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Polaritonic states, which are formed by resonances between a molecular excitation and the photonic mode of a cavity, have a number of useful properties that offer new routes to control molecular photochemistry using electric fields. To provide a theoretical description of how polaritonic states affect the real-time electron dynamics in molecules, a new method is described where the effects of strong light–molecule coupling are implemented using real-time electronic structure theory. The coupling between the molecular electronic states and the cavity is described by the Pauli–Fierz Hamiltonian, and transitions between polaritonic states are induced via an external time-dependent electric field using time-dependent configuration interaction (TDCI) theory, producing quantum electrodynamics TDCI (QED-TDCI). This method is used to study laser-induced ultrafast charge transfer and dipole-switching dynamics of the LiCN molecule inside a cavity. The increase in cavity coupling strength is found to have a significant impact on the energies and transition dipole moments of the molecule–cavity system. The convergence of the polaritonic state energies as a function of the number of included electronic and photonic basis states is discussed. [ABSTRACT FROM AUTHOR]

Orphan nuclear estrogen‐related receptor γ (ERRγ) has been recognized as a potential therapeutic target for cancer, inflammation and metabolic disorder. The ERRγ contains a regulatory AF2 helical tail linked C‐terminally to its ligand‐binding domain (LBD), which is a self‐binding peptide (SBP) and serves as molecular switch to dynamically regulate the receptor alternation between active and inactive states by binding to and unbinding from the AF2‐binding site on ERRγ LBD surface, respectively. Traditional ERRγ modulators are all small‐molecule chemical ligands that can be classified into agonists and inverse agonists in terms of their action mechanism; the agonists stabilize the AF2 in ABS site with an agonist conformation, while the inverse agonists lock the AF2 out of the site to largely abolish ERRγ transcriptional activity. Here, a class of ERRγ peptidic antagonists was described to compete with native AF2 for the ABS site, thus blocking the active state of AF2 binding to ERRγ LBD domain. Self‐inhibitory peptide was derived from the SBP‐covering AF2 region and we expected it can rebind potently to the ABS site by reducing its intrinsic disorder and entropy cost upon the rebinding. Hydrocarbon stapling was employed to do so, which employed an all‐hydrocarbon bridge across the [i, i + 4]‐anchor residue pair in the N‐terminal, middle or C‐terminal region of the self‐inhibitory peptide. As might be expected, it is revealed that the stapled peptides are good binders of ERRγ LBD domain and can effectively compete with the native AF2 helical tail for ERRγ ABS site, which exhibit a basically similar binding mode with AF2 to the site and form diverse noncovalent interactions with the site, thus conferring stability and specificity to the domain–peptide complexes. [ABSTRACT FROM AUTHOR]

Allergen-specific immunotherapy (AIT) induces immune tolerance, showing the highest success rate (>95%) for insect venom while a much lower chance for pollen allergy. However, the molecular switches leading to successful durable tolerance restoration remain elusive. The primary outcome of this observational study is the comprehensive immunological cellular characterization during the AIT initiation phase, whereas the secondary outcomes are the serological and Th2-cell-type-specific transcriptomic analyses. Here we apply a multilayer-omics approach to reveal dynamic peripheral immune landscapes during the AIT-initiation phase in venom allergy patients (VAP) versus pollen-allergic and healthy controls. Already at baseline, VAP exhibit altered abundances of several cell types, including classical monocytes (cMono), CD4+ hybrid type 1-type 17 cells (Th1-Th17 or Th1/17) and CD8+ counterparts (Tc1-Tc17 or Tc1/17). At 8-24 h following AIT launch in VAP, we identify a uniform AIT-elicited pulse of late-transitional/IL-10-producing B cells, IL-6 signaling within Th2 cells and non-inflammatory serum-IL-6 levels. Sequential induction of activation and survival protein markers also immediately occur. A disequilibrium between serum IL-6 and cMono in VAP baseline is restored at day seven following AIT launch. Our longitudinal analysis discovers molecular switches during initiation-phase insect-venom AIT that secure long-term outcomes. Trial number: NCT02931955. Allergen specific immunotherapy (AIT) is both, safe and effective in reducing systemic symptoms of venom allergy in individuals. Here the authors examine the underlying immune cell changes after venom specific AIT in early time points after therapy initiation showing indicative changes in specific immune cell populations. [ABSTRACT FROM AUTHOR]

Although the intrinsic electronic properties of polyoxometalates (POMs) can be greatly influenced by modifying them with organic substituents, their resistive switching behavior on surfaces dependent on the organic substituents remains largely unexplored. In this work, we assessed the importance of electron‐withdrawing and electron‐donating ligand substituents on the material properties of a series of hybrid Lindqvist‐type hexavanadates TBA2[V6O13((OCH2)3CCH2OH)2] (TBA2V6‐OH), TBA2[V6O13((OCH2)3CMe)2] (TBA2V6‐Me), TBA2[V6O13((OCH2)3CNHCOCH2Cl)2] (TBA2V6‐Cl), and TBA2[V6O13((OCH2)3CNHCOCH2‐OOCC10H15)2] (TBA2V6‐Ad) as potential resistive random‐access memory (ReRAM) components. Compared to their redox behavior in solution, changing the ligand substituents on surfaces results in no significant effect on the potential and, thus, no effect on the resistance steps in the current‐voltage profiles. However, while the current‐voltage characteristics do not change, the peripheral metal‐free substituents in the trisalkoxide framework of Lindqvist‐type hexavanadate molecules influence the adsorption and switching stability of these POMs on gold. This work highlights the noticeable differences between hexavanadate's redox properties in solution (which follow the trend observed in the gas phase) and hexavanadate's resistive switching properties on conducting surfaces. Importantly, their multi‐state switching behavior is not significantly altered by the different type of substituent at the periphery of the trisalkoxo ligands. [ABSTRACT FROM AUTHOR]

The lateral wall of the mouse subventricular zone harbors neural stem cells (NSC, B cells) which generate proliferating transient-amplifying progenitors (TAP, C cells) that ultimately give rise to neuroblasts (NB, A cells). Molecular profiling at the single-cell level struggles to distinguish these different cell types. Here, we combined transcriptome analyses of FACS-sorted cells and single-cell RNAseq to demonstrate the existence of an abundant, clonogenic and multipotent population of immature neuroblasts (iNB cells) at the transition between TAP and migrating NB (mNB). iNB are reversibly engaged in neuronal differentiation. Indeed, they keep molecular features of both undifferentiated progenitors, plasticity and unexpected regenerative properties. Strikingly, they undergo important progressive molecular switches, including changes in the expression of splicing regulators leading to their differentiation in mNB subdividing them into two subtypes, iNB1 and iNB2. Due to their plastic properties, iNB could represent a new target for regenerative therapy of brain damage. [ABSTRACT FROM AUTHOR]

