For the first time asymmetric and symmetric carboxytriazoleimidazolium derivatives with different structures were synthesized. The critical micellization concentration (CMC) value was estimated using a pyrene fluorescent probe and the solubility of Orange OT. The complexation ability of carboxytriazoleimidazolium derivatives toward bovine serum albumin (BSA) has been investigated by various physico-chemical methods: fluorescence spectroscopy, electrophoretic light scattering and circular dichroism. The effect of the oxo-bridge and the presence of a hydrophobic fragment in the structure of the molecules and its influence on their aggregation properties and interaction with BSA has also been studied. According to the fluorescence data, only in the case of the asymmetric derivatives with long alkyl fragments a shift of the BSA emission maximum is observed, indicating a change in the BSA microenvironment. The secondary structure of BSA remains virtually unchanged in the presence of carboxytriazoleimidazolium derivatives, as shown by circular dichroism. No significant changes in the structure of BSA were observed in the presence of zwitterionic compounds with an oxo-bridge at concentrations where fluorescence quenching occurs, as shown by time-resolved fluorescence measurements. Electrophoretic light scattering showed a recharging of BSA from a negative to a positive zeta potential in the presence of amphiphilic derivatives.

We announce call for papers for a Special Issue of Biophysical Reviews associated with the Russian Autumn School in Biophysics held in Kazan, Russia, 11–14 November 2024. The autumn school was focused on modern biophysical methods and approaches to study living and model biological systems. It was the most important biophysical meeting within 2024 in Russia, organized for the first time with perspectives to make it regular. The Special Issue accepts reviews on comprehensive analysis of experimental and computational methods currently used to study the dynamical structure of biological systems at all levels of living matter organization—from submolecular, molecular and supramolecular model systems to cells and whole organisms. Here, we describe main themes and sections, types of papers and key dates for the journal issue.

Overall, the school collected presentations on molecular biophysics and experimental techniques, addressed major unresolved challenges in the field, and shared an overall perspective on future directions that might help to clarify the important questions that emerged during the last decade of intensive research. To conclude, we note growing interest in AI applications for biophysical modeling, new physical experimental techniques such as cryo-microscopy, applications of modeling in pharmaceutical research, and drug design. We believe this special journal issue will be of interest to readers.

ABSTRACT The macrolide antibiotic, macrolactin A (McA), has been known for its antimicrobial properties since the late 1980s, but the mechanism of its antibacterial activity is still unknown. In this study, we investigated the microbiological and molecular characteristics of McA antimicrobial activity. McA effect on bacteria was found to be both bacteriostatic and bactericidal, depending on species and strains. Regarding the mechanism of action of McA, the following important results were obtained: 1) using in vivo and in vitro systems, we showed that McA is an inhibitor of protein synthesis in bacteria; 2) the concentration of McA required to inhibit protein synthesis in the E. coli cell-free model was found to be 50 times lower than the concentration required in the S. aureus cell-free model; 3) the toe-printing assay revealed that McA inhibits the first step of elongation stage of protein synthesis; 4) we identified single and multiple nucleotide polymorphisms in the gene encoding the translation elongation factor Tu (EF-Tu) by annotating the genomes of McA-resistant Bacillus pumilus McA R and its parental strain. Molecular modeling showed that the McA molecule can form non-covalent bonds with amino acids at the interface of domains 1 and 2 of EF-Tu, characterized by a relatively high docking score. Overall, our study demonstrated that McA acts as an elfamycin-like antibiotic (targeting EF-Tu), addressing a substantial gap in our understanding of the mechanism of action of macrolactin A, a representative member of macrolides.

The barrier to rotation of the unsubstituted cyclopentadienyl (Cp) ring in the crystal of rac-N, N-dimethyl-1-ferrocenylethylamine (Ugi’s amine) hydrobenzoate was investigated using a combination of density functional theory (DFT) calculations and variable-temperature single-crystal X-ray diffraction (SC XRD). The gas-phase rotational barrier was determined to be 4.2 kJ/mol, which is comparable to that of unsubstituted ferrocene, indicating a negligible effect of the N, N-dimethyl-1-ferrocenylethylammonium substituent on the intramolecular barrier. In contrast, the experimental barrier in the crystalline state, derived from TLS analysis of anisotropic displacement parameters over a temperature range of 150–300 K, was significantly higher, ranging from 8.8 to 10.8 kJ/mol. This increase provides direct evidence for the dominant role of intermolecular interactions, specifically C–H···O and C–H···π contacts, in restricting Cp-ring rotation in the solid state. The obtained barrier values are consistent with those classified as Case I (molecules in general positions), and this study underscores the efficacy of variable-temperature SC XRD coupled with TLS analysis for quantifying molecular dynamics, such as ligand rotation, in molecular crystals.

