Bovine bta-microRNA-1271 Promotes Preadipocyte Differentiation by Targeting Activation Transcription Factor 3
In this study, we used target gene prediction, dual-luciferase reporter assay, and transfection-mediated overexpression and inhibition of bta-miR-1271 in a culture of Yanbian yellow cattle preadipocytes to investigate the role of bta-miR-1271 in adipogenesis. We showed that bta-miR-1271 directly targets the 3 ′-untranslated region (3′-UTR) of the activating transcription factor 3 (ATF3) mRNA and downregulates its expression. Overexpression of bta-miR-1271 enforced by the miRNA mimics promoted triglyceride accumulation and significantly upregulated expression of the adipogenic peroxisome proliferator- activated ...
Source: Biochemistry (Moscow) - July 1, 2020 Category: Biochemistry Source Type: research

Inactivation of Epigenetic Regulators due to Mutations in Solid Tumors
AbstractMain factors involved in carcinogenesis are associated with somatic mutations in oncogenes and tumor suppressor genes representing changes in the DNA nucleotide sequence. Epigenetic changes, such as aberrant DNA methylation, modifications of histone proteins, and chromatin remodeling, are equally important in the development of human neoplasms. From this perspective, mutations in the genes encoding key participants of epigenetic regulation are of particular interest including enzymes that methylate/demethylate DNA, enzymes that covalently attach or remove regulatory signals from histones, components of nucleosome r...
Source: Biochemistry (Moscow) - July 1, 2020 Category: Biochemistry Source Type: research

Characterization of the Altai Maral Chymosin Gene, Production of a Chymosin Recombinant Analog in the Prokaryotic Expression System, and Analysis of Its Several Biochemical Properties
AbstractFor the first time, the chymosin gene (CYM) of a maral was characterized. Its exon/intron organization was established using comparative analysis of the nucleotide sequence. TheCYM mRNA sequence encoding a maral preprochymosin was reconstructed. Nucleotide sequence of theCYM maral mRNA allowed developing an expression vector to ensure production of a recombinant enzyme. Recombinant maral prochymosin was obtained in the expression system ofEscherichiacoli [strain BL21 (DE3)]. Total milk-coagulation activity (MCA) of the recombinant maral chymosin was 2330 AU/ml. The recombinant maral prochymosin relative activity wa...
Source: Biochemistry (Moscow) - July 1, 2020 Category: Biochemistry Source Type: research

Role of Interactions of the CRE Region of Escherichia coli RNA Polymerase with Nontemplate DNA during Promoter Escape
AbstractRNA polymerase (RNAP) recognizes promoter DNA through many interactions that determine specificity of transcription initiation. In addition to the dedicated transcription initiation σ factor in bacteria, the core enzyme of RNAP can also participate in promoter recognition. In particular, guanine residue at the +2 position (+2G) of the nontemplate DNA strand is bound in the CRE pocket formed by the RNAP β subunit. Here, we analyzed the role of these contacts in the process of promoter escape by RNAP by studying point mutations in the β subunit ofEscherichia coli RNAP that disrupted these interactions...
Source: Biochemistry (Moscow) - July 1, 2020 Category: Biochemistry Source Type: research

Spliceosomal Introns: Features, Functions, and Evolution
AbstractSpliceosomal introns, which have been found in most eukaryotic genes, are non-coding sequences excised from pre-mRNAs by a special complex called spliceosome during mRNA splicing. Introns occur in both protein- and RNA-coding genes and can be found in coding and untranslated gene regions. Because intron sequences vary greatly due to a high rate of polymorphism, the functions of intron had been for a long time associated only with alternative splicing, while intron evolution had been viewed not as an evolution of an individual genomic element, but rather considered within a framework of the evolution of the gene int...
Source: Biochemistry (Moscow) - July 1, 2020 Category: Biochemistry Source Type: research

Phytofluene as a Highly Efficient UVA Photosensitizer of Singlet Oxygen Generation
AbstractPhytoene and phytofluene – uncolored C40 carotenoids with short chain of conjugated double bonds (3 and 5, respectively) – are known to be universal precursors in biosynthesis of colored carotenoids in photosynthesizing organisms. It is commonly recognized that C40 carotenoids are photoprotectors of cells and tissues. We have shown that phytofluene is an exception to this rule. By measuring photosensitized phosphorescence of singlet oxygen (1O2) we found out that phytofluene was very effective photosensitizer of1O2 formation in aerated solutions under UVA irradiation (quantum yield of 85 ± 5%), w...
Source: Biochemistry (Moscow) - July 1, 2020 Category: Biochemistry Source Type: research

