Natural photoreceptors as a source of fluorescent proteins, biosensors, and optogenetic tools.

Genetically encoded optical tools have revolutionized modern biology by allowing detection and control of biological processes with exceptional spatiotemporal precision and sensitivity. Natural photoreceptors provide researchers with a vast source of molecular templates for engineering of fluorescent proteins, biosensors, and optogenetic tools. Here, we give a brief overview of natural photoreceptors and their mechanisms of action. We then discuss fluorescent proteins and biosensors developed from light-oxygen-voltage-sensing (LOV) domains and phytochromes, as well as their properties and applications. These fluorescent tools possess unique characteristics not achievable with green fluorescent protein-like probes, including near-infrared fluorescence, independence of oxygen, small size, and photosensitizer activity. We next provide an overview of available optogenetic tools of various origins, such as LOV and BLUF (blue-light-utilizing flavin adenine dinucleotide) domains, cryptochromes, and phytochromes, enabling control of versatile cellular processes. We analyze the principles of their function and practical requirements for use. We focus mainly on optical tools with demonstrated use beyond bacteria, with a specific emphasis on their applications in mammalian cells.

The structure and regulation of human muscle α-actinin.

The spectrin superfamily of proteins plays key roles in assembling the actin cytoskeleton in various cell types, crosslinks actin filaments, and acts as scaffolds for the assembly of large protein complexes involved in structural integrity and mechanosensation, as well as cell signaling. α-actinins in particular are the major actin crosslinkers in muscle Z-disks, focal adhesions, and actin stress fibers. We report a complete high-resolution structure of the 200 kDa α-actinin-2 dimer from striated muscle and explore its functional implications on the biochemical and cellular level. The structure provides insight into the phosphoinositide-based mechanism controlling its interaction with sarcomeric proteins such as titin, lays a foundation for studying the impact of pathogenic mutations at molecular resolution, and is likely to be broadly relevant for the regulation of spectrin-like proteins.

Advances in methods for tRNA sequencing and quantification.

In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows. Other approaches forgo NGS applications in favor of hybridization-based approaches. In this review we provide a brief comparative overview of various tRNA quantification approaches, focusing on the advantages and disadvantages of these methods, which together facilitate reliable tRNA quantification.

Functions of unconventional mammalian translational GTPases GTPBP1 and GTPBP2.

GTP-binding protein 1 (GTPBP1) and GTPBP2 comprise a divergent group of translational GTPases with obscure functions, which are most closely related to eEF1A, eRF3, and Hbs1. Although recent reports implicated GTPBPs in mRNA surveillance and ribosome-associated quality control, how they perform these functions remains unknown. Here, we demonstrate that GTPBP1 possesses eEF1A-like elongation activity, delivering cognate aminoacyl-transfer RNA (aa-tRNA) to the ribosomal A site in a GTP-dependent manner. It also stimulates exosomal degradation of mRNAs in elongation complexes. The kinetics of GTPBP1-mediated elongation argues against its functioning in elongation per se but supports involvement in mRNA surveillance. Thus, GTP hydrolysis by GTPBP1 is not followed by rapid peptide bond formation, suggesting that after hydrolysis, GTPBP1 retains aa-tRNA, delaying its accommodation in the A site. In physiological settings, this would cause ribosome stalling, enabling GTPBP1 to elicit quality control programs; e.g., by recruiting the exosome. GTPBP1 can also deliver deacylated tRNA to the A site, indicating that it might function via interaction with deacylated tRNA, which accumulates during stresses. Although GTPBP2's binding to GTP was stimulated by Phe-tRNAPhe, suggesting that its function might also involve interaction with aa-tRNA, GTPBP2 lacked elongation activity and did not stimulate exosomal degradation, indicating that GTPBP1 and GTPBP2 have different functions.

A Unique ISR Program Determines Cellular Responses to Chronic Stress.

The integrated stress response (ISR) is a homeostatic mechanism induced by endoplasmic reticulum (ER) stress. In acute/transient ER stress, decreased global protein synthesis and increased uORF mRNA translation are followed by normalization of protein synthesis. Here, we report a dramatically different response during chronic ER stress. This chronic ISR program is characterized by persistently elevated uORF mRNA translation and concurrent gene expression reprogramming, which permits simultaneous stress sensing and proteostasis. The program includes PERK-dependent switching to an eIF3-dependent translation initiation mechanism, resulting in partial, but not complete, translational recovery, which, together with transcriptional reprogramming, selectively bolsters expression of proteins with ER functions. Coordination of transcriptional and translational reprogramming prevents ER dysfunction and inhibits "foamy cell" development, thus establishing a molecular basis for understanding human diseases associated with ER dysfunction.