For over 60 years, cyclophanes have inspired the design of novel molecular architectures of different sizes and geometries, unleashing significant advances in supramolecular chemistry and also in biomedical and materials sciences. Reported cyclophanes are countless and more complex molecular structures continue to be spawned. Herein, the study classifies cyclophanes into different families to emphasize and feature their structure‐properties relationships. While neutral cyclophanes have attracted more attention owing to their solid‐state physical properties, water‐soluble anionic cyclophanes have been explored predominantly in drug delivery. In the broad family of cationic cyclophanes, viologen‐based cyclophanes (VBCs) are widely investigated for designing molecular interlocked molecules (MIMs), molecular switches, and machines owing to their unique electrochemical properties. Despite decades of ground‐breaking research in academia, controlling the cationic cyclophanes and MIMs solid‐state structures is still a limiting factor when it comes to introducing them into functional materials. Here, the study draws attention to some current challenges in cyclophane chemistry from a materials sciences perspective and highlights processes that, if overcome, would lead to cyclophanes producing transformational materials. It is envisioned that zwitterionic VBCs can have a seminal impact on host–guest chemistry, MIMs, molecular machines, and supramolecular tessellations, which can pave the way toward next‐generation technologies. [ABSTRACT FROM AUTHOR]

This review highlights important research on anion coordination chemistry for materials applications over the last decade. This field has numerous applications in various areas, such as the environment, industry, and medicine. Despite its enormous potential, real‐world applicability is still pending. However, there has been a new trajectory in the field recently, with rapid advancement in designing sophisticated molecular systems for various materials applications. To keep track of this dynamic advancement, we have discussed some outstanding research work with enormous potential for materials applications soon. [ABSTRACT FROM AUTHOR]

Immune system regulation is a key indicator of the gut microbiota (GM) influencing disease development. The causal role of the GM in Guillain-Barré syndrome (GBS) and whether it can be mediated by immune cells is unknown. Genome-wide association study (GWAS) summary statistics for the GM were obtained from the Dutch Microbiota Project (n = 7,738) and the FINRISK 2002 (FR02) cohort (n = 5,959). Inverse variance weighting method (IVW) were used as the main method to evaluate the causal relationship between GM and GBS. Subsequently, the mediating effects of 731 immune traits were evaluated. Additionally, we also executed the Bayesian Weighting algorithm for verification. Mendelian randomization (MR) analysis determined the protective effect of the pyrimidine deoxyribonucleoside degradation superpathway on GBS (IVW: P = 0.0019, OR = 0.4508). It is worth noting that in the causal effects of pyrimidine deoxyribonucleoside degradation superpathway on GBS, the mediated proportions of herpesvirus entry mediator (HVEM) (HVEM on CM CD4 + , HVEM on naive CD4 + , HVEM on CD45RA − CD4 + , HVEM on CM CD8br) in the T cell maturation stage on GBS were -0.0398, -0.0452, -0.0414, -0.0425, accounting for 5.00%, 5.67%, 5.19% and 5.34% of the total effect. 11 types of intestinal bacteria might be involved in the pyrimidine deoxyriboside degradation superpathway, including Staphylococcus A fleurettii, AR31,CAG-274 sp000432155, Photobacterium, Acetobacteraceae, Dysgonomonadaceae, NK4A144,Leptospirae, CAG-81 sp000435795, Leptospirales and CAG-873 sp001701165. This study suggests that there is a causal relationship between pyrimidine deoxyribonucleoside degradation superpathway and GBS, which may be mediated by HVEM on CD4 + and CD8 + T cells. As a bidirectional molecular switch, HVEM plays an important role in T cell regulation. 11 intestinal flora were found to be involved in pyrimidine deoxyribonucleoside degradation superpathway, and their changes may be related to the occurrence of GBS. However, extensive research is still warranted before microbiome sequencing can be used for prevention and targeted treatment of GBS. [ABSTRACT FROM AUTHOR]

Introduction: Cancer is still a major challenge of human health. The abnormality of intracellular cancer-related signal pathways is an important mechanism for the occurrence of cancer. Methods: We used a molecular-senor to act on the endogenous signal molecules within the cell to redirect the abnormal signal flows in the cell to treat cancer. Based on CRISPR-dCas12f procedures, we combined aptamers and ribozymes to construct riboswitches, which served as molecular switches to reprogram sgRNAs, so that CRISPR-dCas12f redirected the intracellular anti-cancer signal flows after sensing specific input signal molecules. In addition, the activated molecular sensors and the inhibitory molecular sensors were constructed by combining transcription factors (VP64) and transcription inhibitors (KRAB) to specifically activate and inhibit target genes of interest. Results: Our experimental results showed that the molecular sensors that we designed and constructed specifically sensed the endogenous signal molecules and then redirect the cancer related signal networks of cancer cells. In addition, corresponding logic gates were constructed to distinguish cancer cells from normal cells and redirect anticancer signal flows to trigger specific cancer immunotherapy. Conclusion: The constructed molecular sensors constructed specifically recognized the signal molecules within the cell and redirected the endogenous signal pathway to reprogram the fate of cancer cells. [ABSTRACT FROM AUTHOR]

Oligo‐adenine (polyA) is primarily known for its critical role in mRNA stability, translational status, and gene regulation. Beyond its biological functions, extensive research has unveiled the diverse applications of polyA. In response to environmental stimuli, single polyA strands undergo distinctive structural transitions into diverse secondary configurations, which are reversible upon the introduction of appropriate counter‐triggers. In this review, we systematically summarize recent advances of noncanonical structures derived from polyA, including A‐motif duplex, A‐cyanuric acid triplex, A‐coralyne‐A duplex, and T ⋅ A‐T triplex. The structural characteristics and mechanisms underlying these conformations under specific external stimuli are addressed, followed by examples of their applications in stimuli‐responsive DNA hydrogels, supramolecular fibre assembly, molecular electronics and switches, biosensing and bioengineering, payloads encapsulation and release, and others. A detailed comparison of these polyA‐derived noncanonical structures is provided, highlighting their distinctive features. Furthermore, by integrating their stimuli‐responsiveness and conformational characteristics, advanced material development, such as pH‐cascaded DNA hydrogels and supramolecular fibres exhibiting dynamic structural transitions adapting environmental cues, are introduced. An outlook for future developments is also discussed. These polyA derived, stimuli‐responsive, noncanonical structures enrich the arsenal of DNA "toolbox", offering dynamic DNA frameworks for diverse future applications. [ABSTRACT FROM AUTHOR]