Recombinant Spidroin Films Attenuate Individual Markers of Glucose Induced Aging in NIH 3T3 Fibroblasts
AbstractThe effect of bioresorbable materials on aging in cultured mouse NIH 3T3 fibroblasts treated with elevated glucose concentration was investigated. The cells were grown on films produced from the silkworm fibroin and rS1/9, a recombinant analog ofNephila clavipes spidroin 1. Exposure to 50 mM glucose of the cells grown on uncoated glass support resulted in the cell growth retardation. The average areas of the cells and nuclei and the percentage of apoptotic cells increased, whereas the amount of soluble collagen decreased. In contrast, on the fibroin and spidroin films, the cell density and the percentage of 5-bromo...
Source: Biochemistry (Moscow) - July 1, 2020 Category: Biochemistry Source Type: research

Electric Cables of Living Cells. I. Energy Transfer along Coupling Membranes
AbstractThe concept of “electric cables” involved in bioenergetic processes in a living cell was proposed half a century ago [Skulachev, V. P. (1971)Curr. Top.Bioenerg., Elsevier, pp. 127-190]. Membrane structures of a cell were considered as probable pathways for transferring transmembrane electrochemical potential. Further studies have shown that coupling membranes (inner mitochondrial membrane or bacterial cell membrane), i.e., those involved in the generation of membrane potential, can also serve for its transfer. A wide range of organisms from almost all major taxa have been discovered to employ the energy...
Source: Biochemistry (Moscow) - July 1, 2020 Category: Biochemistry Source Type: research

Molecular Pathway Activation Markers Are Associated with Efficacy of Trastuzumab Therapy in Metastatic HER2-Positive Breast Cancer Better than Individual Gene Expression Levels
AbstractIncreased expression or amplification of HER2 receptor tyrosine kinase geneERBB2 is well-known and widely used as a prognostic biomarker of breast cancer (BC) response to the targeted treatment with trastuzumab and its analogs. Considering that part of the BC patients overexpressing HER2 does not respond to trastuzumab, clinical trial NCT03521245 was initiated to identify additional gene expression and molecular pathway activation response biomarkers to trastuzumab treatment in HER2-positive BC. Using RNA sequencing gene expression in 23 formalin-fixed, paraffin embedded HER2 positive BC tissue blocks from patients...
Source: Biochemistry (Moscow) - July 1, 2020 Category: Biochemistry Source Type: research

Regulation of Thiamine (Vitamin B1)-Dependent Metabolism in Mammals by p53
AbstractTranscriptional factor p53 is a master regulator of energy metabolism. Energy metabolism strongly depends on thiamine (vitamin B1) and/or its natural derivatives. Thiamine diphosphate (ThDP), which is a major thiamine derivative, affects p53 binding to DNA. In order to elucidate the mechanism of regulation of thiamine-dependent metabolism by p53, we assessed putative p53-binding sites near transcription starting points in genes coding for transporters and enzymes, whose function is associated with thiamine and/or its derivatives. The predictions were validated by studying cell metabolic response to the p53 inducer ...
Source: Biochemistry (Moscow) - July 1, 2020 Category: Biochemistry Source Type: research

Transcription Factor Nrf2 as a Potential Therapeutic Target for Prevention of Cytokine Storm in COVID-19 Patients
This article suggests rationale for the use of Nrf2 inducers to prevent development of an excessive inflammatory response in COVID-19 patients. (Source: Biochemistry (Moscow))
Source: Biochemistry (Moscow) - July 1, 2020 Category: Biochemistry Source Type: research

Manipulating Cellular Energetics to Slow Aging of Tissues and Organs
AbstractUp to now numerous studies in the field of gerontology have been published. Nevertheless, a well-known food restriction remains the most reliable and efficient way of lifespan extension. Physical activity is also a well-documented anti-aging intervention being especially efficient in slowing down the age-associated decline of skeletal muscle mass. In this review we focus on the molecular mechanisms of the effect of physical exercise on muscle tissues. We also discuss the possibilities of pharmacological extension of this effect to the rest of the tissues. During the exercise, the level of ATP decreases triggering a...
Source: Biochemistry (Moscow) - June 1, 2020 Category: Biochemistry Source Type: research

