Search

Products from rolling smoking tobacco, they are also “hand-rolled”, are currently a trending phenomenon in the development of the tobacco products market, both in the Russian Federation and abroad. In view of the fact that maximum allowable values for the content of nicotine, tar and carbon monoxide in smoke are set for cigarettes, manufacturers produce tobacco blendings for cigarettes with a high content of components such as reconstituted tobacco and extended stem, on the one hand, regulating toxicity, and on the other hand, reducing flavoring properties. This leads to the fact that modern cigarettes, in terms of taste and aroma of tobacco smoke, poorly meet consumer taste preferences. By creating products from rolling smoking tobacco, combining different types of tobacco, using paper for self-rolling paper of different composition and breathability, as well as changing the mass of tobacco and the diameter of the product, the consumer can create an ideal product that meets all his taste preferences. In connection with the growing popularity of hand-rolled cigarettes, the relevance of research on their qualitative characteristics is growing. This article discusses such qualitative characteristics as the chemical composition and technological properties of samples: raw tobacco; tobacco blendings with and without a vein; rolling smoking tobacco of various brands. The main purpose of the research is to study the influence of the design of the product (diameter, weight, air permeability of paper) on the tasting assessment. For each type of smoking tobacco, products (hand-rolled) of various weights and diameters have been made, using four types of paper, differing in composition and air permeability. The dependence of the tasting evaluation of products from rolling smoking tobacco on the air permeability of the paper and the design features of the products (fiber width, weight and diameter of the products) has been established.

The method of high-voltage paper electrophoresis may be applied not only for peptide separation, but also in modifications and combinations with other methods, so, by means of aminoethylation and maleylation it is possible to broaden or narrow the range of trypsin action. This, in its turn, makes it possible to isolate preparatively lysin- and arginine-containing peptides, oxidation with performic acid enables the thyol-containing fragments to be isolated and application of carboxypeptidase A-C-terminal peptide of protein. When studying the primary structure of proteins the method has already found its widest application but with an increase in the number of methods of protein specific modification its potentiabilities will be even wider.

The paper presents the results concerning the application of docking programs FLM to combined use of the MMFF94 force field and the semiempirical quantum-chemical method PM7 in the docking procedure. At the first step of this procedure a fairly wide range of low-energy minima of the protein-ligand complex is found in the frame of the MMFF94 force field using the FLM program. The energies of all these minima are recalculated using the PM7 method and the COSMO solvent continuum model at the second step. On the basis of these calculations the deepest minimum of the protein-ligand energy, calculated by the PM7 method with COSMO solvent, is determined, which gives the position of the ligand closest to its position in the crystal of the protein-ligand complex. It is shown that the first step of the combined procedure is performed more quickly and more efficiently in vacuum, rather than with a solvent model.

The paper focuses on intermolecular interactions, particularly interactions between proteins and natural intermediates (small molecules). Molecules with a molecular weight of up to 1000 Da are free in cytoplasmic solution and form a pool of intermediates. Methods of computer modeling for prediction of protein-proteinaceous, protein-ligand, protein - a small molecule of interactions are presented. The program for modeling predicted biological activity in silico is Prediction of Activity Spectrum for Substances (PASS). In the Search Tool for Interacting Chemicals (STITCH) system, it is possible to identify potential protein interaction partners for small molecules. A review of the literature presents modern data on small molecules - metabolic switches, such as α-glycerophosphatedihydroxyacetone phosphate, pyruvate-lactate, oxaloacetate-malate. The molecules we study have different and multiple effects on metabolism and on intercellular interaction systems. Natural intermediates are at the intersection of metabolic pathways of metabolism of proteins, carbohydrates, lipids; they are signal molecules, participate in regulation of protein function, gene expression, enzyme activity. An increasing interest in deciphering protein-small molecule/metabolite interactions at the systemic level will lay a conceptual foundation that provides insight into complex epigenetic regulation under various environmental influences. A complete interplay, including a protein-small molecule interaction, will be crucial to eventually unraveling the complex relationships between the genotype and phenotype and to provide a deeper understanding of health and disease., Competing Interests: The authors declare no conflict of interest.