The study investigates the impact of thionation on N,N'‐di(dodecyl)‐4,5,8,9‐naphthalene diimide (NDI) through computational methods such as density functional theory (DFT/TD‐DFT), quantum theory of atoms in molecules (QTAIM), and Landauer theory (LT). Thionation, involving the replacement of diamide oxygens with sulfurs in NDI, significantly enhances quantum‐electronic/thermoelectric properties. Computational analyzes of energy of frontier orbitals HOMO/LUMO, dipole moment, polarizability, first superpolarizability, UV spectrum, and cohesive energy show the superior performance of the thione structure (M2) compared to the pristine structure (M1). Thionation decreased the energy gap from 01.3 eV (in M1 structure) to 1.87 eV (in M2 structure). The absorption wavelength in the pristine structure (M1) is calculated to be 507 nm, which increased to 1067 nm after thionation (M2). Cohesive energy values for each of M1 and M2 structures are calculated as 12.76 and 12.89 Kcal mol−1, respectively, which indicates the improvement of stability after thionation. After connecting M1 and M2 to gold electrodes (Au‐M1‐Au and Au‐M2‐Au) and applying electric fields, the Au‐M2‐Au structure shows a lower energy gap, lower thermoelectric activity and higher conductivity at field intensities with higher than 140 × 10−4 (a.u.), indicating its use as a field‐effect molecular device (such as molecular wire or molecular switch). [ABSTRACT FROM AUTHOR]

G protein-coupled receptors (GPCRs) are sensors for the G protein complex to sense changes in environmental factors and molecular switches for G protein complex signal transduction. In this study, the homologous gene of GPCR-like proteins was identified from maize and named as ZmCOLD1. Subcellular analysis showed that the ZmCOLD1 protein is localized to the cell membrane and endoplasmic reticulum. A CRISPR/Cas9 knock-out line of ZmCOLD1 was further created and its plant height was significantly lower than the wild-type maize at both the seedling and adult stages. Histological analysis showed that the increased cell number but significantly smaller cell size may result in dwarfing of zmcold1, indicating that the ZmCOLD1 gene could regulate plant height development by affecting the cell division process. Additionally, ZmCOLD1 was verified to interact with the maize Gα subunit, ZmCT2, though the central hydrophilic loop domain by in vivo and in vitro methods. Abscisic acid (ABA) sensitivity analysis by seed germination assays exhibited that zmcold1 were hypersensitive to ABA, indicating its important roles in ABA signaling. Finally, transcriptome analysis was performed to investigate the transcriptional change in zmcold1 mutant. Overall, ZmCOLD1 functions as a GPCR-like protein and an important regulator to plant height. [ABSTRACT FROM AUTHOR]

Multifunctional molecular switches have attracted much attention because of their unique stimulus response behavior and advanced applications. However, precise regulation of the structure for property enrichment is still a great challenge. Herein, the first case of a single‐molecule switch BN‐S with multiple structurally tunable and full‐color fluorescent properties is reported. Interestingly, BN‐S exhibits a butterfly‐like "metamorphosis" crystal growth process accompanied by full‐color fluorescence emission (including white light, CIE = 0.33, 0.33; 456 nm → 610 nm). It is shown that this is related to the reversible B←N bonding and the tunability of the spatial structure of the BN‐S. Thus, BN‐S exhibits superior multicolor tunability in different states (solid, liquid, and film), and its applications in white‐light optical light emitting diodes (OLEDs) and multicolor fluorescent inks also show great promise. This will provide a new strategy for designing and synthesizing the development of multifunctional molecular switching materials and enriching the variety of organoboron luminescent materials. [ABSTRACT FROM AUTHOR]

The phosphoproteome is vast and intricate, with many aspects of its extent and site-specific functional roles still largely unexplored. While traditional studies have primarily focused on Ser/Thr and Tyr phosphorylation, new methodologies are emerging to study non-canonical phosphorylation events. Protein phosphatases play critical roles in cellular signaling, with recent studies highlighting their complexity and involvement in various biological processes. A significant portion of the kinome, referred to as the 'dark' kinome, remains understudied and holds great potential for novel discoveries. Pseudokinases and pseudophosphatases, despite lacking catalytic activity, play crucial roles in cell signaling. Recent advances in experimental and computational analyses have improved the understanding of kinase–substrate and phosphatase–substrate interactions. Protein phosphorylation is a crucial regulatory mechanism in cell signaling, acting as a molecular switch that modulates protein function. Catalyzed by protein kinases and reversed by phosphoprotein phosphatases, it is essential in both normal physiological and pathological states. Recent advances have uncovered a vast and intricate landscape of protein phosphorylation that include histidine phosphorylation and more unconventional events, such as pyrophosphorylation and polyphosphorylation. Many questions remain about the true size of the phosphoproteome and, more importantly, its site-specific functional relevance. The involvement of unconventional actors such as pseudokinases and pseudophosphatases adds further complexity to be resolved. This review explores recent discoveries and ongoing challenges, highlighting the need for continued research to fully elucidate the roles and regulation of protein phosphorylation. [ABSTRACT FROM AUTHOR]

Multifunctional magnetic materials have broad application prospects in molecular switches and information storage. In this study, four mononuclear Fe(II) complexes are synthesized using a series of pyrenylhydrazone ligands HL1–4. Two deprotonated ligands are coordinated to the iron(II) ions in an enolic form, leading to neutral complexes FeII(Lx)2·xsol with a FeIIN4O2 octahedral coordination environment. Magnetic measurements suggest that complex Fe(L1)2·2ACE (1·2ACE, ACE = acetone) is mainly low spin below 300 K and complex Fe(L3)2·ACE (3·ACE) is high spin, whereas complexes Fe(L2)2 (2) and Fe(L4)2·6H2O (4·6H2O) exhibit gradual spin crossover behavior. The spin states of complexes 1–4 are confirmed by single-crystal X-ray diffraction analysis. The substituent effect on the magnetic properties of the complexes is significant in this system. Temperature-dependent fluorescence emission spectra show the coexistence but no coupling effect of spin crossover and fluorescence for complexes 2 and 4·6H2O. [ABSTRACT FROM AUTHOR]

Synthetic molecular photoswitches have taken center stage as high‐precision tools to introduce light‐responsiveness at the smallest scales. Today they are found in all areas of applied chemistry, covering materials research, chemical biology, catalysis, or nanotechnology. For a next step of applicability truly orthogonal photoswitching is highly desirable but to date such independent addressability of different photoswitches remains highly challenging. Herein we present the first example of all‐visible, all‐light responsive, and path‐ independent orthogonal photoswitching. By combining two recently developed indigoid photoswitches ‐ peri‐anthracenethioindigo and a rhodanine‐based chromophore ‐ a four‐state system is established and each state can be accessed in high yields completely independently and also with visible light irradiation only. The four states give rise to four different colors, which can be transferred to a solid polymer matrix to yield a versatile multi‐state photochromic material. Further, combination with a fluorescent dye as a third component is possible, demonstrating the applicability of this orthogonal photoswitching system in all‐photonic molecular logic behavior and information processing. [ABSTRACT FROM AUTHOR]