Highly-Active Recombinant Formate Dehydrogenase from Pathogenic Bacterium Staphylococcus aureus : Preparation and Crystallization
AbstractNAD+-dependent formate dehydrogenase fromStaphylococcus aureus (SauFDH) is one of the key enzymes responsible for the survival of this pathogen in the form of biofilms. 3D structure of the enzyme might be helpful in the search for highly specific SauFDH inhibitors that can be used as antibacterial agents exactly againstS. aureus biofilms. Here, we prepared a recombinant SauFDH inEscherichia coli cells with a yield of 1 g target protein per liter medium. The developed procedure for the enzyme purification allowed to obtain 400 mg of homogenous enzyme with 61% yield. The specific activity of the purified recombinant ...
Source: Biochemistry (Moscow) - June 1, 2020 Category: Biochemistry Source Type: research

The Role of Liquid –Liquid Phase Separation in the Compartmentalization of Cell Nucleus and Spatial Genome Organization
AbstractFunctional compartmentalization of the cell nucleus plays an important role in the regulation of genome activity by providing accumulation of enzymes and auxiliary factors in the reaction centers, such as transcription factories, Cajal bodies, speckles, etc. The mechanisms behind the nucleus functional compartmentalization are still poorly understood. There are reasons to believe that the key role in the nucleus compartmentalization belongs to the process of liquid –liquid phase separation. In this brief review, we analyze results of experimental studies demonstrating that liquid–liquid phase separation...
Source: Biochemistry (Moscow) - June 1, 2020 Category: Biochemistry Source Type: research

Creation of Chitinase Producer and Disruption of Micromycete Cell Wall with the Obtained Enzyme Preparation
AbstractA recombinant strain producing a complex of extracellular enzymes including chitinase fromMyceliophtora thermophila was created based on the fungusPenicillium verruculosum. The activity of the enzyme preparations obtained from the cultural fluid of the producer strain was 0.55, 0.53, and 0.66 U/mg protein with chitin and chitosans with the molecular weight of 200 and 1000 kDa, respectively. The temperature optimum for the recombinant chitinase was 52-65 °C; the pH optimum was 4.5-6.2, which corresponded to the published data for this class of the enzymes. The content of heterologous chitinase in the obtained en...
Source: Biochemistry (Moscow) - June 1, 2020 Category: Biochemistry Source Type: research

Ommochromes from the Compound Eyes of Insects: Physicochemical Properties and Antioxidant Activity
The objective of this study was screening of ommochromes from the compound eyes of insects and comparison of their antioxidant properties. Ommochromes were isolated in preparative quantities from insects of five different families: Stratiomyidae, Sphingidae, Blaberidae, Acrididae, and Tenebrionidae. The yield of ommochromes (dry pigment weight) was 0.9-5.4% of tissue wet weight depending on the insect species. Isolated pigments were analyzed by high-performance liquid chromatography and represented a mixture of several ommochromes of the ommatin series. The isolated ommochromes displayed a pronounced fluorescence with the ...
Source: Biochemistry (Moscow) - June 1, 2020 Category: Biochemistry Source Type: research

Effect of Cysteine Residue Substitution in the GCSAG Motif of the PMGL2 Esterase Active Site on the Enzyme Properties
AbstractThe gene coding for PMGL2 esterase, which belongs to the family of mammalian hormone-sensitive lipases (HSLs), was discovered by screening a metagenomic DNA library from a permafrost soil. The active site of PMGL2 contains conserved GXSXG motif which includes Cys173 residue next to the catalytic Ser174. In order to clarify the functional role of the cysteine residue in the GCSAG motif, we constructed a number of PMGL2 mutants with Cys173 substitutions and studied their properties. The specific activity of the C173D mutant exceeded the specific activity of the wild-type enzyme (wtPMGL2) by 60%, while the C173T/C202S...
Source: Biochemistry (Moscow) - June 1, 2020 Category: Biochemistry Source Type: research

