We have previously shown that the thermal stability of animal collagens correlates with the number of hydrophobic amino acid residues in their composition: the more hydrophobic residues in a molecule, the higher the denaturation temperature of collagen. In addition, it was found that with the same hydrophobicity, the thermal stability of collagens of cold-blooded animals can be several degrees lower than that of warm-blooded animals. To understand the reasons for this, we studied the amino acid composition and sequences of α1, α2, and α3 chains of type I collagen in warm-blooded and cold-blooded animals. The α3 chain is found only in cold-blooded animals and is represented by sequences for only 6 fish species. The results of the study show that differences in the thermal stability of collagens of warm-blooded and cold-blooded animals may be due to differences in the number of Gly-Gly pairs, Pro, Ala, Met, Ser in collagen subunits. A negative correlation was observed between the number of GGY (Gly-Gly-Yaa, pair Gly-Gly is before Yaa in the sequence) and GGX (pair Gly-Gly is before Xaa in the sequence) and collagen thermal stability. Differences in the amounts of GGY and GGX were also observed between the different types of α1, α2, and α 3 chains. A negative correlation with thermal stability was also observed for Ser. For all chain types, the amount of Pro at position Xaa and Pro at position Yaa was shown to correlate with collagen denaturation temperatures. Moreover, in the α1 and α2 chains of warm-blooded and cold-blooded animals, the positive correlation with Pro(Yaa) was higher than with Pro (Xaa). Similarities were found between the α1 and α3 chains and their differences from the α2 chain in the amount and ratio of Pro (Xaa) and Pro (Yaa).

African swine fever virus (ASFV) is a large DNA virus that causes a highly lethal disease in pigs and currently has no effective vaccines or antiviral treatments available. We designed a protein switch that combines the DNase domain of colicin E9 (DNase E9) and its inhibitor Im9 with the viral protease cleavage site. The complex is only destroyed in the presence of an ASFV pS273R protease, which releases DNase activity. Several Im9 variants were constructed by inserting the pS273R protease cleavage sequence into different exposed loops. From these, we identified an optimized variant (Im9-1.4) that remains highly stable and tightly bound to DNase E9, suppressing its activity in the absence of protease. Exposure to the ASFV protease results in cleavage of Im9-1.4, rendering it unable to inhibit DNase E9 activity. In vitro assays confirmed that the DNase E9/Im9-1.4 complex becomes catalytically active upon proteolytic digestion with pS273R protease. This virus-triggered 'kill switch' is designed to render pig cells nonpermissive to ASFV by aborting infection via viral DNA degradation. Our study offers a generalizable synthetic biology strategy that uses virus-encoded proteases to trigger dormant effectors, exemplified by this protease-sensing DNase. This synthetic restriction system might be used to develop ASFV-resistant pigs.

In this study, a database of the thermal stability of collagens and their synthetic analogues has been compiled taking into account literature sources. In total, our database includes 1200 records. As a result of a comparative theoretical analysis of the collected experimental data, the relationship between the melting temperature (Tm) or denaturation temperature (Td) of collagens and the fraction of hydrophobic residues (f) in their molecules has been established. It is shown that this relationship is linear: the larger the f value, the higher the denaturation or melting temperature of a given collagen.

In this study, we analyze the occurrence of the unique structural motif, the 3β-corner, belonging to the Structural Classification of Proteins (SCOP) folds, in proteins of various origins. We further assess the structural and functional role of this motif as well as the clustering of the biological functions of proteins in which it occurs. It has been shown previously that the 3β-corner occurs with different probabilities in all beta proteins, alpha and beta proteins (α + β and α/β), and alpha classes occur most often in the composition of β-proteins. The 3β-corner is often found as a building block in protein structures, such as β-barrels, -sandwiches, and -sheets/-layers.