Background: Normal cells express functional tumor suppressor WW domain-containing oxidoreductase (WWOX), designated WWOXf. UV irradiation induces WWOXf cells to undergo bubbling cell death (BCD) — an event due to the accumulation of nuclear nitric oxide (NO) gas that forcefully pushes the nuclear and cell membranes to form one or two bubbles at room temperature (22 °C) and below. In contrast, when WWOX-deficient or -dysfunctional (WWOXd) cells are exposed to UV and/or cold shock, the cells undergo nuclear pop-out explosion death (POD). We aimed to determine the morphological and biochemical changes in WWOXf cells during BCD versus apoptosis. Methods: WWOXf and WWOXd cells were exposed to UV followed by measuring BCD or POD by time-lapse microscopy and/or time-lapse holographic microscopy at 4, 22, or 37 °C to visualize morphological changes. Live cell stains were used to measure the kinetics of nitric oxide (NO) production and Ca2+ influx. Extent of cell death was measured by uptake of propidium iodide and by internucleosomal DNA fragmentation using agarose gel electrophoresis. Results: WWOXf cells were exposed to UV and then cold shock, or cold shock and then UV, and cultured at 4, 10, and 22 °C, respectively. Initially, UV induced calcium influx and NO production, which led to nuclear bubbling and final death. Cold shock pretreatment completely suppressed UV-mediated bubbling at 37 °C, so the UV/cold shock-treated cells underwent apoptosis. Without cold shock, UV only induced bubbling at all temperatures, whereas the efficiency of bubbling at 37 °C was reduced by greater than 50%. Morphologically, the WWOXf cell height or thickness was significantly increased during cell division or apoptosis, but the event did not occur in BCD. In comparison, when WWOXd cancer cells received UV or UV/cold shock, these cells underwent NO-independent POD. UV/cold shock effectively downregulated the expression of many proteins such as the housekeeping α-tubulin (> 70%) and β-actin (< 50%), and cortactin (> 70%) in WWOXf COS7 cells. UV/cold shock induced relocation of α-tubulin to the nucleus and nuclear bubbles in damaged cells. UV induced co-translocation of the WWOX/TRAF2 complex to the nuclei, in which the prosurvival TRAF2 blocked the proapoptotic WWOX via its zinc finger domain. Without WWOX, TRAF2 did not relocate to the nuclei. Cold shock caused the dissociation of the WWOX/TRAF2 complex in the nucleus needed for BCD. In contrast, the formation of the WWOX/TRAF2 complex, plus p53, was strengthened at 37 °C required for apoptosis. Conclusions: The temperature-sensitive nuclear WWOX/TRAF2 complex acts as a molecular switch, whose dissociation favors BCD at low temperatures, and the association supports apoptosis at 37 °C in UV-treated WWOXf cells. [ABSTRACT FROM AUTHOR]

Rho/Rac of plant (ROP) GTPases are plant-specific proteins that function as molecular switches, activated by guanine nucleotide exchange factors (GEFs) and inactivated by GTPase-activating proteins (GAPs). The bryophyte Marchantia polymorpha contains single copies of ROP (MpROP), GEFs [ROPGEF and SPIKE (SPK)] and GAPs [ROPGAP and ROP ENHANCER (REN)]. MpROP regulates the development of various tissues and organs, such as rhizoids, gemmae and air chambers. The ROPGEF KARAPPO (MpKAR) is essential for gemma initiation, but the functions of other ROP regulatory factors are less understood. This study focused on two GAPs: MpROPGAP and MpREN. Mpren single mutants showed defects in thallus growth, rhizoid tip growth, gemma development, and air-chamber formation, whereas Mpropgap mutants showed no visible abnormalities. However, Mpropgap Mpren double mutants had more severe phenotypes than the Mpren single mutants, suggesting backup roles of MpROPGAP in processes involving MpREN. Overexpression of MpROPGAP and MpREN resulted in similar gametophyte defects, highlighting the importance of MpROP activation/inactivation cycling (or balancing). Thus, MpREN predominantly, and MpROPGAP as a backup, regulate gametophyte development, likely by controlling MpROP activation in M. polymorpha. [ABSTRACT FROM AUTHOR]

The reversible photo-induced conformation transition of a single molecule with a [5]helicene backbone has garnered considerable interest in recent studies. Based on such a switching process, one can build molecular photo-driven switches for potential applications of nanoelectronics. But the achievement of high-performance reversible single-molecule photoswitches is still rare. Here, we theoretically propose a 13,14-dimethylcethrene switch whose photoisomerization between the ring-closed and ring-open forms can be triggered by ultraviolet (UV) and visible light irradiation. The electronic structure transitions and charge transport characteristics, concurrent with the photo-driven electrocyclization of the molecule, are calculated by the non-equilibrium Green's function (NEGF) in combination with density functional theory (DFT). The electrical conductivity bears great diversity between the closed and open configurations, certifying the switching behavior and leading to a maximum on–off ratio of up to 103, which is considerable in organic junctions. Further analysis confirms the evident switching behaviors affected by the molecule–electrode interfaces in molecular junctions. Our findings are helpful for the rational design of organic photoswitches at the single-molecule level based on cethrene and analogous organic molecules. [ABSTRACT FROM AUTHOR]

The evaluation of the Z/E photoisomerization efficiency is an essential task to design photoactive molecular devices. Nevertheless, this photoreactivity can be correctly described only by applying extensive and expensive computational methods. In this study, a predictive tool to screen the photoinduced Z/E isomerization efficiency of molecular switches is presented, based on three key properties: the structure of the ground state minimum, the nature of the electronic transition populating the optically bright state, and the presence of crossings between the optically bright state and the one lower in energy. Our methodology allows evaluating these properties by few and affordable calculations, potentially enabling the screening of large sets of photoswitches. After presenting the formal aspects, the tool is applied to model systems of paradigmatic classes of photoswitches (retinal, green fluorescent protein, hemithioindigo, chiroptical, and stilbene compounds) including derivatives. A comparison with the available experimental data is performed to validate our approach. Cis-trans photoisomerization is a key process for many processes in biology and materials science, but only careful and time-consuming quantum chemistry methods can describe such reaction in detail. Here, a predictive tool is presented requiring few and affordable calculations, evaluating the efficiency of paradigmatic and modified photoswitches. [ABSTRACT FROM AUTHOR]

Many researchers have focused on molecular electronics, and this field can progress faster by applying semiconductors to molecular modeling. In this work, two middle rings of a bipyridine–biborinine molecular diode are rotated from 25∘ to 90∘ such that the current along the molecule is reduced. The current is minimum and almost zero at 90∘, while it is maximum at 25∘. Accordingly, considering these two angles, the molecule can act as a switching device when the two middle rings are rotated. The bipyridine–biborinine molecular diode is modeled considering the effect of rotation by including two resistors in the model. Two parallel diodes are used in this modeling for pyridine and borinine rings. The ideality factors of these diodes are varied based on the electronegativity of pyridine and borinine rings. This model is then applied to consider different molecular logic gates such as NAND, NOR, NOT, OR and AND gates, as well as molecular logic circuits (half adder and full adder), using the unique capabilities of the LTspice software. [ABSTRACT FROM AUTHOR]

