RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures.

Recent advances in Cryo-EM led to a surge of ribosome structures deposited over the past years, including structures from different species, conformational states, or bound with different ligands. Yet, multiple conflicts of nomenclature make the identification and comparison of structures and ortholog components challenging. We present RiboXYZ (available at https://ribosome.xyz), a database that provides organized access to ribosome structures, with several tools for visualisation and study. The database is up-to-date with the Protein Data Bank (PDB) but provides a standardized nomenclature that allows for searching and comparing ribosomal components (proteins, RNA, ligands) across all the available structures. In addition to structured and simplified access to the data, the application has several specialized visualization tools, including the identification and prediction of ligand binding sites, and 3D superimposition of ribosomal components. Overall, RiboXYZ provides a useful toolkit that complements the PDB database, by implementing the current conventions and providing a set of auxiliary tools that have been developed explicitly for analyzing ribosome structures. This toolkit can be easily accessed by both experts and non-experts in structural biology so that they can search, visualize and compare structures, with various potential applications in molecular biology, evolution, and biochemistry.

Creative destruction: New protein folds from old.

Mechanisms of emergence and divergence of protein folds pose central questions in biological sciences. Incremental mutation and stepwise adaptation explain relationships between topologically similar protein folds. However, the universe of folds is diverse and riotous, suggesting more potent and creative forces are at play. Sequence and structure similarity are observed between distinct folds, indicating that proteins with distinct folds may share common ancestry. We found evidence of common ancestry between three distinct ß-barrel folds: Scr kinase family homology (SH3), oligonucleotide/oligosaccharide-binding (OB), and cradle loop barrel (CLB). The data suggest a mechanism of fold evolution that interconverts SH3, OB, and CLB. This mechanism, which we call creative destruction, can be generalized to explain many examples of fold evolution including circular permutation. In creative destruction, an open reading frame duplicates or otherwise merges with another to produce a fused polypeptide. A merger forces two ancestral domains into a new sequence and spatial context. The fused polypeptide can explore folding landscapes that are inaccessible to either of the independent ancestral domains. However, the folding landscapes of the fused polypeptide are not fully independent of those of the ancestral domains. Creative destruction is thus partially conservative; a daughter fold inherits some motifs from ancestral folds. After merger and refolding, adaptive processes such as mutation and loss of extraneous segments optimize the new daughter fold. This model has application in disease states characterized by genetic instability. Fused proteins observed in cancer cells are likely to experience remodeled folding landscapes and realize altered folds, conferring new or altered functions.

Vortex ring reconnections in elliptic Gaussian beams.

We study theoretically accessible optical vortex rings and their topological transformations in superpositions of elliptic and astigmatic Gaussian beams with a plane wave. We demonstrate the birth and death of vortex rings at isolated points on and off the optical axis and their pairwise and higher-order three- and four-ring reconnections.

Preparation of Langmuir-Blodgett Films from Quinoxalines Exhibiting Aggregation-Induced Emission and Their Acidochromism.

The development of aggregation-induced emission (AIE)-exhibiting compounds heavily relies on our evolving comprehension of their behavior at interfaces, an understanding that still remains notably limited. In this study, we explored the preparation of two-dimensional (2D) sensing films from 2,3-diphenylquinoxaline-based diazapolyoxa- and polyazamacrocycles displaying AIE via the Langmuir-Blodgett (LB) technique. This systematic investigation highlights the key role of the heteroatom-containing tether of 2,3-diphenylquinoxalines in the successful fabrication of Langmuir layers at the air-water interface and the transfer of AIE-emitting supramolecular aggregates onto solid supports. Using both diazapolyoxa- and polyazamacrocycles, we prepared AIE-exhibiting monolayer films containing emissive supramolecular aggregates on silica, mica, and quartz glass and characterized them using ultraviolet-visible (UV-vis) and photoluminescence (PL) spectroscopies, atomic force microscopy (AFM) imaging, and fluorescence microscopy. We also obtained multilayer AIE-emitting films through the LB technique, albeit with increased complexity. Remarkably, by employing the smallest macrocycle N2C3Q, we successfully prepared LB films suitable for the visual detection of acidic vapors. This sensing material, which contains a much lesser amount of organic dye compared with traditional drop-cast films, can be regenerated and utilized for real-life sample analysis, such as monitoring the presence of ammonia in the air and the freshness of meat.