Biological activity regulation by protein post-translational modification (PTM) is critical for cell function, development, differentiation, and survival. Dysregulation of PTM proteins is present in various pathological conditions, including rheumatoid arthritis (RA). RA is a systemic autoimmune disease that primarily affects joints, and there are three main types of protein PTMs associated with the development of this disease, namely, glycosylation, citrullination, and carbamylation. Glycosylation is important for the processing and presentation of antigen fragments on the cell surface and can modulate immunoglobulin activity. The citrullination of autoantigens is closely associated with RA, as evidenced by the presence of antibodies specific to citrullinated proteins in the serum of patients. Carbamylation and dysregulation have recently been associated with RA development in humans.In this study, we performed an overview analysis of proteins with post-translational modifications associated with the development of RA adverted in peer-reviewed scientific papers for the past 20 years. As a result of the search, a list of target proteins and corresponding amino acid sequences with PTM in RA was formed. Structural characteristics of the listed modified proteins were extracted from the Protein Data Bank. Then, molecular dynamics experiments of intact protein structures and corresponding structures with PTMs were performed regarding structures in the list announced in the ProtDB service. This study aimed to conduct a molecular dynamics study of intact proteins and proteins, including post-translational modification and protein citrullination, likely associated with RA development. We observed another exhibition of the fundamental physics concept, symmetry, at the submolecular level, unveiled as the autonomous repetitions of outside the protein structural motif performance globule corresponding to those in the whole protein molecule.

In this study, we conducted a comparative analysis of the structure of agonists and antagonists of transmembrane (TM) β-adrenoceptors (β-ARs) and their interactions with the β-ARs and proposed the mechanism of receptor activation. A characteristic feature of agonist and antagonist molecules is the presence of a hydrophobic head (most often, one or two aromatic rings) and a tail with a positively charged amino group. All β-adrenergic agonists have two carbon atoms between the aromatic ring of the head and the nitrogen atom of the amino group. In antagonist molecules, this fragment can be either reduced or increased to four atoms due to the additional carbon and oxygen atoms. The agonist head, as a rule, has two H-bond donors or acceptors in the para- and meta-positions of the aromatic rings, while in the antagonist heads, these donors/acceptors are absent or located in other positions. Analysis of known three-dimensional structures of β-AR complexes with agonists showed that the agonist head forms two H-bonds with the TM5 helix, and the tail forms an ionic bond with the D3.32 residue of the TM3 helix and one or two H-bonds with the TM7 helix. The tail of the antagonist can form similar bonds, but the interaction between the head and the TM5 helix is much weaker. As a result of these interactions, the agonist molecule acquires an extended "strained string" conformation, in contrast to the antagonist molecule, which has a longer, bended, and flexible tail. The "strained string" of the agonist interacts with the TM6 helix (primarily with the W6.48 residue) and turns it, which leads to the opening of the G protein-binding site on the intracellular side of the receptor, while flexible and larger antagonist molecules do not have the same effect on the receptor.

This study explored the mechanisms by which the stability of super-secondary structures of the 3β-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3β-corner structures of various origins. We focused on geometric parameters such as change in gyration radius, solvent-accessible area, major conformer lifetime and torsion angles, and the number of hydrogen bonds. Ultimately, a set of 3β-corners from 330 structures was characterized by a root mean square deviation (RMSD) of less than 5 Å, a change in the gyration radius of no more than 5%, and the preservation of amino acid residues positioned within the allowed regions on the Ramachandran map. The studied structures retained their topologies throughout the MD experiments. Thus, the 3β-corner structure was found to be rather stable per se in a water environment, i.e., without the rest of a protein molecule, and can act as the nucleus or “ready-made” building block in protein folding. The 3β-corner can also be considered as an independent object for study in field of structural biology.

This study investigated the stability of structural motifs via molecular dynamics, using α-α-corners as an example. A molecular dynamics experiment was performed on a sample of α-α-corners selected by the authors from the PDB database. For the first time during a molecular dynamics experiment, we investigated the characteristics of structural motifs by describing their geometry, including the interplanar distance, area of polygon of the helices projections intersection, and torsion angles between axes of helices in helical pairs. The torsion angles for the constriction amino acids in the equilibrium portion of the molecular dynamics trajectory were analyzed. Using the molecular dynamics method, α-α-corners were found to be autonomous structures that are stable in aquatic environments.