Crystallization of organic materials can lead to different assembly structure with different reactivity, but this phenomenon is rarely observed for delocalized hydrocarbon radicals. This report introduces a crystallization‐induced radical–radical coupling reaction, which employs a series of stable nonplanar organic π‐radicals as reactants. Six stable radical congeners are synthesized, resulting in radical–radical coupling at the allenyl radical site during crystallization to produce close‐shell dimers. This coupling reaction is absent in the solution phase, which highlights the importance of preorganization in the lattice. Remarkably, the attempts of cocrystallization of different congeners yielded homocoupling products instead of cross‐coupling products. In specific cases, two distinct polymorphs are observed and their reactivity is different according to the distance of the reaction sites. Theoretical calculations indicate that the transition from a metastable preorganized monomer to a dimer is barrierless and spontaneous. The dimer could regenerate free radicals by heating or photoirradiation in the solution phase. This discovery may lead to controllable molecular switches. [ABSTRACT FROM AUTHOR]

Summary: At present, many DNA logic circuits have been successfully constructed. However, advanced complex DNA computing tasks with simple structure, fast response, and modularization still remain a huge challenge. In this paper, molecular switch circuits (MSCs) are constructed based on DNA strand displacement to improve above problems. At first, molecular switch is constructed, which is the basic element for building logic circuits. Next, the functions of AND, OR, Fan‐in, and Fan‐out are realized through switches cascading in series or parallel. Furthermore, switch canvas strategy is explored to obtain the shortest reaction path and highest output concentration for circuits. Finally, a novel strategy of integrating computing module using molecular switches is proposed. Here, we construct a half‐adder, half‐subtractor, and a 9‐bit parity checking circuits to verify its feasibility. Compared with the classical monorail and dual‐track logic circuits, the structure scale is reduced by more than two times, and the DNA strands are decreased by more than four times, which effectively reduces the circuit complexity and raises the reaction speed. The above results show that MSC strategy has a great potential to construct large‐scale DNA circuits and provides a development model for the scalability and modularity of biological computing. [ABSTRACT FROM AUTHOR]

Toxin–antitoxin (TA) systems in bacteria are key regulators of the cell cycle and can activate a death response under stress conditions. Like other bacterial elements, TA modules have been widely exploited for biotechnological purposes in diverse applications, such as molecular cloning and anti-cancer therapies. However, their use in plants has been limited, leaving room for the development of new approaches. In this study, we examined two TA systems previously tested in plants, MazEF and YefM-YoeB, and identified interesting differences between them, likely related to their modes of action. We engineered modifications to these specific modules to transform them into molecular switches that can be activated by a protease, inducing necrosis in the plant cells where they are expressed. Finally, we demonstrated the antiviral potential of the modified TA modules by using, as a proof-of-concept, the potyvirus plum pox virus as an activator of the death phenotype. [ABSTRACT FROM AUTHOR]

The incorporation of molecular switches into polymer networks has been a powerful approach for the development of functional polymer materials that display macroscopic actuation and function enabled directly by molecular changes. However, such materials sometimes require harsh conditions to perform their functions, and the design of new molecular photoswitches that can function under physiological conditions is highly needed. Here, we report the design and synthesis of a spiropyridine-based photoswitchable hydrogel that exhibits light-driven actuation at physiological pH. Owing to its high pKa, spiropyridine maintains its ring-open protonated form at neutral pH, and the resulting hydrogel remains in a swollen state. Upon irradiation with visible light, the ring closure of spiropyridine leads to a decrease in the charge and a reduction in the volume of the hydrogel. The contracted gel could spontaneously recover to its expanding state in the dark, and this process is highly dynamic and reversible when the light is switched on and off. Furthermore, the hydrogel shows switchable fluorescence in response to visible light. Bending deformation is observed in the hydrogel thin films upon irradiation from one side. Importantly, the independence of this spiropyridine hydrogel from the acidic environment makes it biotolerant and shows excellent biocompatibility. This biocompatible spiropyridine hydrogel might have important biorelated applications in the future. [ABSTRACT FROM AUTHOR]

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(η5‐tetrahydroindenyl), two cyclo‐1,3‐diphospha‐pentane‐1,3‐diyls were successfully introduced, which finally led to the isolation of a deep green zirconcene‐bridged bis(biradicaloid) complex (5) that can act as a double molecular switch. Under the influence of light (570 nm), this tetraradical forms a transannular bond in each of the two five‐membered biradical units, leading to the formation of housane 5 h. Upon irradiation at 415 nm, the reverse reaction is observed, fully recovering tetraradical 5. Through single‐crystal‐to‐single‐crystal transformation, 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. [ABSTRACT FROM AUTHOR]

Bioorthogonal reactions that enable switching molecular functions by breaking chemical bonds have gained prominence, with the tetrazine‐mediated cleavage of trans‐cyclooctene caged compounds (click‐to‐release) being particularly noteworthy for its high versatility, biocompatibility, and fast reaction rates. Despite several recent advances, the development of highly reactive tetrazines enabling quantitative elimination from trans‐cyclooctene linkers remains challenging. In this study, we present the synthesis and application of sulfo‐tetrazines, a class of derivatives featuring phenolic hydroxyl groups with increased acidity constants (pKa). This unique property leads to accelerated elimination and complete release of the caged molecules within minutes. Moreover, the inclusion of sulfonate groups provides a valuable synthetic handle, enabling further derivatization into sulfonamides, modified with diverse substituents. Significantly, we demonstrate the utility of sulfo‐tetrazines in efficiently activating fluorogenic compounds and prodrugs in living cells, offering exciting prospects for their application in bioorthogonal chemistry. [ABSTRACT FROM AUTHOR]

The booming demand on data security has aroused great interest for developing smart materials with temporal display feature and dynamic multicolor fluorescence. However, it remains challenging to implement both features on most responsive molecules. Herein, we construct a polymer free volume‐controlled "molecular clock and emitter" via covalently embedding a multi‐stimuli responsive molecular switch (i.e. spiropyran) into a polymer network (i.e. poly(pentafluorophenyl acrylate)) with programmable crosslink density and free volume. By the aminolysis of pentafluorophenyl ester with different amount of diamine crosslinkers, pPFPA‐co‐SP networks with controllable crosslink densities are generated, which have different confinement effects on the rate constant of SP/MC isomerization, thus leading to time‐dependent photochromism. In addition, PTF1, a fluorescent probe that is sensitive to polymer rigidity, is introduced to further endow pPFPA‐co‐SP system with phototunable dynamic full‐color emission. Therefore, relying on their synergistical responses to the rigidity of the polymer network, we have successfully developed a versatile molecular clock and emitter via an "one stone two birds" manner, which shows time‐dependent data display along with dynamic multicolor fluorescence switching, providing great potential for advanced encryption and anticounterfeiting with a high security level. [ABSTRACT FROM AUTHOR]