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.

Phenoxaphosphonium Mixed Ylides in Ring Expansion Reaction.

Treatment of mixed phosphonium-iodonium ylides featuring a six-membered phenoxaphosphonium fragment with aqueous tetrafluoroboronic acid induces a rearrangement, resulting in expansion of the phosphacycle and oxidation of the phosphorus atom. The target difficult-to-access dibenzo[b,f][1,4]oxaphosphepine oxides (3 examples) were isolated in excellent yields (up to 95%) as mixtures of stereoisomers. Hydrolysis of a five-membered mixed ylide, a dibenzophosphole derivative, predominantly preserves the phosphole system with cycle expansion occurring as a side process.

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.

Quinoxaline-based azamacrocycles: synthesis, AIE behavior and acidochromism.

The development of luminescent molecular materials has advanced rapidly in recent decades, primarily driven by the synthesis of novel emissive compounds and a deeper understanding of excited-state mechanisms. Herein, we report a streamlined synthetic approach to light-emitting diazapolyoxa- and polyazamacrocycles N2CnOxQ and NyCnQ (n = 3-10; x = 2, 3; y = 2-5), incorporating a 2,3-diphenylquinoxaline residue (DPQ). This synthetic strategy based on macrocyclization through Pd-catalyzed amination reaction yields the target macrocycles in good or high yields (46-92%), enabling precise control over their structural parameters. A key role of the PhPF-tBu ligand belonging to the JosiPhos series in this macrocyclization was elucidated through DFT computation. This macrocyclization reaction eliminates the need for complex protecting-deprotecting procedures of secondary amine groups, offering a convenient and scalable method for the preparation of target compounds. Moreover, it boasts a potentially broad substrate scope, making it promising for structure-properties studies within photophysics, sensor development, and material synthesis. Photophysical properties of representative macrocycles were investigated, employing spectroscopic techniques and DFT computation. It was demonstrated that DPQ-containing macrocycles display aggregation-induced emission in a DCM-hexane solvent mixture despite the presence of flexible tethers within their structures. Single-crystal X-ray diffraction analysis of a representative compound N2C8O3Q allowed us to gain deeper insight into its molecular structure and AIE behaviour. The emissive aggregates of the N2C10O3Q macrocycle were immobilized on filter paper yielding AIE-exhibiting test strips for measuring acidity in vapors and in aqueous media.

Unveiling the electronic structure peculiarities of phosphine selenides as NMR probes for non-covalent interactions: an experimental and theoretical study.

In this work, R3PSe (R = Me, Et, n-Bu, t-Bu and Ph) were studied experimentally using NMR spectroscopy in solution and the solid-state in combinaton with quantum chemical methods. The study shows that the NMR parameters of these phosphine selenides, such as δP, δSe, and 1JPSe, are sensitive to subtle changes in the electronic environment of the P and Se atoms. Consequently, phosphine selenides R3PSe can serve as promising spectral probes for the detection and quantitative investigation of various non-covalent interactions. Additionally, the variations of R in phosphine selenides influence the observed NMR spectral parameters, primarily through effects such as π-backdonation and hyperconjugation, which have been observed experimentally and confirmed theoretically.

Searching for stable copper borozene complexes in CuB7- and CuB8.

Copper has been shown to be an important substrate for the growth of borophenes. Copper-boron binary clusters are ideal platforms to study the interactions between copper and boron, which may provide insight about the underlying growth mechanisms of borophene on copper substrates. Here we report a joint photoelectron spectroscopy and theoretical study on two copper-doped boron clusters, CuB7- and CuB8-. Well resolved photoelectron spectra are obtained for the two clusters at different wavelengths and are used to understand the structures and bonding properties of the two CuBn- clusters. We find that CuB8- is a highly stable borozene complex, which possesses a half-sandwich structure with a Cu+ species interacting with the doubly aromatic η8-B82- borozene. The CuB7- cluster is found to consist of a terminal copper atom bonded to a double-chain B7 motif, but it has a low-lying isomer composed of a half-sandwich structure with a Cu+ species interacting with an open-shell η7-B72- borozene. Both ionic and covalent interactions are found to be possible in the binary Cu-B clusters, resulting in different structures.