Transition metal dichalcogenide nanospheres for high-refractive-index nanophotonics and biomedical theranostics.

Recent developments in the area of resonant dielectric nanostructures have created attractive opportunities for concentrating and manipulating light at the nanoscale and the establishment of the new exciting field of all-dielectric nanophotonics. Transition metal dichalcogenides (TMDCs) with nanopatterned surfaces are especially promising for these tasks. Still, the fabrication of these structures requires sophisticated lithographic processes, drastically complicating application prospects. To bridge this gap and broaden the application scope of TMDC nanomaterials, we report here femtosecond laser-ablative fabrication of water-dispersed spherical TMDC (MoS2 and WS2) nanoparticles (NPs) of variable size (5 to 250 nm). Such NPs demonstrate exciting optical and electronic properties inherited from TMDC crystals, due to preserved crystalline structure, which offers a unique combination of pronounced excitonic response and high refractive index value, making possible a strong concentration of electromagnetic field in the NPs. Furthermore, such NPs offer additional tunability due to hybridization between the Mie and excitonic resonances. Such properties bring to life a number of nontrivial effects, including enhanced photoabsorption and photothermal conversion. As an illustration, we demonstrate that the NPs exhibit a very strong photothermal response, much exceeding that of conventional dielectric nanoresonators based on Si. Being in a mobile colloidal state and exhibiting superior optical properties compared to other dielectric resonant structures, the synthesized TMDC NPs offer opportunities for the development of next-generation nanophotonic and nanotheranostic platforms, including photothermal therapy and multimodal bioimaging.

Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages.

Mouse (Mus musculus) models have been heavily utilized in developmental biology research to understand mammalian embryonic development, as mice share many genetic, physiological, and developmental characteristics with humans. New explorations into the integration of temporal (stage-specific) and transcriptional (tissue-specific) data have expanded our knowledge of mouse embryo tissue-specific gene functions. To better understand the substantial impact of synonymous mutational variations in the cell-state-specific transcriptome on a tissue's codon and codon pair usage landscape, we have established a novel resource-Mouse Embryo Codon and Codon Pair Usage Tables (Mouse Embryo CoCoPUTs). This webpage not only offers codon and codon pair usage, but also GC, dinucleotide, and junction dinucleotide usage, encompassing four strains, 15 murine embryonic tissue groups, 18 Theiler stages, and 26 embryonic days. Here, we leverage Mouse Embryo CoCoPUTs and employ the use of heatmaps to depict usage changes over time and a comparison to human usage for each strain and embryonic time point, highlighting unique differences and similarities. The usage similarities found between mouse and human central nervous system data highlight the translation for projects leveraging mouse models. Data for this analysis can be directly retrieved from Mouse Embryo CoCoPUTs. This cutting-edge resource plays a crucial role in deciphering the complex interplay between usage patterns and embryonic development, offering valuable insights into variation across diverse tissues, strains, and stages. Its applications extend across multiple domains, with notable advantages for biotherapeutic development, where optimizing codon usage can enhance protein expression; one can compare strains, tissues, and mouse embryonic stages in one query. Additionally, Mouse Embryo CoCoPUTs holds great potential in the field of tissue-specific genetic engineering, providing insights for tailoring gene expression to specific tissues for targeted interventions. Furthermore, this resource may enhance our understanding of the nuanced connections between usage biases and tissue-specific gene function, contributing to the development of more accurate predictive models for genetic disorders.

The effect of linker conformation on performance and stability of a two-domain lytic polysaccharide monooxygenase.