The single‐molecule localization concept MINFLUX has triggered a reevaluation of the features of fluorophores for attaining nanometer‐scale resolution. MINFLUX nanoscopy benefits from temporally controlled fluorescence ("on"/"off") photoswitching. Combined with an irreversible switching behavior, the localization process is expected to turn highly efficient and quantitative data analysis simple. The potential in the recently reported photoactivable xanthone (PaX) dyes is recognized to extend the list of molecular switches used for MINFLUX with 561 nm excitation beyond the fluorescent protein mMaple. The MINFLUX localization success rates of PaX560, PaX+560, and mMaple are quantitatively compared by analyzing the effective labeling efficiency of endogenously tagged nuclear pore complexes. The PaX dyes prove to be superior to mMaple and on par with the best reversible molecular switches routinely used in single‐molecule localization microscopy. Moreover, the rationally designed PaX595 is introduced for complementing PaX560 in dual color 561 nm MINFLUX imaging based on spectral classification and the deterministic, irreversible, and additive‐independent nature of PaX photoactivation is showcased in fast live‐cell MINFLUX imaging. The PaX dyes meet the demands of MINFLUX for a robust readout of each label position and fill the void of reliable fluorophores dedicated to 561 nm MINFLUX imaging. [ABSTRACT FROM AUTHOR]

Quantum chemistry methods have been enacted to characterize the second‐order nonlinear optical (NLO) properties of a multi‐state molecular switch containing dihydroazulene and spiropyran units. They have demonstrated that the first hyperpolarizabilities constitute a novel output signal from the viewpoint of molecular logic, owing to the contrasts of NLO responses between the different forms of the dyad. On the one hand, the DFT calculations demonstrate that switching either unit has only a negligible impact on the geometrical parameters of the other one, as well as on the thermodynamics of their transformations. Similarly, as determined by time‐dependent DFT calculations, the UV/vis absorption spectra are in good approximation a superposition of those from the parent units. On the other hand, this additivity trend is not consistently observed for the NLO responses. However, an interpretation of these NLO responses has been proposed by using the unit sphere representation of the first hyperpolarizability tensors to address their orientational aspects as well as by resorting to the few‐state approximation and the missing state analysis to highlight the localized or charge‐transfer nature of the dominant excited states. [ABSTRACT FROM AUTHOR]

The tendency for cell fate to be robust to most perturbations, yet sensitive to certain perturbations raises intriguing questions about the existence of a key path within the underlying molecular network that critically determines distinct cell fates. Reprogramming and trans-differentiation clearly show examples of cell fate change by regulating only a few or even a single molecular switch. However, it is still unknown how to identify such a switch, called a master regulator, and how cell fate is determined by its regulation. Here, we present CAESAR, a computational framework that can systematically identify master regulators and unravel the resulting canalizing kernel, a key substructure of interconnected feedbacks that is critical for cell fate determination. We demonstrate that CAESAR can successfully predict reprogramming factors for de-differentiation into mouse embryonic stem cells and trans-differentiation of hematopoietic stem cells, while unveiling the underlying essential mechanism through the canalizing kernel. CAESAR provides a system-level understanding of how complex molecular networks determine cell fates. [ABSTRACT FROM AUTHOR]

The fabrication of materials that can switch between circularly polarized luminescence (CPL) signals is both essential and challenging. Here, two new halogen‐bonded fluorescent molecular photoswitches, namely, HB‐switch 1 and HB‐switch 2, containing α‐cyano‐substituted diarylethene compounds with different end groups were developed. Upon exposure to specific UV or visible light wavelengths, they exhibited controllable and reversible Z/E photoisomerization. When these switches were integrated into blue‐phase liquid crystals (BPLCs), the temperature range of BP significantly expanded. Notably, the BP system incorporating HB‐switch 1 exclusively achieved reversible polarization inversion of CPL signals under irradiation with specific UV/Visible light and during cooling/heating. The photo/thermal dual‐response behavior of the CPL signals can be attributed to the phase transition from a high‐symmetry 3D BP Icubic lattice to a low‐symmetry 1D helical superstructure induced by the Z/E photoisomerization of HB‐switch 1 and temperature changes. This study underscores the significance of employing halogen‐bond assembly strategies to design materials with switchable CPL signals, opening new possibilities for CPL‐active systems. [ABSTRACT FROM AUTHOR]

Molecular‐level understanding of photoinduced processes is critically important for breakthroughs in transformative technologies utilizing light, ranging from photomedicine to photoresponsive materials. Theory and simulation play a crucial role in this task. Despite great advances in hardware and computational methods, the theoretical description of photoinduced phenomena in the presence of complex environments and external photoexcitation conditions still poses formidable challenges for theoreticians and there are numerous formal and computational difficulties that must be overcome. The development of predictive, accurate, and at the same time, computationally efficient theoretical approaches to describe complex problems in photochemistry and photophysics is an active field of research in contemporary theoretical and computational chemistry. In this advanced review, we discuss modern computational advances and novel approaches that have been recently developed in excited‐electronic structure methods, and multiscale modeling, with a special emphasis on coupled electron‐nuclear dynamics and spectroscopy, from fully quantum to semi‐classical methodologies—including dissipative effects, the explicit light field interaction, femtosecond time‐resolved spectroscopy, and software infrastructure. This article is categorized under:Software > Quantum ChemistryElectronic Structure Theory > Combined QM/MM MethodsTheoretical and Physical Chemistry > SpectroscopySoftware > Molecular Modeling [ABSTRACT FROM AUTHOR]

The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the dark matter of MD — data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 files and 2000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on files produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identified systems with specific molecular composition and were able to characterize essential parameters of MD simulation such as temperature and simulation length, and could identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore the MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and to report and standardize metadata to reuse this valuable matter. [ABSTRACT FROM AUTHOR]

The morphology of dendritic spines, the postsynaptic compartment of most excitatory synapses, decisively modulates the function of neuronal circuits as also evident from human brain disorders associated with altered spine density or morphology. Actin filaments (F-actin) form the backbone of spines, and a number of actin-binding proteins (ABP) have been implicated in shaping the cytoskeleton in mature spines. Instead, only little is known about the mechanisms that control the reorganization from unbranched F-actin of immature spines to the complex, highly branched cytoskeleton of mature spines. Here, we demonstrate impaired spine maturation in hippocampal neurons upon genetic inactivation of cyclase-associated protein 1 (CAP1) and CAP2, but not of CAP1 or CAP2 alone. We found a similar spine maturation defect upon overactivation of inverted formin 2 (INF2), a nucleator of unbranched F-actin with hitherto unknown synaptic function. While INF2 overactivation failed in altering spine density or morphology in CAP-deficient neurons, INF2 inactivation largely rescued their spine defects. From our data we conclude that CAPs inhibit INF2 to induce spine maturation. Since we previously showed that CAPs promote cofilin1-mediated cytoskeletal remodeling in mature spines, we identified them as a molecular switch that control transition from filopodia-like to mature spines. [ABSTRACT FROM AUTHOR]