A method for estimating the gas-dynamic characteristics of supersonic plasma jets based on the minimum number of plasma parameters (electron number density and temperature) that are easily measured by spectral diagnostic methods is considered. The course of the most important parameters characterizing the gas dynamics of the nonequilibrium plasma flow in the shock-wave region of a supersonic plasma jet created by a pulsed capillary discharge is revealed, and their values are estimated. A significant difference between the electron and gas temperatures was found in the vicinity of the central shock wave.

Communicated by Ramaswamy H. Sarma.

Communicated by Ramaswamy H. Sarma.

Abstract—Mutual arrangement, or packing, of α-helices in proteins depends on several factors, but, tight packing and the chemical nature of the polypeptide chain are the most important. This study shows, for the first time, that the torsion packing angles between axes of α-helices depend on their length. A database of helical pairs formed by two connected and juxtaposed α-helices has been compiled using the Protein Data Bank. These helical pairs have been subdivided into four types: (1) 10474 pairs formed by long helices; (2) 3665 pairs in which the first α-helix is long and the second is short; (3) 3648 pairs in which the first α‑helix is short and the second is long; 4) 1895 pairs in which both helices are short. Analysis of the database showed that most helical pairs in which both the helices are long form α-hairpins having interhelical packing angles of Ω ≈ 20°. Most helical pairs in which one α-helix is long and the other is short or both helices are short form αα-corners having orthogonal (Ω ≈ –70°…–90°) or slanted (Ω ≈ –50°) packing of α-helices. The possible reasons for this relationship between interhelical angles (Ω) and the length of α-helices are discussed. These results are of great importance in protein modeling and prediction since they enable the determination of the mutual arrangement of α-helices in protein molecules.

The paper presents the results of spectroscopic studies of the initial segment of a supersonic plasma jet formed by a pulsed discharge in a capillary made of carbon-containing polymer. Detection of the emission properties of the high-temperature core of the jet (the intensities and contours of the H α and H β Balmer lines and the relative intensities of C II ion lines) with high temporal (1–50 μs) and spatial (30–50 μm) resolutions allowed the authors to reveal specific features of the longitudinal distributions of the electron density and temperature caused by the flow nonisobaricity along the initial segment of the supersonic jet.

A novel L-shaped repeat module whose structure can be represented as β-strand–loop–β-strand has been identified in a stereochemical analysis of nonhomologous SH3-like folds. β-Strands of the L-module are positioned at a ~90° angle to each other in different orthogonally packed β-layers. Together with a crossover loop, they form a half-turn of a right-handed superhelix. A database of 60 nonhomologous SH3-like domains has been compiled using the Protein Data Bank to study structural similarities and differences of L-modules. Occurrence frequencies of L-modules have been determined depending on the length of their loops. It has been shown that L-modules with βmαααβn- and βmαααβαβn-conformations, where m and n are numbers of β-residues in the first and second β-strands, occur most often (57 and 8%, respectively). Spatial structures of L-modules of the same type are very similar, demonstrated through superimposing them using computer programs. Structural alignment of the amino acid sequences encoding L-modules has been performed, making it possible to identify key positions for hydrophobic, hydrophilic, and proline residues.

In proteins, the polypeptide chain forms a number of right-and left-handed helices and superhelices, right-and left-turned hairpins, and some other structures that are nonsuperimposable, although they are not mirror images of each other as the Lamino acids are not converted to the Damino acids. This property of protein structures will be referred to here as pseudo-chirality–or handedness. It has been shown that there are two kinds of handedness in proteins–helical handedness and handedness of arrangement. Some protein structures exhibit both the kinds of handedness. Handedness is observed at all levels of protein structural organization–from α-helices, β-strands, hairpins, βαβ-units up to complex structural motifs, superhelices, and supramolecular structures in fibrous and polymer proteins. There are several structures that have unique handedness in proteins, for example, α-helices, αα-corners, βαβ-units, abcd-units, and so on. This property of the polypeptide chain is of particular value in protein folding and protein modeling, because it drastically reduces the number of possible folds.

