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.

The behavior of a dimer isolated from the crystal structure of tetragonal lysozyme has been simulated using the accelerated molecular dynamics method. The simulation time was 240 ns. The simulation data are compared with the data obtained previously using classical molecular dynamics. It is shown that the dimer studied is stable in both experiments, but the accelerated molecular dynamics method made it possible to reveal additional conformational changes in lysozyme molecules.

STRUCTURAL BIOINFORMATICS STUDY OF THE STRUCTURAL BASIS OF SUBSTRATE SPECIFICITY OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS Исследование структурных основ субстратной специфичности пуриннуклеозидфосфорилазы из Thermus Thermophilus методами структурной биоинформатики

Molecular dynamics simulations were performed for wild-type purine nucleoside phosphorylase in complexes with two substrates (adenosine and guanosine). The MD simulations were also performed for the mutant form of the enzyme with the same substrates. The free energy changes upon the formation of the complexes were evaluated from the molecular dynamics trajectories by the MM-GBSA method.