Allostery is a fundamental way to regulate the function of biomolecules playing crucial roles in cell metabolism and proliferation and is deemed the second secret of life. Given the limited understanding of the structure of natural allosteric molecules, the development of artificial allosteric molecules brings a huge opportunity to transform the allosteric mechanism into practical applications. In this study, the concept of bionics is introduced into the design of artificial allosteric molecules and an allosteric DNA switch with an activity site and an allosteric site based on two aptamers for selective inhibition of thrombin activity. Compared with the single aptamer, the allosteric switch possesses a significantly enhanced inhibition ability, which can be precisely regulated by converting the switch states. Moreover, the dynamic allosteric switch is further subjected to the control of the DNA threshold circuit for realizing automatic concentration determination and activity inhibition of thrombin. These compelling results confirm that this allosteric switch equipped with self‐sensing and information‐processing modules puts a new slant on the research of allosteric mechanisms and further application of allosteric tactics in chemical and biomedical fields. [ABSTRACT FROM AUTHOR]

Optoacoustic (or photoacoustic) imaging promises micron‐resolution noninvasive bioimaging with much deeper penetration (>cm) than fluorescence. However, optoacoustic imaging of enzyme activity would require loud, photostable, NIR‐absorbing molecular contrast agents, which remain unknown. Most organic molecular contrast agents are repurposed fluorophores, with severe shortcomings of photoinstability or phototoxicity under optoacoustic imaging, as consequences of their slow S1→S0 electronic relaxation. We now report that known fluorophores can be rationally modified to reach ultrafast S1→S0 rates, without much extra molecular complexity, simply by merging them with molecular switches. Here, we merge azobenzene switches with cyanine dyes to give ultrafast relaxation (<10 ps, >100‐fold faster). Without even adapting instrument settings, these azohemicyanines display outstanding improvements in signal longevity (>1000‐fold increase of photostability) and signal loudness (>3‐fold even at time zero). We show why this simple but unexplored design strategy can still offer stronger performance in the future, and can also increase the spatial resolution and the quantitative linearity of photoacoustic response over extended longitudinal imaging. By bringing the world of molecular switches and rotors to bear on problems facing optoacoustic agents, this practical strategy will help to unleash the full potential of optoacoustic imaging in fundamental studies and translational uses. [ABSTRACT FROM AUTHOR]

Rotaxanes are mechanically interlocked molecules where a ring (macrocycle) is threaded onto a linear molecule (thread). The position of the macrocycle on different stations on the thread can be controlled in response to external stimuli, making rotaxanes applicable as molecular switches. Here we show that bistable rotaxanes based on the combination of a Zn(II) tetraphenylporphyrin photosensitizer, attached to the macrocycle, and a black-hole-quencher, attached to the thread, are capable of singlet oxygen production which can be switched on/off by the addition of base/acid. However, we found that only a sufficiently long linker between both stations on the thread enabled switchability, and that the direction of switching was inversed with regard to the original design. This unexpected behavior was attributed to intramolecular folding of the rotaxanes, as indicated by extensive theoretical calculations. This evidences the importance to take into account the conformational flexibility of large molecular structures when designing functional switchable systems. Singlet oxygen is a highly useful reagent for organic synthesis, disinfection and photodynamic therapy, but its high reactivity calls for systems where its photochemical generation can be switched on and off on demand. Here, the authors report porphyrin-decorated pH-switchable [2]rotaxanes for singlet oxygen photoproduction, finding that molecular folding of the rotaxanes influences the on/off switching in an unforeseen way. [ABSTRACT FROM AUTHOR]

Electronic switches have been considered to be one of the most important components of contemporary electronic circuits for processing and storing digital information. Fabricating functional devices with building blocks of atomic/molecular switches can greatly promote the minimization of the devices and meet the requirement of high integration. This review highlights key developments in the fabrication and application of molecular switching devices. This overview offers valuable insights into the switching mechanisms under various stimuli, emphasizing structural and energy state changes in the core molecules. Beyond the molecular switches, typical individual metal atomic switches are further introduced. A critical discussion of the main challenges for realizing and developing practical molecular/atomic switches is provided. These analyses and summaries will contribute to a comprehensive understanding of the switch mechanisms, providing guidance for the rational design of functional nanoswitch devices toward practical applications. [ABSTRACT FROM AUTHOR]

RAS proteins are conserved guanosine triphosphate (GTP) hydrolases (GTPases) that act as molecular binary switches and play vital roles in numerous cellular processes. Upon GTP binding, RAS GTPases adopt an active conformation and interact with specific proteins termed RAS effectors that contain a conserved ubiquitin-like domain, thereby facilitating downstream signaling. Over 50 effector proteins have been identified in the human proteome, and many have been studied as potential mediators of RAS-dependent signaling pathways. Biochemical and structural analyses have provided mechanistic insights into these effectors, and studies using model organisms have complemented our understanding of their role in physiology and disease. Yet, many critical aspects regarding the dynamics and biological function of RAS-effector complexes remain to be elucidated. In this review, we discuss the mechanisms and functions of known RAS effector proteins, provide structural perspectives on RAS-effector interactions, evaluate their significance in RAS-mediated signaling, and explore their potential as therapeutic targets. RAS proteins act as molecular switches by binding GTP and interacting with effectors to facilitate downstream signaling. This review by Mozzarelli et al. discusses the mechanisms, structures, and functions of RAS effectors, their roles in signaling, and their potential as therapeutic targets, emphasizing the need for deeper insights into RAS-effector interactions. [ABSTRACT FROM AUTHOR]

Summary: Switched on surfaces Molecular spin switches have been known for almost a hundred years. Their response to various excitations and the physical properties that can be changed by switching make them attractive for a wide range of applications. Recently, it became possible to manipulate individual molecules in a controlled manner in order to understand the influence of the local environment on switching. The interdisciplinary collaboration between chemistry and physics allows spin switches based on different mechanisms to be designed, synthesized and tested on surfaces. [ABSTRACT FROM AUTHOR]

Light irradiation is an external stimulus, rapidly developed in switchable atom transfer radical polymerization (ATRP) via photo‐activation methods in recent years. Herein, a photo‐deactivation strategy is introduced to regulate ATRP with the assistance of photoswitchable hexaarylbiimidozole (HABI). Under visible light irradiation and in the presence of HABI, ATRP is greatly decelerated or quenched depending on the concentration of HABI. Interestingly, with visible light off, ATRP can proceed smoothly and follow a first‐order kinetics. Moreover, photo‐switchable ATRP alternatively with light off and on is demonstrated. Besides, the mechanism of photo‐deactivation ATRP involving radical quenching is proposed in the presence of HABI. [ABSTRACT FROM AUTHOR]