We discuss the effect of isothermal and adiabatic evaporation of water on the state of a water-protein droplet. The discussed problem is of current importance due to development of techniques to perform single molecule experiments using free electron lasers. In such structure-dynamic experiments the delivery of a sample into the X-ray beam is performed using the microdroplet injector. The time between the injection and delivery is in the order of microseconds. In this paper we developed a specialized variant of all-atom molecular dynamics simulations for the study of irreversible isothermal evaporation of the droplet. Using in silico experiments we determined the parameters of isothermal evaporation of the water-protein droplet with the sodium and chloride ions in the concentration range of 0.3 M at different temperatures. The energy of irreversible evaporation determined from in silico experiments at the initial stages of evaporation virtually coincides with the specific heat of evaporation for water. For the kinetics of irreversible adiabatic evaporation an exact analytical solution was obtained in the limit of high thermal conductivity of the droplet (or up to the droplet size of -100 Å). This analytical solution incorporates parameters that are determined using in silico. experiments on isothermal droplet evaporation. We show that the kinetics of adiabatic evaporation and cooling of the droplet scales with the droplet size. Our estimates of the water-protemi droplet. freezing rate in the adiabatic regime in a vacuum chamber show that additional techniques for stabilizing the temperature inside the droplet should be used in order to study the conformational transitions of the protein in single molecules. Isothermal and quasi-isothermal conditions are most suitable for studying the conformational transitions upon object functioning. However, in this case it is necessary to take into account the effects of dehydration and rapid increase of ionic strength in an aqueous microenvironment surrounding the protein.

Although there is a progress in understanding the causes and consequences of genetic and epigenetic changes in glioma malignant transformation, many details remain obscure and need further investigation. It is known that process of malignant transformation of gliomas is accompanied by gradual loss of LGI1 gene expression. However, genetic defects causing LGI1 inactivation have not been revealed. In this paper, we have analyzed the LGI1 gene expression in primary cultures of malignant gliomas, and compared these data with epigenetic indicators of transcriptional activity — posttranslational H3 histone modifications. We have show the presence of an epigenetic marker of gene repression H3K9me3 near the site of LGI1 transcription initiation in most (5 from 6) studied gliomas. There was not LGI1 expression in these gliomas. Only one glioma showed LGI1 expression, and in this glioma there was no association of LGI1gene with H3K9me3 modification. Thus, we are the first to show a correlation between LGI1 gene expression and the epigenetic indicator H3K9met3 in malignant gliomas. Marker of actively transcribed chromatin Í3K4àñ have not been found in this area of the genome. The data obtained strongly suggest the possibility of gene LGL1 inactivation by epigenetic mechanism: modified «histone code».

Achievement of the concentration detection limit for proteins at the level of the reverse Avogadro number determines the modern development of proteomics. In this review, the possibility of approximating the reverse Avogadro number by using nanotechnological methods (AFM-based fishing with mechanical and electrical stimulation, nanowire detectors, and other methods) are discussed. The ability of AFM to detect, count, visualize and characterize physico-chemical properties of proteins at concentrations up to 10(-17)-10(-18) M is demonstrated. The combination of AFM-fishing with mass-spectrometry allows the identification of proteins not only in pure solutions, but also in multi-component biological fluids (serum). The possibilities to improve the biospecific fishing efficiency by use of SOMAmers in both AFM and nanowire systems are discussed. The paper also provides criteria for evaluation of the sensitivity of fishing-based detection systems. The fishing efficiency depending on the detection system parameters is estimated. The practical implementation of protein fishing depending on the ratio of the sample solution volume and the surface of the detection system is discussed. The advantages and disadvantages of today's promising nanotechnological protein detection methods implemented on the basis of these schemes.

The paper analyzes data on how physical exercise as a standard test of cosmonaut's performance, affects the renal function and urine protein profile. The investication involved 10 normal human subjects. Following exercise, rate of renal excretion of proteins increased. The occurrence of 4 proteins out of 9 in urine did not alter and of 2 (alpha-methylacyl coenzyme A racemase and cubilin) increased; occurrence of 3 proteins (kallikrein-1, osteopontin and vitamin K-dependent protein Z) decreased. Out of 24 proteins with molecular weights higher than albumin, 7 were detected in urine after exercise more frequently, 6 with same frequency as before the test and none less frequently which demonstrates lowered selectivity of the glomerular barrier during exercise.

