In order to elucidate the effect of modification of the hinge region on structural polymorphism associated with conformational transitions, structural studies of hinge-modified oligopeptidase B from Serratia proteamaculans (SpOpBmod) in the crystalline state and solution were carried out. A new crystal structure of SpOpBmod in the intermediate conformation was obtained, and a molecular model of SpOpBmod in the open conformation was created using a combination of small-angle X-ray scattering with MD simulations. The improved electron density of the mobile H-loop carrying the catalytic H652 distinguished the obtained crystal structure from that which was previously reported. Good electron density in this region was previously found only in the inhibitor-bound SpOpBmod structure, in which one of the inhibitor molecules was covalently bound to H652. Comparison of the above structures of free and inhibitor-bound enzymes showed that both tertiary folds are the result of the internal conformational dynamics of SpOpBmod, which were captured by inhibitor binding. Comparison of the SpOpBmod structures with the structures of the same enzyme with a native hinge peptide made it possible to establish the influence of hinge modification on the rearrangement of the interdomain interface during conformational transitions. The above analysis also used models of native and hinge-modified enzymes in open conformations. We found that the interdomain interface observed in the crystal structures of hinge-modified enzymes could be considered an extreme version of the H-loop arrangement, in which closure of the domains does not lead to the assembly of the catalytic triad, whereas the intermediate conformation observed in the structure of the enzyme with the native hinge sequence illustrates a productive transition to the catalytically active closed conformation.

Currently, there is great interest in the development of highly sensitive bioanalytical systems for diagnosing diseases at an early stage, when pathological biomarkers are present in biological fluids at low concentrations and there are no clinical manifestations. A promising direction is the use of molecular detectors―highly sensitive devices that detect signals from single biomacromolecules. A typical detector in this class is the atomic force microscope (AFM). The high sensitivity of an AFM-based bioanalysis system is determined by the size of the sensing element of an atomic force microscope―the cantilever―the radius of the curvature of which is comparable to that of a biomolecule. Biospecific molecular probe–target interactions are used to ensure detection system specificity. Antibodies, aptamers, synthetic antibodies, and peptides can be used as molecular probes. This study has demonstrated the possibility of using aptamers as molecular probes for AFM-based detection of the ovarian cancer biomarker CA125. Antigen detection in a nanomolar solution was carried out using AFM chips with immobilized aptamers, commercially available or synthesized based on sequences from open sources. Both aptamer types can be used for antigen detection, but the availability of sequence information enables additional modeling of the aptamer structure with allowance for modifications necessary for immobilization of the aptamer on an AFM chip surface. Information on the structure and oligomeric composition of aptamers in the solution was acquired by combining small-angle X-ray scattering and molecular modeling. Modeling enabled pre-selection, before the experimental stage, of aptamers for use as surface-immobilized molecular probes.

A multichannel microfluidic cell (MFC) obtained using 3D printing for studying the structure of complex solutions by small-angle X-ray scattering (SAXS) is described. MFC was tested at the BioMUR beamline of the Kurchatov synchrotron. A comparative analysis of SAXS signal from the standard capillary and from the developed MFC was carried out, with MFC showing significant advantages. The dynamics of SAXS scattering curves for lysozyme solutions with NaCl precipitant were studied when the protein and precipitant concentrations changed. The obtained time series of data are well consistent with the known data for the lysozyme solution.

Elementary building blocks for the growth of KDP crystals were established. The solution of potassium dihydrogen phosphate (KH2PO4–KDP) has been experimentally studied by the small-angle X-ray scattering (SAXS) method. The analysis of SAXS data in the temperature range of 2.5–90 °C using a set of models of 3D fragments of the crystal structure showed that the saturated solution contains above K⁺, H₂PO₄⁻ and KH₂PO₄ monomers, as well as mainly octamers. The 3D model of the octamer isolated from the crystal structure has dimensions of 17.443 Å along the [001] axis and 5.963 Å along the [100] and [010] axes. As the temperature is decreased, starting from the saturation temperature of the solution, the volume fraction of octamers sharply increases while the volume fraction of monomers decreases. The results indicate that the monomers and octamers represent major components in the solution with the presence of minor populations of other oligomers. The significant dominance of octamers in the supersaturated solution indicates that they are elementary building blocks for the growth of KDP crystals of tetragonal modification.

The structure of an aqueous solution of potassium dihydrogen phosphate (KH₂PO₄, KDP) was studied by small-angle X-ray scattering (SAXS) and molecular dynamics (MD). According to SAXS data, the octameric species (KH₂PO₄)₈ are formed in solution in addition to K⁺, (H₂PO₄)⁻, and KH₂PO₄, while the presence of other types of oligomers is not observed. When the temperature drops below the saturation temperature (~60 °C), the volume fraction of octamers increases sharply, reaching 50% at 4 °C. The results of MD calculations of the temporal stability relationships of dimers (KH₂PO₄)₂, tetramers (KH₂PO₄)₄, and octamers (KH₂PO₄)₈ show that the dimers and tetramers disintegrate rapidly (50–100 ps), while the octamers remain stable. A comparative analysis of the bonds between the octamers and the KDP crystal lattice was carried out when the octamer was inserted during crystal growth in the directions [001] and [100]. The possible relationship of the obtained results with the changes in the anisotropy of growth rates (habitus) of KDP crystals at different degrees of supersaturation is discussed.