Here we review the functions of ribosomal proteins (RPs) in the nucleolar stages of large ribosomal subunit assembly in the yeast Saccharomyces cerevisiae. We summarize the effects of depleting RPs on pre-rRNA processing and turnover, on the assembly of other RPs, and on the entry and exit of assembly factors (AFs). These results are interpreted in light of recent near-atomic-resolution cryo-EM structures of multiple assembly intermediates. Results are discussed with respect to each neighborhood of RPs and rRNA. We identify several key mechanisms related to RP behavior. Neighborhoods of RPs can assemble in one or more than one step. Entry of RPs can be triggered by molecular switches, in which an AF is replaced by an RP binding to the same site. To drive assembly forward, rRNA structure can be stabilized by RPs, including clamping rRNA structures or forming bridges between rRNA domains. [ABSTRACT FROM AUTHOR]

The interaction between different types of substituents in dicarbollide ligands and their influence on the stabilization of various rotational conformers (rotamers) of transition metal bis(dicarbollide) complexes [3,3′-M(1,2-C2B9H11)2]− are considered. It has been shown that the formation of intramolecular CH···X hydrogen bonds between dicarbollide ligands is determined by the size of the proton acceptor atom X rather than its electronegativity. Due to the stabilization of rotamers with different dipole moments, intramolecular hydrogen bonds between ligands in transition metal bis(dicarbollide) complexes can have a significant impact on the biological properties of their derivatives. In the presence of external complexing metals, weak intramolecular CH···X hydrogen bonds can be broken to form stronger X—>M donor-acceptor bonds. This process is accompanied by the mutual rotation of dicarbollide ligands and can be used in sensors and molecular switches based on transition metal bis(dicarbollide) complexes. [ABSTRACT FROM AUTHOR]

Coronaviruses constitute a global threat to human and animal health. It is essential to investigate the long-distance RNA-RNA interactions that approximate remote regulatory elements in strategies, including genome circularization, discontinuous transcription, and transcriptional enhancers, aimed at the rapid replication of their large genomes, pathogenicity, and immune evasion. Based on the primary sequences and modeled RNA-RNA interactions of two experimentally defined coronaviral enhancers, we detected via an in silico primary and secondary structural analysis potential enhancers in various coronaviruses, from the phylogenetically ancient avian infectious bronchitis virus (IBV) to the recently emerged SARS-CoV-2. These potential enhancers possess a core duplex-forming region that could transition between closed and open states, as molecular switches directed by viral or host factors. The duplex open state would pair with remote sequences in the viral genome and modulate the expression of downstream crucial genes involved in viral replication and host immune evasion. Consistently, variations in the predicted IBV enhancer region or its distant targets coincide with cases of viral attenuation, possibly driven by decreased open reading frame (ORF)3a immune evasion protein expression. If validated experimentally, the annotated enhancer sequences could inform structural prediction tools and antiviral interventions. [ABSTRACT FROM AUTHOR]

Protein kinases act as central molecular switches in the control of cellular functions. Alterations in the regulation and function of protein kinases may provoke diseases including cancer. In this study we investigate the conformational states of such disease-associated kinases using the high sensitivity of the kinase conformation (KinCon) reporter system. We first track BRAF kinase activity conformational changes upon melanoma drug binding. Second, we also use the KinCon reporter technology to examine the impact of regulatory protein interactions on LKB1 kinase tumor suppressor functions. Third, we explore the conformational dynamics of RIP kinases in response to TNF pathway activation and small molecule interactions. Finally, we show that CDK4/6 interactions with regulatory proteins alter conformations which remain unaffected in the presence of clinically applied inhibitors. Apart from its predictive value, the KinCon technology helps to identify cellular factors that impact drug efficacies. The understanding of the structural dynamics of full-length protein kinases when interacting with small molecule inhibitors or regulatory proteins is crucial for designing more effective therapeutic strategies. [ABSTRACT FROM AUTHOR]

Fibril formation is a key feature in neurodegenerative diseases like Alzheimer's, Parkinson's, and systemic amyloidosis. Polyphenols, found in plant-based foods, show promise in inhibiting fibril formation and disrupting disease progression. The ability of polyphenols to break the amyloid fibrils of many disease-linked proteins has been tested in numerous studies. Polyphenols have their distinctive mechanism of action. They behave differently on various events in the aggregation pathway. Their action also differs for different proteins. Some polyphenols only inhibit the formation of fibrils whereas others break the preformed fibrils. Some break the fibrils into smaller species, and some change them to other morphologies. This article delves into the intricate molecular mechanisms underlying the inhibitory effects of polyphenols on fibrillogenesis, shedding light on their interactions with amyloidogenic proteins and the disruption of fibril assembly pathways. However, addressing the challenges associated with solubility, stability, and bioavailability of polyphenols is crucial. The current strategies involve nanotechnology to improve the solubility and bioavailability, thus showing the potential to enhance the efficacy of polyphenols as therapeutics. Advancements in structural biology, computational modeling, and biophysics have provided insights into polyphenol–fibril interactions, offering hope for novel therapies for neurodegenerative diseases and amyloidosis. [ABSTRACT FROM AUTHOR]

Electronic characterization of bio-molecular nanoscale devices is important in the new edge of nanotechnology and the field of nanoelectronics. In this new era, the molecular transmission properties of the Adenine bio-molecular optical switch are predicted using Density Functional Theory along with Non-Equilibrium Green's Function-based First Principle approach and this phenomenon is supported with Machine Learning based algorithms. The photo-induced switching characteristics are observed for the bi-directional bio-molecular switch for both forward and reverse bias conditions. This switching behaviour converts the position of the bio-molecular switch to its straightened and 60° twisted form. The electrical doping process plays an important role in generating p and n regions at the two ends of the switch. In this experiment, gold electrodes are used as the supporting anchor of the Adenine molecules. The HOMO–LUMO gap and I–V characteristics of the bio-molecular switch are analyzed using first principle formalisms and compared with the Machine learning approach. This ML approach helps design the future-generation prediction model for the nano-scale electronic device simulation process. This prediction model can be obtained without knowing the switching characteristics and also without knowing all-time sequence generating waveforms but only observing the waveform prediction for up to a certain period sequence. [ABSTRACT FROM AUTHOR]

Indolino‐oxazolidine derivatives are a new and pretty confidential family of multimodal molecular switches. Indeed, acid, electrochemical potential, and UV light irradiation can be used to convert these compounds form their colorless closed form to a colorful open form. In this publication, we have investigated the influence of the extension of the π‐conjugated system beared by the indolino moiety on their halo‐, electro‐ and photochromic properties. In this context, we have demonstrated that only their photochemical properties are strongly affected by this structural modification. Moreover, quantum chemistry calculations have allowed to rationalize our experimental observations and, noticeably, evidenced an oxidative quenching process in presence of chlorobenzene, which enhances their photoreactivity. [ABSTRACT FROM AUTHOR]