive, with a limit of detection of 69.95 nM. The decrease in peak fluorescence intensity shows a linear dependence, with the concentration of As(III) in the range of 0.1 µM to 2.5 µM. The whole detection process takes 30 min. Moreover, the THMS-based aptasensor was also successfully used to detect As(III) in a real sample of Huangpu River water with good recoveries. The aptamer-based THMS also presents distinct advantages in stability and selectivity. The proposed strategy developed herein can be extensively applied in the field of food inspection.