The medusa, Aurelia aurita (Scyphozoa, Cnidaria), is considered to be a cosmopolitan species with a worldwide distribution in most seas from the poles to the tropics. Cnidarian is thought to possess two tissue layers: endoderm (gastroderm) and ectoderm, which are separated by huge mesoglea in medusa. The basic morphology of medusa is similar in different populations. Previously we have determined a new protein "mesoglein" as one of the main components of mesoglea. Deduced amino acid sequence of mesoglein contains Zona Pellucida (ZP) domain. In this paper, we have comparied of mesoglein and its gene in medusa from three habitats (White Sea (WsA), Black Sea (BsA), Japonic Sea (JsA)). The set of the mesoglea protein bands after SDS-PAGE is similar in all samples. Nevertheless, JsA mesogleins' M(r) is 53-55 kDa, while WsA and BsA mesogleins have M(r) of 47 kDa. Antibodies raised against WsA mesoglein recognize only mesogleins with M(r) of 47 kDa, but not 53-55 kDa, both on immunoblot and immunocytochemistry. Mesogleal cells and elastic fibrils are stained intensively in the mesoglea both from WsA and BsA but not from JsA. The possibility of gene divergency was checked by PCR with primers specific for WsA mesoglein gene. PCR products of expected length obtained on polyA-cDNA template from mesogleal cells of WsA and BsA medusa but not on cDNA of JsA medusa. Our results evidence that there are two different species in genus Aurelia: Aurelia aurita inhabits White and Black Seas while Aurelia sp. inhabits Japonic Sea. This is consistent with findings of other recept molecular biological studies.

The present paper features a comparative analysis of the biological value of milk obtained from cows, goats, mares, and camels. The biological value of the milk was estimated by protein and lipid components using computational methods of food combinatorics. According to the chemical composition of the milk, camel’s milk proved to have the highest protein content (4.0%). Cow’s and goat’s milk were much poorer in protein: its content was by 0.8 and 1% lower, respectively. The lowest weight fraction of protein was in mare’s milk, which was by 1.8% lower than in camel’s milk, and also by 0.8 and 1% lower if compared to goat’s and cow’s milk. In addition, mare’s milk differed from other types of dairy raw products by its lowest fat content (1.0%), which was 4.1, 3.2, and 2.6% lower than the fat content of the milk obtained from camels, goats, and cows, respectively. The high fat content of camel’s milk was associated with its highest energy content (82 kcal), while the energy content in goat’s milk was 14 kcal, cow’s milk – 17 kcal and mare’s milk – 41 kcal. Camel’s and goat’s milk had a high content of solids (15% and 13.4%, respectively), whereas mare’s milk had only 10.7% and cow’s milk – 11%. The paper also introduces some data on the protein component of the milk obtained by using the amino acid scoring method. Mare’s milk proved to have the highest value of the amino acid composition index (0.6), which over-indexed the values for cow’s, goat’s, and camel’s milk by 0.13, 0.14 and 0.18, respectively. The biological value of the lipid component of the product is characterized by its qualitative composition of fatty acids. The highest values of the index of fatty acid composition belonged to mare’s milk: 0.58 and 0.42, taking into account the 3 and 5 calculation components. Camel’s milk was found inferior to mare’s milk by 0.9. The lowest values of the lipid composition index were observed for cow’s and goat’s milk. The research involved a complex calculation of the level of balance in the composition of milk. All the livestock animals were rated according to the Harrington’s scale of desirability as ‘satisfactory’ by the third component of the estimation, but the highest numerical values of the level of balance belonged to mare’s milk. To optimize this indicator, the authors recommend livestock animal milk as an ingredient of complex raw commodity products.