Phycoerythrin Association with Photosystem II in the Cryptophyte Alga Rhodomonas salina
AbstractCryptophyte algae belong to a special group of oxygenic photosynthetic organisms containing pigment combination unique for plastids – phycobiliproteins and chlorophylla/c-containing antenna. Despite the progress in investigation of morphological and ecological features, as well as genome-based systematics of cryptophytes, their photosynthetic apparatus remains poorly understood. The ratio of the photosystems (PS)s I and II is unknown and information on participation of the two antennal complexes in functions of the two photosystems is inconsistent. In the present work we demonstrated for the first time that t...
Source: Biochemistry (Moscow) - June 1, 2020 Category: Biochemistry Source Type: research

Involvement of SASH1 in the Maintenance of Stable Cell –Cell Adhesion
We examined localization of SASH1 in cultures of normal IAR-20 epithelial cells and HT-29 colorectal cancer cells using immunofluorescence staining and confocal microscopy. IAR-20 normal epithelial cells and HT-29 cells with epithelial phenotype formed stable linear adherens junctions (AJs) associated with circumferential actin bundles. In both IAR-20 and HT-29 cells, SASH1 was co-localized with zones of circumferential actin bundles and linear AJs. SASH1 was not detected in lamellipodia. IAR-20 and HT-29 cells tre ated with Epidermal Growth Factor underwent epithelial-mesenchymal transition (EMT). We observed significant ...
Source: Biochemistry (Moscow) - June 1, 2020 Category: Biochemistry Source Type: research

Evolutionary Loss of the Ability of the Photosystem I Primary Electron Donor for the Redox Interaction with Mn-Bicarbonate Complexes
In this study, we investigated redox interactions between Mn2+-bicarbonate complexes and PSI. Such interactions were almost absent in the original PSI preparations and emerged only in preoxidized PSI preparations containing ~50% oxidized RCs. The interaction between Mn2+-bicarbonate complexes and PSI required increased Mn2+ concentrations, while its dependence on the HCO3– concentration indicated involvement of electroneutral low-potential [Mn(HCO3)2] complex in the process. Analysis of the PSI crystal structure revealed steric hindrances on the RC donor side, which could block the redox interaction between Mn2+-bica...
Source: Biochemistry (Moscow) - June 1, 2020 Category: Biochemistry Source Type: research

Mitochondrial Transplantation: A Critical Analysis
Abstract“Mitochondrial transplantation” refers to a procedure for introducing isolated mitochondria into a damaged area of a heart or other organ. A considerable amount of data has been accumulated on the therapeutic effects of “mitochondrial transplantation” in animals with ischemic heart damage. I n 2017, the first attempts were made to apply this procedure in a clinic. The authors of the method suggest that exogenous mitochondria penetrate into cardiomyocytes, retaining functional activity, and compensate for impaired energy output of endogenous mitochondria. This hypothesis contradicts the well-...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

In vitro Reconstitution of the S. aureus 30S Ribosomal Subunit and RbfA Factor Complex for Structural Studies
This article describes protocols for preparation of RbfA and the small 30S ribosomal subunits and reconstitution and optimization of the 30S–RbfA complex to obtain samples suitable for cryo-electron microsc opy studies. (Source: Biochemistry (Moscow))
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

Molecular Targets in the Chemotherapy of Coronavirus Infection
This article considers six major chemotherapeutic classes aimed at certain viral targets: inhibitors of viral RNA polymerase, inhibitors of viral protease Mpro, inhibitors of proteolytic activation of viral protein S allowing virus entry into the target cell, inhibitors of virus uncoating in cellular endosomes, compounds of exogenous interferons, and compounds of natural and recombinant virus-neutralizing antibodies. In the second stage, when the multiplication of the virus decreases and threatening pathological processes of excessive inflammation, acute respiratory distress syndrome, pulmonary edema, hypoxia, and secondar...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

Mechanisms of Acinetobacter baumannii Capsular Polysaccharide Cleavage by Phage Depolymerases
AbstractAerobic gram-negative bacteriumAcinetobacter baumannii has recently become one of the most relevant pathogens associated with hospital-acquired infections worldwide.A. baumannii produces a capsule around the cell, which represents a thick viscous layer of structurally variable capsular polysaccharide (CPS). The capsule protects the bacteria against unfavorable environmental factors and biological systems, including bacteriophages and host immune system. ManyA. baumannii phages have structural depolymerases (tailspikes) that specifically recognize and digest bacterial CPS. In this work, we studied the interaction of...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