Possible combinations of βαβ-units and Π-like modules in proteins in both right- and left-handed forms have been analyzed in detail. The correlation between the mutual arrangement of the structural elements in the polypeptide chain and their handedness has been shown. In the βαβП combinations, which is encountered most frequently in proteins, the П-module follows the βαβ unit along the chain and both elements are right-handed. In the Пβαβ combinations, where the П-module is located at the N end and the βαβ-unit follows it, the former is left-handed and the latter is right-handed. In relatively rare combinations of the left-handed βαβ-units and right-handed П-modules, the βαβ-unit follows П-module in the chain. The combinations of left-handed П-modules and the left-handed βαβ-units are unobservable in proteins. It has also been shown that the П-modules with a β-strand-α-helix-arch-β-strand structure are observed in proteins only in a right-handed form and half of them (51%) contains cis-prolines in their arches. These arches of nonhomologous proteins, as well as the positions of cis-prolines, nearly coincide when superimposed. The superimposed П-modules also demonstrate that their overall folds are very similar. Structural alignment of their amino acid sequences has shown that the П-modules have very similar sequence patterns of the key hydrophobic, hydrophilic, glycine, and cis-proline residues.

The results of a complex study of the destructive effect of a nitrogen plasma jet at atmospheric pressure onto the surface of the MPG-6 graphite are presented. The space-time changes in the rate of decrease in the samples material, the temperature of their surface, the electron temperature of plasma in the oncoming flow and the plasma composition in the region of 'injection' were all experimentally determined. Using spectroscopic methods with high spatial (50 mu m) and time (0.5 s) resolutions changes in the concentration of emitting carbon atoms (line CI 247.9 nm) and CN (transition B2 Sigma(+) - X-2 Sigma(+)) near the surface of isotropic graphite were recorded, which occur in the process of intense and long (100-150s) exposure of graphite to a nitrogen plasma jet. The change in the vibrational and rotational temperatures of the radical CN and the molecular ion N-2(+) in the near-surface region of the plasma is determined by the method of 2D matrix spectroscopy. An analysis of the relative populations of the excited NI states in the interaction region at the quasistationary stage of sample heating revealed spatial-temporal changes in the electron temperature in the near-surface plasma, indicating an increase in its enthalpy caused by the rapid exothermic CN + N -> C + N-2 substitution process, which leads to a decrease in the heat flow acting on sample. The analytical solution of the problem of temperature change in a relaxing nitrogen plasma jet in the absence of graphite confirmed the experimentally observed slow cooling of it, caused by a number of exothermic recombination processes taking place in the plasma.

We present the results of spectroscopic investigations of the plasma of an impulse discharge in a capillary with an ablation wall made of carbon-containing polymer, within the discharge pulse parameters providing the supersonic flow regime of a plasma jet. Based on a 2D-matrix high resolution spectra containing Hα, Cu I, Cu II, C I, C II, and CN and the Swan molecular bands, we obtain spatiotemporal distributions of the electron number density and the plasma temperature in the capillary and the supersonic plasma jet. We reveal the peculiarities of the spatial distribution of the electron number density and of the spectral component intensity within both above stated zones, conditioned, in particular, by achievement, in the hot central zone, of an electron temperature above the “normal” temperature, as well as by essential nonisobaricity of the initial section of the plasma jet. The emission properties of the high-temperature jet core–the intensities and the profiles of the Hα and Hβ Balmer lines, relative intensities of the C II and O II ion lines–registered with high temporal (10 μs) and spatial (20–30 μm) resolution make it possible to discover the main regularities in the spatiotemporal distributions of pressure, temperature, and ionization degree in the capillary and in the supersonic heterogeneous jet of the erosion discharge. Due to the presence in the flow of the molecular components displaying their emission properties at the jet periphery, we manage to obtain information on the plasma parameters within the zone of formation of the “intercepting” shocks in the supersonic jet.