Kinetic features of solvent extraction by N,O-donor ligands of f-elements: a comparative study of diamides based on 1,10-phenanthroline and 2,2'-bipyridine.

A variant of microfluidic setup design for the study of extraction kinetics has been proposed. Mass transfer constants for Am(III) and Eu(III) and observed rate constants were obtained for N-,O-donor ligands featuring phenanthroline and bipyridyl cores. The possibility of determining rate constants for cations independently of each other makes it possible to observe the kinetic effect of separation. The extraction rate was found to be lower for the bipyridyl ligand, compared to phenanthroline. The values of the rotation barriers for the ligands were calculated using the DFT method. The values correlate with the obtained low extraction rate for the bipyridyl ligand. Also, crystallographic data showing anti-conformation for the bipyridyl ligand align with the kinetic data. Surface tension was also determined for the systems with the studied ligands. It is shown that at equal ligand concentrations, the value of surface tension agrees with the extraction rate. Furthermore, it is shown that for the bipyridyl ligand, prior contact of the organic phase with nitric acid significantly affects the surface tension.

Unique Role of Vimentin in the Intermediate Filament Proteins Family.

Intermediate filaments (IFs), being traditionally the least studied component of the cytoskeleton, have begun to receive more attention in recent years. IFs are found in different cell types and are specific to them. Accumulated data have shifted the paradigm about the role of IFs as structures that merely provide mechanical strength to the cell. In addition to this role, IFs have been shown to participate in maintaining cell shape and strengthening cell adhesion. The data have also been obtained that point out to the role of IFs in a number of other biological processes, including organization of microtubules and microfilaments, regulation of nuclear structure and activity, cell cycle control, and regulation of signal transduction pathways. They are also actively involved in the regulation of several aspects of intracellular transport. Among the intermediate filament proteins, vimentin is of particular interest for researchers. Vimentin has been shown to be associated with a range of diseases, including cancer, cataracts, Crohn's disease, rheumatoid arthritis, and HIV. In this review, we focus almost exclusively on vimentin and the currently known functions of vimentin intermediate filaments (VIFs). This is due to the structural features of vimentin, biological functions of its domains, and its involvement in the regulation of a wide range of basic cellular functions, and its role in the development of human diseases. Particular attention in the review will be paid to comparing the role of VIFs with the role of intermediate filaments consisting of other proteins in cell physiology.

rRNA expansion segment 7 in eukaryotes: from Signature Fold to tentacles.

The ribosomal core is universally conserved across the tree of life. However, eukaryotic ribosomes contain diverse rRNA expansion segments (ESs) on their surfaces. Sites of ES insertions are predicted from sites of insertion of micro-ESs in archaea. Expansion segment 7 (ES7) is one of the most diverse regions of the ribosome, emanating from a short stem loop and ranging to over 750 nucleotides in mammals. We present secondary and full-atom 3D structures of ES7 from species spanning eukaryotic diversity. Our results are based on experimental 3D structures, the accretion model of ribosomal evolution, phylogenetic relationships, multiple sequence alignments, RNA folding algorithms and 3D modeling by RNAComposer. ES7 contains a distinct motif, the 'ES7 Signature Fold', which is generally invariant in 2D topology and 3D structure in all eukaryotic ribosomes. We establish a model in which ES7 developed over evolution through a series of elementary and recursive growth events. The data are sufficient to support an atomic-level accretion path for rRNA growth. The non-monophyletic distribution of some ES7 features across the phylogeny suggests acquisition via convergent processes. And finally, illustrating the power of our approach, we constructed the 2D and 3D structure of the entire LSU rRNA of Mus musculus.

Mono- and bis(steroids) containing a cyclooctane core: Synthesis, antiproliferative activity, and action on cell cytoskeleton microtubules.