α-Synuclein Overexpression in SH-SY5Y Human Neuroblastoma Cells Leads to the Accumulation of Thioflavin S-positive Aggregates and Impairment of Glycolysis
AbstractDeterioration of energy metabolism in affected cells is an important feature of synucleinopathies, including Parkinson's disease. Here, we studied the association between α-synuclein accumulation and glycolysis using SH-SY5Y neuroblastoma cell lines stably expressing wild-type α-synuclein or its A53T mutant linked to the autosomal dominant form of the disease. Overexpression of both proteins led to the accumulation of thioflavin S-positive aggregates, more pronounc ed for α-synuclein A53T. It also caused changes in the cell energy metabolism manifested as a decrease in the lactate accumulation and...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

Two Glycosyl 1-Phosphate Polymers and Teichulosonic Acid from Glutamicibacter protophormiae VKM Ac-2104 T Cell Wall
AbstractTwo glycosyl 1-phosphate polymers containing monoglycosyl 1-phosphate, -6)- α-D-Glcp-(1-P., and diglycosyl 1-phosphate, -6)- α-D-GalpNAc-(1 →6)-α-D-GlcpNAc-(1-P., in the repeating unit were identified in the cell wall ofGlutamicibacter protophormiae VKM Ac-2104T (formerly,Arthrobacter protophormiae). The structures of these polymers were described for the first time in prokaryotes. Teichulosonic acid, the third identified polymer, with 3-deoxy-D-glycero- α-D-galacto-non-2-ulopyranosonic acid (Kdn) and β-D-glucopyranose residues in the main chain, →6)-β-D-Glcp-(1 →8)-...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

Immune Response and Protective Efficacy of Inactivated and Live Influenza Vaccines Against Homologous and Heterosubtypic Challenge
AbstractInactivated (whole-virion, split, subunit, and adjuvanted) vaccines and live attenuated vaccine were tested in parallel to compare their immunogenicity and protective efficacy. Homologous and heterosubtypic protection against the challenge with influenza H5N1 and H1N1 viruses in a mouse model were studied. Single immunization with live or inactivated whole-virion H5N1 vaccine elicited a high level of serum antibodies and provided complete protection against the challenge with the lethal A/Chicken/Kurgan/3/05 (H5N1) virus, whereas application of a single dose of the split vaccine was much less effective. Adjuvants i...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

Role of Arg243 and His239 Residues in the Recognition of Damaged Nucleotides by Human Uracil-DNA Glycosylase SMUG1
In this study, we investigated the kinetics of conformational transitions in the protein and in various DNA substrates during enzymatic catalysis using the stopped-flow method based on changes in the fluorescence intensity of enzyme ’s tryptophan residues and 2-aminopurine in DNA or fluorescence resonance energy transfer (FRET) between fluorophores in DNA. The kinetic mechanism of interactions between reaction intermediates was identified, and kinetic parameters of the intermediate formation and dissociation were calculated. The obtained data help in elucidating the functions of His239 and Arg243 residues in the reco...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

Melanin from the Lichens Cetraria islandica and Pseudevernia furfuracea : Structural Features and Physicochemical Properties
AbstractLichens are symbiotic photosynthesizing organisms with thalli formed by fungi and algae/cyanobacteria that possess high stress tolerance. One of the factors that contributes to the ability of a lichen to tolerate harsh environmental conditions is the presence of unique metabolites, including high-molecular-weight dark pigments termed melanins. The chemical composition and structure of lichen melanins remain poorly studied. We analyzed the elemental composition, the main functional groups, and the physicochemical properties of melanin extracted fromCetraria islandica andPseudevernia furfuracea lichens. Based on the ...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

Lymphocyte Activation in the Development of Immune Tolerance in Women with Recurrent Pregnancy Loss
AbstractAssociation between lymphocyte activation and formation of immune tolerance, as well as pregnancy outcome, in the case of immunocytotherapy (ICT) was studied in women with idiopathic recurrent pregnancy loss (IRPL). The content and phenotypic characteristics of activated T lymphocytes and NK cells were investigated in the peripheral blood of IRPL patients with different pregnancy outcomes (pregnancy prolongation to the full term and habitual miscarriage). The fraction of activated cells in the subpopulation of cytotoxic T lymphocytes (CD3+CD8+/CD3+CD8+CD69+) before ICT was significantly lower in women who lost the ...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