The YsxC protein from Staphylococcus aureus is a GTP-binding protein from the TRAFAC superfamily of the TrmE-Era-EngA-EngB-Septin-like GTPase class, EngB family of GTPases. Recent structural and biochemical studies of YsxC function show that it is an integral part of the pathogenic microorganism life cycle, as it is involved in the assembly of the large 50S ribosomal subunit. Structural studies of this protein with its specific functional features make it an attractive target for further development of new selective antimicrobials. In this study, we cloned the ysxC protein gene from S. aureus, overexpressed the protein in E. coli, and subsequently purified and crystallized it. Protein crystals were successfully grown using the vapor diffusion method, yielding diffraction data with a resolution of up to 2 Å. Comparative analysis of the structure of SaYsxC with known three-dimensional structures of homologs from other microorganisms showed the presence of structural differences for the apo form.

Triazole derivatives of fluorescein-containing N,N-dimethylaminopropyl fragments and their ammonium salts were synthesized with yields of 74–85%. The resulting compounds exhibit fluorescent properties in the green region of the visible spectrum. The critical aggregation concentration (CAC) was estimated using a pyrene fluorescent probe corresponding to a range of 0.28–1.43 mM, and at concentrations above the CAC, the compounds form stable aggregates ranging from 165 to 202 nm. A relative quantum yield of 5–24% has been calculated based on fluorescence and UV spectra. The best value is shown by a derivative containing a tetradecyl substituent. When studying the photocatalytic properties of synthesized compounds through the reaction between N-substituted 1,2,3,4-tetrahydroisoquinoline and malonic ester, the mono-tetradecyl derivative demonstrated the best results. According to gas chromatography–mass spectrometry (GC-MS) data, the conversion of the initial heterocycle reached 95%. Therefore, these resulting compounds have the potential to act as an effective photocatalysts.

The synthesis and characterization of previously unknown azides, iminophosphoranes and amines from commercially available mucochloric and mucobromic acids is reported. The reaction of 5-alkoxy-3,4-dihalo-2(5H)-furanones with sodium azide resulted in the regioselective formation of furanone 4-azidoderivatives. A series of novel iminophosphoranes was obtained from the reaction of corresponding azides with triphenylphosphine. Reduction of iminophosphoranes with stannous chloride dihydrate led to the heterocycles, possessing an amino group at the C4 carbon atom of the unsaturated γ-lactone ring.

GTPase Era from Staphylococcus aureus belongs to the TRAFAC superfamily of the TrmE-Era-EngA-EngB-Septin-like GTPases class and plays a significant role in the vital activity of this pathogenic microorganism as a maturation factor of the 30S ribosome subunit. However, the functions of this protein are not fully understood, making it a promising object for further study. Here, the 2.76 Å resolution crystal structure of Staphylococcus aureus Era in complex with GDP is presented. Structural comparison with other GTP-bound and GDP-bound homologous proteins, GTPase domain and the KH domain revealed a mutual orientation in S. aureus which has not been described before. The GDP-bound Era structure presented here will facilitate efforts to elucidate its interactions with its regulators and lay the foundation for a structure-based search for specific inhibitors.

Four new NiII, CoII, ZnII, and CuII complexes with the promising anti-tuberculosis drug (E/Z)-N′-((5-Hydroxy-3,4-bis(hydroxymethyl)-6-methylpyridin-2-yl)methylene)-isonicotino-hydrazide (LH) were synthesized and characterized by structural methods: single-crystal X-ray diffraction, vibrational spectroscopy, and mass spectrometry. The NiII, CoII, and ZnII metal ions form only amorphous phases with various morphologies according to mass spectrometry and IR spectroscopy. The CuII forms a crystalline 1D coordination polymer with the relative formula {[CuLCl]·0.5H2O}∞1. Even though the LH ligand in the crystalline state includes a mixture of E-/Z-isomers, only the tautomeric iminol E-/Z-form is coordinated by CuII in the crystal. The copper(II) complex crystallizes in the monoclinic P21/n space group with the corresponding cell parameters a = 16.3539(11) Å, b = 12.2647(6) Å, and c = 17.4916(10) Å; α = 90°, β = 108.431(7)°, and γ = 90°. DFT calculations showed that the Z-isomer of the LH ligand in solution has the lowest formation energy due to intramolecular hydrogen bonds. According to the quantum chemical calculations, the coordination environment of the CuII atom during the transfer of the molecule into the solution remains the same as in the crystal, except for the polymeric bond, namely, distorted trigonal bipyramidal. Some of the complexes investigated can be used as effective sensors in biosystems.