A considerable number of lytic polysaccharide monooxygenases (LPMOs) and other carbohydrate-active enzymes are modular, with catalytic domains being tethered to additional domains, such as carbohydrate-binding modules, by flexible linkers. While such linkers may affect the structure, function, and stability of the enzyme, their roles remain largely enigmatic, as do the reasons for natural variation in length and sequence. Here, we have explored linker functionality using the two-domain cellulose-active ScLPMO10C from Streptomyces coelicolor as a model system. In addition to investigating the WT enzyme, we engineered three linker variants to address the impact of both length and sequence and characterized these using small-angle X-ray scattering, NMR, molecular dynamics simulations, and functional assays. The resulting data revealed that, in the case of ScLPMO10C, linker length is the main determinant of linker conformation and enzyme performance. Both the WT and a serine-rich variant, which have the same linker length, demonstrated better performance compared with those with either a shorter linker or a longer linker. A highlight of our findings was the substantial thermostability observed in the serine-rich variant. Importantly, the linker affects thermal unfolding behavior and enzyme stability. In particular, unfolding studies show that the two domains unfold independently when mixed, whereas the full-length enzyme shows one cooperative unfolding transition, meaning that the impact of linkers in biomass-processing enzymes is more complex than mere structural tethering.

Synthesis and antiproliferative activity of cisplatin-3-chloropiperidine conjugates.

We report the synthesis and characterization of two novel cisplatin- alkylating agents conjugates. Combining a platinum based cytostatic agent with a sterically demanding alkylating agent could potentially induce further DNA damage, block cell repair mechanisms and keep the substrate active against resistant tumor cell lines. The 3-chloropiperidines utilized as ligands in this work are cyclic representatives of the N-mustard family and were not able to coordinate platinum on their own. The introduction of a second coordination site, in form of a pyridine moiety, led to the isolation of the desired conjugates. They were characterized with HRMS, CHN-analyses and XRD. We concluded this work by examining the cytotoxicity of the ligands and the obtained complexes with MTT assays in human cancer cell lines. While the ligands showed hardly any activity, the novel conjugates both displayed a high antiproliferative and cytotoxic potency in a panel of three cell lines. Moreover, both complexes were able to largely circumvent the acquired cisplatin resistance of A2780cisR ovarian cancer cells, both in the MTT assay and a flow-cytometric apoptosis assay.

Exploration of Vitamin B6-Based Redox-Active Pyridinium Salts Towards the Application in Aqueous Organic Flow Batteries.

Pyridoxal hydrochloride, a vitamin B6 vitamer, was synthetically converted to a series of diverse redox-active benzoyl pyridinium salts. Cyclic voltammetry studies demonstrated redox reversibility under basic conditions, and two of the most promising salts were subjected to laboratory-scale flow battery tests involving galvanostatic cycling at 10 mM in 0.1 M NaOH. In these tests, the battery was charged completely, corresponding to the transfer of two electrons to the electrolyte, but no discharge was observed. Both CV analysis and electrochemical simulations confirmed that the redox wave observed in the experimental voltammograms corresponds to a two-electron process. To explain the irreversibility in the battery tests, we conducted bulk electrolysis with the benzoyl pyridinium salts, affording the corresponding benzylic secondary alcohols. Computational studies suggest that the reduction proceeds in three consecutive steps: first electron transfer (ET), then proton-coupled electron transfer (PCET) and finally proton transfer (PT) to give the secondary alcohol. 1H NMR deuterium exchange studies indicated that the last PT step is not reversible in 0.1 M NaOH, rendering the entire redox process irreversible. The apparent reversibility observed in CV at the basic media likely arises from the slow rate of the PT step at the timescale of the measurement.

Pore-Fiber Transport Dynamics of Aqueous Cosolvent Solutions in Paper.

After inkjet printing onto uncoated and unsized paper, the ink is first imbibed into the interfiber pores and subsequently absorbed by the cellulose fibers. The achievable print quality depends on the rate of this pore-fiber transport. The latter is accompanied by mechanical expansion of the fibers and the paper sheet. Therefore, we systematically monitored the swelling dynamics of several paper types as a function of ink composition by means of four different measurement techniques. Using aqueous cosolvent solutions as model inks, we found an approximately exponential relation of the time scales of pore-fiber transport with the cosolvent concentration and an approximately linear relation with its molecular weight. Addition of surfactants can substantially speed-up pore-fiber transport.

Photoredox Activation of Fluorinated Organozinc Reagents: Hydrofluoroalkylation of Unactivated and Electron Deficient Alkenes.

Hydrofluoroalkylation of alkenes with organozinc reagents under photocatalytic conditions is described. The fluorinated alkyl radicals were generated from organozincs by the single electron oxidation of the carbon-zinc bond. The radical addition step is followed either by hydrogen atom transfer for unactivated olefins or by a reduction/protonation sequence for strongly accepting arylidenemalononitriles.

Oxidative Transformation of 2-Furylanilines into Indolin-3-ones.