Steroid dimers of natural and synthetic origin possess an unusual and complex molecular architecture that may lead to the realization of peculiar effects in biological systems, in particular in different cancer cell lines. In the present work, diastereoselective ring-opening of mono- and polyoxiranes, containing a cyclooctane core, by azide-anion was performed to yield a series of azidoalcohols with different types of symmetry. The products were involved in copper-catalyzed azyde-alkyne cycloaddition (CuAAC) reaction with ethinylestradiol and ethinyltestosterone, and the resulting steroids and steroid dimers with triazole linkers were screened for their antiproliferative activity via (3-(4,5-dimethylthiazol-2-yl)2,5-diphenyl tetrazolium bromide) assay. All the compounds revealed cytotoxicity toward several cancer cell lines. The effect of the most potent compound, containing two estradiol moieties, on the microtubules (MT) dynamics was investigated by immunofluorescent microscopy. The disruption of the majority of interphase cell cytoplasmic MT and mitotic event disturbances in the presence of the studied compound were observed. The latter effect caused the appearance of numerous multinucleated cells.

One-Pot Synthesis of Affordable Redox-Responsive Drug Delivery System Based on Trithiocyanuric Acid Nanoparticles.

Redox-responsive drug delivery systems present a promising avenue for drug delivery due to their ability to leverage the unique redox environment within tumor cells. In this work, we describe a facile and cost-effective one-pot synthesis method for a redox-responsive delivery system based on novel trithiocyanuric acid (TTCA) nanoparticles (NPs). We conduct a thorough investigation of the impact of various synthesis parameters on the morphology, stability, and loading capacity of these NPs. The great drug delivery potential of the system is further demonstrated in vitro and in vivo by using doxorubicin as a model drug. The developed TTCA-PEG NPs show great drug delivery efficiency with minimal toxicity on their own both in vivo and in vitro. The simplicity of this synthesis, along with the promising characteristics of TTCA-PEG NPs, paves the way for new opportunities in the further development of redox-responsive drug delivery systems based on TTCA.

Molecular Insights into Adhesion at Interface of Geopolymer Binder and Cement Mortar.

The degradation of concrete and reinforced concrete structures is a significant technical and economic challenge, requiring continuous repair and rehabilitation throughout their service life. Geopolymers (GPs), known for their high mechanical strength, low shrinkage, and durability, are being increasingly considered as alternatives to traditional repair materials. However, there is currently a lack of understanding regarding the interface bond properties between new geopolymer layers and old concrete substrates. In this paper, using advanced computational techniques, including quantum mechanical calculations and stochastic modeling, we explored the adsorption behavior and interaction mechanism of aluminosilicate oligomers with different Si/Al ratios forming the geopolymer gel structure and calcium silicate hydrate as the substrate at the interface bond region. We analyzed the electron density distributions of the highest occupied and lowest unoccupied molecular orbitals, examined the reactivity indices based on electron density functional theory, performed Mulliken charge population analysis, and evaluated global reactivity descriptors for the considered oligomers. The results elucidate the mechanisms of local and global reactivity of the oligomers, the equilibrium low-energy configurations of the oligomer structures adsorbed on the surface of C-(A)-S-H(I) (100), and their adsorption energies. These findings contribute to a better understanding of the adhesion properties of geopolymers and their potential as effective repair materials.

Expression features of T-lymphocytes, B-lymphocytes and macrophages in the post-traumatic regenerate of the mandible rats under conditions of filling a bone defect with hydroxyapatite-containing osteotropic material and thymalin injecting the surrounding soft tissues.