Optimization of Method for Human Sex Determination Using Peptidome Analysis of Teeth Enamel from Teeth of Different Biological Generation, Archeological Age, and Degrees of Taphonomic Preservation
AbstractDetermination of biological sex to human remains is a fundamental requirement in anthropological, archeological, and forensic anthropological studies. Sex determination based on morphological criteria is significantly limited in the cases of juvenile remains and adult skeletons in a poor state of preservation. Regular attempts have been made to use alternative techniques to resolve this issue, including analysis of tooth enamel peptides by liquid chromatography/mass spectrometry. Optimization of this method involving acid etching of tooth enamel for 10 min followed by desalting of the products of etching on SDB-RPS...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

Membrane Contacts in Plasmodesmata: Structural Components and Their Functions
AbstractPlasmodesmata (PD) are intercellular channels in plant tissues providing continuity of the cytoplasm, the plasma membrane (PM) and the endoplasmic reticulum (ER) of neighboring cells. These channels allow the active transport of macromolecules such as proteins or RNAs. Thus, PD are believed to play a critical role in the functional unity of plant tissues and the transport of signals required for plant development and responses to external stimuli. Recent findings indicate that the PD channel contains a specialized type of ER-PM membrane contact sites (MCSs), structural links formed between ER and PM with tethering ...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

Effect of His 6 -tag Position on the Expression and Properties of Phenylacetone Monooxygenase from Thermobifida fusca
AbstractPhenylacetone monooxygenase (EC 1.14.13.92, PAMO) catalyzes oxidation of ketones with molecular oxygen and NADPH with the formation of esters. PAMO is a promising enzyme for biotechnological processes. In this work, we generated genetic constructs coding for PAMO fromThermobifida fusca, containingN- orC-terminal His6-tags (PAMO N and PAMO C, respectively), as well as PAMO L with the His6-tag attached to the enzymeC-terminus via a 19-a.a. spacer. All PAMO variants were expressed as catalytically active proteins inEscherichia coli BL21(DE3) cells; however, the expression level of PAMO N was 3 to 5 times higher than f...
Source: Biochemistry (Moscow) - May 1, 2020 Category: Biochemistry Source Type: research

Protein Complex NDC80: Properties, Functions, and Possible Role in Pathophysiology of Cell Division
AbstractMitotic division maintains genetic identity of any multicellular organism throughout an entire lifetime. Each time a parent cell divides, chromosomes are equally distributed between the daughter cells due to the action of mitotic spindle. Mitotic spindle is formed by the microtubules that represent dynamic polymers of tubulin protein. Spindle microtubules are attached end-on to kinetochores – large multi-protein complexes on chromosomes. This review focuses on the four-subunit NDC80 complex, one of the most important kinetochore elements that plays a major role in the attachment of assembling/disassembling mi...
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

Analysis of Glycosyl-Enzyme Intermediate Formation in the Catalytic Mechanism of Influenza Virus Neuraminidase Using Molecular Modeling
AbstractUsing classical molecular dynamics, constant-pH molecular dynamics simulation, metadynamics, and combined quantum mechanical and molecular mechanical approach, we identified an alternative pathway of glycosyl-enzyme intermediate formation during oligosaccharide substrate conversion by the influenza H5N1 neuraminidase. The Asp151 residue located in the enzyme mobile loop plays a key role in catalysis within a wide pH range due to the formation of a network of interactions with water molecules. Considering that propagation of influenza virus takes place in the digestive tract of birds at low pH values and in the huma...
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

Inorganic Polyphosphate and Physiological Properties of Saccharomyces cerevisiae Yeast Overexpressing Ppn2
AbstractThe effect of the yeast endopolyphosphatase Ppn2 overproduction on the metabolism of inorganic polyphosphates inSaccharomyces cerevisiae yeast was studied. Expression of thePPN2 gene under control of the strong constitutive promoter of glyceraldehyde 3-phosphate dehydrogenase gene (PKG1) led to a significant increase in the endopolyphosphatase activity stimulated by cobalt/zinc ions. This activity was present in both soluble and membrane subcellular fractions; it was higher toward long-chain polyphosphates and could be stimulated by ADP. The content of short-chain polyphosphates in the cells of the overexpressing s...
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