Oxidation of 2-furylaninlies with m-CPBA followed by treatment with a base provides access to functionalized indolin-3-ones. The designed oxidative transformation utilizes an underassessed chemical behavior of furyl-containing amines to form a C-N bond via engaging a ß-carbon atom of the furan core upon a ring-forming step, thereby providing an alternative disconnection toward nitrogen-containing heterocycles.

Introduction of Niobium in the Chemistry of Octahedral Chalcogenide Clusters: Synthesis and Detailed Study of Compounds Based on Condensed and Discrete {Re5NbQ8} (Q = S or Se) Cores.

It is known that niobium practically does not form cluster chalcogenide compounds of the {M6(µ3-Q8)} type, which are widespread in the chemistry of group 6 and 7 metals. This work reports the preparation of a series of polymeric and discrete niobium-containing heterometallic clusters based on the {Re5Nb(µ3-S8)} and {Re5Nb(µ3-Se8)} cores. The compounds were prepared by the high-temperature reaction between rhenium and niobium dichalcogenides in a KCN melt. The 1D polymers K5[Re5NbQ8(CN)5] (Q = S or Se), which were formed as a result of the reaction, crystallize in the structural type of K6[Mo6Se8(CN)5], similar to the previously reported heterometallic clusters K6[Re6-xMoxQ8(CN)5] (x = 2-3). The polymers were solubilized to form discrete anionic clusters [Re5NbQ8(CN)6]4-. The structure and properties of the new clusters were investigated using a combination of X-ray diffraction analysis, UV/vis spectroscopy, high-resolution electrospray mass spectrometry, cyclic voltammetry, and DFT calculations. Among other features, the compounds showed high electrochemical activity, being able to form three redox states in solution with reversible transitions. It was found that redox potentials of the isoelectronic octahedral clusters demonstrate a strong cathodic shift in the sequence [Re5OsSe8(CN)6]3- > [Re6Se8(CN)6]4- > [Re5MoSe8(CN)6]5- > [Re5NbSe8(CN)6]6-, illustrating the effect of systematic changes in the composition of octahedral cluster cores on their properties.

Understanding Alkene Interaction with Metal-Modified Zeolites: Thermodynamics and Mechanism of Bonding in the π-Complex.

Zeolites modified with metal cations are perspective catalysts for converting light alkenes to valuable chemicals. A crucial step of the transformation is an alkene interaction with zeolite to afford π-complex with metal cations. The mechanism of alkene bonding with cations is still unclear. To address this problem, propene adsorption on H+ (BroÌ·nsted acid site), Na+, Ca2+, Zn2+, Co2+, Cu2+, Cu+, and Ag+ cationic sites in ZSM-5 zeolite has been studied by quantum chemical calculations in terms of adsorption enthalpy, νC═C frequency, and natural bond orbital (NBO) analysis together with natural energy decomposition analysis (NEDA). It is revealed that the conventional concept of σ- and π-bonding is only partially applicable to alkene interaction with metal cations in zeolites. The orbital interaction between an alkene molecule and a metal site is more complex. Several different bonding mechanisms have been identified depending on the nature and electron configuration of the metal cation. This finding explains the complex correlations observed for propene π-complex stability and νC═C frequency shift or charge transfer from the alkene molecule. The results provide the basis for further understanding the interactions between alkenes and inorganic solid BroÌ·nsted and Lewis acids.

Exploring the Frontiers of Heterometallic Systems: the {FeW5} Octahedral Cluster Complex.

This research presents the first examples of heterometallic octahedral cluster complexes incorporating both 5d and 3d metals, specifically, tungsten and iron. The key compound, (TBA)2[FeW5Br14] (TBA = tetrabutylammonium), exhibits selective ligand substitution reactions at the iron site when exposed to various solvents. Several {FeW5}-type anions, namely, [FeW5Br14]2-, [FeW5Br13(L)]- (L = H2O, DMSO, CH3CN), and [(FeW5Br13)2O]4-, were revealed and characterized by single-crystal X-ray diffraction analysis. The redox properties of [FeW5Br14]2- were studied and compared with those of [W6Br14]2-. Density functional theory calculations demonstrated that the bonding between Fe and W atoms is fundamentally different from the bonding between 4d (Mo-Mo) or 5d (W-W) metals in isotypic {M6} clusters.

Catalyst- and solvent-free regiospecific SNHAr phosphinylation of pyridines with H-phosphinates mediated by benzoylphenylacetylene.