OBJECTIVE: Aim: The purpose of the study was to determine the features of the expression of T-lymphocytes, B-lymphocytes, macrophages in the post-traumatic regenerate of the mandible rats under conditions of filling a bone defect with hydroxyapatite-containing osteotropic material and thymalin injecting the surrounding soft tissues. PATIENTS AND METHODS: Materials and Methods: An experiment was conducted on 48 mature rats of the WAG population weighing 160-180 grams. Four groups were formed. Group 1 included 12 rats with a simulated holey defect in the lower jaw. Group 2 included 12 rats with a simulated holey defect in the lower jaw followed by its closure with hydroxyapatite-containing osteotropic material (bone graft "Biomin GT"). Group 3 included 12 rats with a simulated holey defect in the lower jaw with injecting the surrounding soft tissues with thymalin. Group 4 included 12 rats with a simulated holey defect in the lower jaw followed by its closure with hydroxyapatite-containing osteotropic material (bone graft "Biomin GT") and injecting the surrounding soft tissues with thymalin. The material for the morphological study was a fragment of the lower jaw from the area of the simulated holey defect. An immunohistochemical study was aperformed using monoclonal antibodies to CD68, CD20, CD163, CD86, CD3. RESULTS: Results: A comprehensive experimental and morphological study conducted by the authors revealed that thymalin injection of the soft tissues surrounding the bone defect of the lower jaw, filled with hydroxyapatite-containing osteotropic material "Biomin GT", stimulates local immune reactions in the post-traumatic regenerate, which is manifested, firstly, by an increase in the number T-lymphocytes on the 3rd day of the experiment and their increase up to the 28th day; secondly, by increasing the number of B-lymphocytes on the 14th day of the experiment with their further increase up to the 28th day; thirdly, by increasing the number of macrophages on the 3rd day of the experiment and their growth up to the 28th day; fourth, changes in macrophages phenotypes (decrease in the number of M1-macrophages and increase in the number of M2-macrophages). CONCLUSION: Conclusions: Stimulation of local immune reactions in the post-traumatic regenerate can be one of the mechanisms that activate reparative osteogenesis in the lower jaw of rats under the conditions of filling bone defects with hydroxyapatite-containing osteotropic material "Biomin GT" and thymalin injecting the surrounding soft tissues.

TCR-Pred: A new web-application for prediction of epitope and MHC specificity for CDR3 TCR sequences using molecular fragment descriptors.

The search for the relationships between CDR3 TCR sequences and epitopes or MHC types is a challenging task in modern immunology. We propose a new approach to develop the classification models of structure-activity relationships (SAR) using molecular fragment descriptors MNA (Multilevel Neighbourhoods of Atoms) to represent CDR3 TCR sequences and the naïve Bayes classifier algorithm. We have created the freely available TCR-Pred web application (http://way2drug.com/TCR-pred/) to predict the interactions between α chain CDR3 TCR sequences and 116 epitopes or 25 MHC types, as well as the interactions between ß chain CDR3 TCR sequences and 202 epitopes or 28 MHC types. The TCR-Pred web application is based on the data (more 250 000 unique CDR3 TCR sequences) from VDJdb, McPAS-TCR, and IEDB databases and the proposed approach. The average AUC values of the prediction accuracy calculated using a 20-fold cross-validation procedure varies from 0.857 to 0.884. The created web application may be useful in studies related with T-cell profiling based on CDR3 TCR sequences.

Multilevel selection in the evolution of sexual dimorphism in phenotypic plasticity.

Phenotypes are partly shaped by the environment, which can impact both short-term adaptation and long-term evolution. In dioecious species, the two sexes may exhibit different degrees of phenotypic plasticity and theoretical models indicate that such differences may confer an adaptive advantage when the population is subject to directional selection, either because of a systematically varying environment or a load of deleterious mutations. The effect stems from the fundamental asymmetry between the two sexes: female fertility is more limited than male fertility. Whether this asymmetry is sufficient for sexual dimorphism in phenotypic plasticity to evolve is, however, not obvious. Here, we show that even in conditions where it provides an adaptive advantage, dimorphic phenotypic plasticity may be evolutionarily unstable due to sexual selection. This is the case, in particular, for panmictic populations where mating partnerships are formed at random. However, we show that the effects of sexual selection can be counteracted when mating occurs within groups of related individuals. Under this condition, sexual dimorphism in phenotypic plasticity can not only evolve but offset the twofold cost of males. We demonstrate these points with a simple mathematical model through a combination of analytical and numerical results.

Vortex rings in paraxial laser beams.

Interference of a fundamental vortex-free Gaussian beam with a co-propagating plane wave leads to nucleation of a series of vortex rings in the planes transverse to the optical axis; the number of rings grows with vanishing amplitude of the plane wave. In contrast, such interference with a beam carrying on-axis vortex with winding number l results in the formation of |l| rings elongated and gently twisted in propagation direction. The twist handedness of the vortex lines is determined by the interplay between dynamic and geometric phases of the Gaussian beam and the twist angle grows with vanishing amplitude of the plane wave. In the counter-propagating geometry the vortex rings nucleate and twist with half-wavelength period dominated by the interference grating in propagation direction.