Frediction of the three-dimensional structure of a protein from its amino acid sequence can be considered as a global optimization problem. In this paper, the Chaotic Artificial Bee Colony (CABC) algorithm was introduced and applied to 3D protein structure prediction. Based on the 3D off-lattice AB model, the CABC algorithm combines global search and local search of the Artificial Bee Colony (ABC) algorithm with the Chaotic search algorithm to avoid the problem of premature convergence and easily trapping the local optimum solution. The experiments carried out with the popular Fibonacci sequences demonstrate that the proposed algorithm provides an effective and high-performance method for protein structure prediction.

Proteomic technologies enable to identify thousands of proteins in biological samples. These data require appropriate means for storage, dissemination and analytical processing to decipher the new knowledge. Automatic processing of high-efficient experiment results is powered by the controlled vocabularies, such as Medical Subjects Headings and GeneOntology. While ontology and vocabularies undergo constant evolution, it is necessary to provide the centralized storage of proteomic data for further revision in accordance with the updated knowledge domain. Proteomic repositories like PRIDE, The Global Proteome Machine, PeptideAtlas etc. are available to harbor the wealth of mass spectral data and appropriate protein identifications. The existing repositories facilitate the development of knowledge extraction technologies to compare the list of identified proteins with the GeneOntology annotations, Medical Subjects Headings, metabolic and regulatory pathways. This paper reviews modern analytical tools that exploit the knowledge-based technologies for proteome research.

Knowledge of 3D-structure of protein-ligand complex is a major prerequisite for understanding the functioning mechanism of cellular proteins and membrane receptors. This is also of a great help in rational drug design projects. In the present paper we briefly review the molecular docking approaches used to predict possible orientation of a ligand in the protein binding site. The recent trends to improve the accuracy and efficiency of docking algorithms are demonstrated with the results obtained in Laboratory of Biomolecular Modeling. Particular attention is paid to protein-ligand hydrophobic and stacking interactions responsible for molecular recognition of ligand fragments. Such type of interactions are not always adequately represented in scoring criteria of docking applications that leads to mismatch in 3D-structure complexes predictions. That is why further inquiry of methods to account for these interactions is now the area of active research.

The paper describes creation and analysis of a database 3Dfold_test. This database consists of a large set of pairs of spatially-similar structures of protein domains and of an accompanying, much larger control set of "decoys", i.e., spatially-dissimilar protein structures, having approximately the same size and compactness as each member of a pair of spatially-similar proteins. The database 3Dfold_test can be found at the site http://phys.protres.ru/resources/prediction analogy/3Dfold/.

The paper describes results of testing of "recognition ability" of different substitution matrices and various pseudo-potentials (taken from literature or designed by us) to recognize protein structures and produce the sequence-to-structure alignments. Numerical estimates of "identifying power" of various matrices and pseudo-potentials are obtained for different levels of similarity between amino acid sequences of spatially-similar proteins. It is shown that substitution matrices work much better than pseudo-potentials at a high level of similarity of sequences of spatially-similar proteins, but some pseudo-potentials overcome substitution matrices at a low level of sequence similarity.

In the present paper we highlight the dependence of normalized mass spectrometry intensity on protein concentration. We have defined dynamic range of concentrations from 1 nM to 1 mcM. It has been shown that the dependence holds linearity along the whole concentration range as for pure proteins as for proteins mixtures. Our observation revealed that the correlation curve possess protein-specific tangent between 1 nM and 1 mcM. The efficacy of the method evaluated by AQUA and 18O-labelling techniques of quantitative proteomics.

Generalized literature data covering principal mechanisms of oxidative modification of protein and its role in various pathologies are presented in the paper. It is emphasized that due to peculiarities of protein structure organization the process of oxidative modification is of complicated and specific character, which is determined by amino acid composition of the protein. Oxidative modification of protein can be connected with impairment of not only a polypeptide chain itself, but also particular amino acid residues with formation of several types of radicals. Mechanisms of formation of long-life hydroperoxides and their role in oxidative stress are discussed. The role of electron-transfer (migratory) reactions in formation of radical centers on a protein molecule surface is elucidated. Oxidative modification of protein is considered as a process of regulation of their synthesis and degradation connected with activation of multicatalytic proteases. Oxidative destruction of protein is one of early and most reliable markers of tissue lesion in reactive species pathology.