Ribosome biogenesis is an energy-intense multistep process where even minimal defects can cause severe phenotypes up to cell death. Ribosome assembly is facilitated by biogenesis factors such as ribosome assembly factors. These proteins facilitate the interaction of ribosomal proteins with rRNA and correct rRNA folding. One of these maturation factors is RimP which is required for efficient 16S rRNA processing and 30S ribosomal subunit assembly. Here, we describe the binding mode of Staphylococcus aureus RimP to the small ribosomal subunit and present a 4.2 Å resolution cryo-EM reconstruction of the 30S-RimP complex. Together with the solution structure of RimP solved by NMR spectroscopy and RimP-uS12 complex analysis by EPR, DEER, and SAXS approaches, we show the specificity of RimP binding to the 30S subunit from S. aureus. We believe the results presented in this work will contribute to the understanding of the RimP role in the ribosome assembly mechanism.

Protein crystal structure studies are an important tool for drug design. The growth of high-quality crystals suitable for X-ray diffraction is the limiting factor and the bottleneck in obtaining the structural data. Here we report the extraction, purification, and crystallization of the protein GTPase Era from the pathogenic bacterium Staphylococcus aureus . In bacterial cells, GTPase Era acts as a ribosome assembly factor. This enzyme is responsible for the cell growth and division. However, its structure is poorly understood. We obtained crystals of Staphylococcus aureus GTPase Era, which can be used in further structural studies by single-crystal X-ray diffraction analysis.

Study of the structures of various biological macromolecules is one of the main directions that are intensively developed using physical methods. Since proteins are an elementary unit of the structural and functional organization of a cell, the strategies for combating pathogenic microorganisms include the analysis of the bacterial protein synthesis apparatus and related systems. The extraction, purification, and small-angle X-ray scattering analysis of the structure of YsxC protein from the Staphylococcus aureus pathogenic bacterium are reported. This protein is involved in the cell growth and division processes, serves an energy-dependent factor, and participates in the assembly of large ribosome subunit. The structural study of this protein opens up a possibility of searching for small molecules capable of inhibiting its function. Since the structural variability of protein factors is higher than that of the conservative ribosome sites, their inhibition makes it possible to selectively affect a pathogenic microorganism.

New amphiphilic surfactant-transition metal complexes [Ag(L)(NO3)2], [Ag(2L)(NO3)3] and [Gd(L)Br (NO3)3H2O] (where L is 1-cetyl-4-aza-1-azoniabicyclo[2.2.2]octane) were synthesized and characterized. The composition and 3D structure of the complexes were determined using IR and 1H NMR spectroscopy, elemental analysis, and X-ray diffractometry. Self-assembly and adsorption properties of the amphiphiles in an aqueous medium were studied by tensiometry, conductometry, potentiometry, dynamic and electrophoretic light scattering, transmission electron microscopy and fluorescence of pyrene. The Kraft temperature, the critical micelle concentration, the degree of bromide ion binding with aggregates, the aggregation numbers, the aggregate size, the zeta-potential of the systems, and the adsorption characteristics at the water-air interface were determined. The results obtained were compared with data for single ligand solutions and ligand-inorganic salt mixtures. A high aggregation capacity and morphological rearrangements in metallosurfactant solutions (vesicle-micelle transition) were established. The antimicrobial activity of metallosurfactants (including antibiotic-resistant strains), as well as low hemolytic and cytotoxic effects were shown, which allows them to be classified as potential drugs with a wide spectrum of activity.

It is known that four peptide fragments of predominant protein in human semen Semenogelin 1 (SEM1) (SEM1(86–107), SEM1(68–107), SEM1(49–107) and SEM1(45–107)) are involved in fertilization and amyloid formation processes. In this work, the structure and dynamic behavior of SEM1(45–107) and SEM1(49–107) peptides and their N-domains were described. According to ThT fluorescence spectroscopy data, it was shown that the amyloid formation of SEM1(45–107) starts immediately after purification, which is not observed for SEM1(49–107). Seeing that the peptide amino acid sequence of SEM1(45–107) differs from SEM1(49–107) only by the presence of four additional amino acid residues in the N domain, these domains of both peptides were obtained via solid-phase synthesis and the difference in their dynamics and structure was investigated. SEM1(45–67) and SEM1(49–67) showed no principal difference in dynamic behavior in water solution. Furthermore, we obtained mostly disordered structures of SEM1(45–67) and SEM1(49–67). However, SEM1(45–67) contains a helix (E58-K60) and helix-like (S49-Q51) fragments. These helical fragments may rearrange into β-strands during amyloid formation process. Thus, the difference in full-length peptides’ (SEM1(45–107) and SEM1(49–107)) amyloid-forming behavior may be explained by the presence of a structured helix at the SEM1(45–107) N-terminus, which contributes to an increased rate of amyloid formation.