Pyridines undergo a facile SNHAr phosphinylation with H-phosphinates under catalyst- and solvent-free conditions (50-55 °C) in the presence of benzoylphenylacetylene to afford 4-phosphinylpyridines in up to 68% yield. In this reaction, benzoylphenylacetylene activates the pyridine ring by the formation of a 1,3(4)-dipolar complex, deprotonates H-phosphinates to generate P-centered anions and finally acts as an oxidizer, being eliminated from an intermediate ion pair. Terminal electron-deficient acetylenes (methyl propiolate and benzoylacetylene) are inefficient as mediators in the above SNHAr process.

Application of the intramolecular Diels-Alder vinylarene (IMDAV) reaction for the synthesis of benzo-, carbocyclo-, thienothiopheneisoindolecarboxylic acids and its limitations.

Thienylallylamines, readily accessible from the corresponding thienyl aldehydes, react with maleic and trifluoromethylmaleic anhydrides leading to the formation of acids with a thieno[2,3-f]isoindole core. The reaction sequence involves two successive steps: acylation of the nitrogen atom of the initial allylamine and the intramolecular Diels-Alder vinylarene (IMDAV) reaction. The scope and limitations of the proposed method were thoroughly investigated. It has been revealed with the aid of X-ray analysis and DFT calculations that the key step, the IMDAV reaction, proceeds through an exo-transition state, giving rise to the exclusive formation of a single diastereomer of the target heterocycle. The obtained functionally substituted thieno[2,3-f]isoindole carboxylic acids are potentially useful substrates for further transformations and bioscreening. The antimicrobial evaluation of the obtained compounds revealed that 1-oxo-2-(3-(trifluoromethyl)phenyl)hexahydrobenzo[4,5]thieno[2,3-f]isoindole-10-carboxylic acid is the most active sample in the synthesized library. It exhibits antibacterial activity against sensitive strains of Gram-positive bacteria, including S. aureus, Enterococcus faecium, Bacillus cereus, and Micrococcus luteus, as well as the Gram-negative bacteria E. coli and Pseudomonas fluorescens, with MIC values ranging from 4 to 64 µg mL-1. 9-Oxo-8-phenyloctahydronaphtho[2,1-d]thieno[2,3-f]isoindole-10-carboxylic acid showed antifungal activity against yeast culture C. albicans with a MIC value of 32 µM.

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations.

In all genomes, most amino acids are encoded by more than one codon. Synonymous codons can modulate protein production and folding, but the mechanism connecting codon usage to protein homeostasis is not known. Here we show that synonymous codon variants in the gene encoding gamma-B crystallin, a mammalian eye-lens protein, modulate the rates of translation and cotranslational folding of protein domains monitored in real time by Förster resonance energy transfer and fluorescence-intensity changes. Gamma-B crystallins produced from mRNAs with changed codon bias have the same amino acid sequence but attain different conformations, as indicated by altered in vivo stability and in vitro protease resistance. 2D NMR spectroscopic data suggest that structural differences are associated with different cysteine oxidation states of the purified proteins, providing a link between translation, folding, and the structures of isolated proteins. Thus, synonymous codons provide a secondary code for protein folding in the cell.

Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses.

During packaging in positive-sense single-stranded RNA (+ssRNA) viruses, coat proteins (CPs) interact directly with multiple regions in genomic RNA (gRNA), but the underlying physicochemical principles remain unclear. Here we analyze the high-resolution cryo-EM structure of bacteriophage MS2 and show that the gRNA/CP binding sites, including the known packaging signal, overlap significantly with regions where gRNA nucleobase-density profiles match the corresponding CP nucleobase-affinity profiles. Moreover, we show that the MS2 packaging signal corresponds to the global minimum in gRNA/CP interaction energy in the unstructured state as derived using a linearly additive model and knowledge-based nucleobase/amino-acid affinities. Motivated by this, we predict gRNA/CP interaction sites for a comprehensive set of 1082 +ssRNA viruses. We validate our predictions by comparing them with site-resolved information on gRNA/CP interactions derived in SELEX and CLIP experiments for 10 different viruses. Finally, we show that in experimentally studied systems CPs frequently interact with autologous coding regions in gRNA, in agreement with both predicted interaction energies and a recent proposal that proteins in general tend to interact with own mRNAs, if unstructured. Our results define a self-consistent framework for understanding packaging in +ssRNA viruses and implicate interactions between unstructured gRNA and CPs in the process.