Mechanisms of TGF β3 Action as a Therapeutic Agent for Promoting the Synthesis of Extracellular Matrix Proteins in Hyaline Cartilage
AbstractHyaline cartilage is a nonvascular connective tissue covering the joint surface. It consists mostly of the extracellular matrix proteins and a small number of highly differentiated chondrocytes. At present, various techniques for repairing joint surfaces damage, for example, the use of modified cell cultures and biodegradable scaffolds, are under investigation. Molecular mechanisms of cartilage tissue proliferation have been also actively studied in recent years. TGF β3, which plays a critical role in the proliferation of normal cartilage tissue, is one of the most important protein among cytokines and growth ...
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

An Assay for the Activity of Base Excision Repair Enzymes in Cellular Extracts Using Fluorescent DNA Probes
AbstractDamaged DNA bases are removed by the base excision repair (BER) mechanism. This enzymatic process begins with the action of one of DNA glycosylases, which recognize damaged DNA bases and remove them by hydrolyzingN-glycosidic bonds with the formation of apurinic/apyrimidinic (AP) sites. Apurinic/apyrimidinic endonuclease 1 (APE1) hydrolyzes the phosphodiester bond on the 5 ′-side of the AP site with generation of the single-strand DNA break. A decrease in the functional activity of BER enzymes is associated with the increased risk of cardiovascular, neurodegenerative, and oncological diseases. In this work, w...
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

Ouabain and Marinobufagenin: Physiological Effects on Human Epithelial and Endothelial Cells
AbstractLong-term study on the identification of Na,K-ATPase endogenous inhibitors in mammalian tissues has resulted in the discovery of ouabain, marinobufagenin (MBG), and other cardiotonic steroids (CTS) in the blood plasma. Production of ouabain and MBG is increased in essential hypertension and other diseases associated with hypervolemia. Here, we compared the effects of ouabain and MBG on the Na,K-ATPase activity (measured as the transport of Na+, K+, and Rb+ ions) and proliferation and death of human renal epithelial cells (HRECs) and human umbilical vein endothelial cells (HUVEC) expressing α1-Na,K-ATPase. Oua...
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

Amino Acids as Regulators of Cell Metabolism
AbstractIn this review, we discuss the principles of regulation and synchronization of metabolic processes in mammalian cells using a two-component model of cell metabolism consisting of a controlling signaling system that regulates major enzymatic cascades and executive metabolic system that directly performs biosynthetic reactions. This approach has allowed us to distinguish two transitional metabolic states (from catabolism to anabolism and vice versa) accompanied by major rearrangements in the signaling system. The signaling system of natural amino acids was selected, because amino acids are involved in both signaling ...
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

Translesion DNA Synthesis and Carcinogenesis
AbstractTens of thousands of DNA lesions are formed in mammalian cells each day. DNA translesion synthesis is the main mechanism of cell defense against unrepaired DNA lesions. DNA polymerases iota (Pol ι), eta (Pol η), kappa (Pol κ), and zeta (Pol ζ) have active sites that are less stringent toward the DNA template structure and efficiently incorporate nucleotides opposite DNA lesions. However, these polymerases display low accuracy of DNA synthesis and can introduce mutations in genomic DNA. Impaired functioning of these enzymes can lead to an increased risk of cancer. (Source: Biochemistry (Moscow))
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

High Level of Gene Transcription at the Embryonic Stage Leads to the Suppression of Heterochromatic Trans -Inactivation in Drosophila melanogaster Adults
AbstractIn some cases, gene transfer from euchromatin to constitutive heterochromatin as a result of chromosomal rearrangement is accompanied by epigenetic inactivation of this gene (cis-inactivation). In the case oftrans-inactivation, transgenes in the normal chromosome are repressed by thecis-inactivation-causing rearranged homologous chromosome.Trans-inactivation is a result of the somatic pairing of homologs and the transfer of the normal chromosomal segment to the heterochromatic compartment of the nucleus. Previously, we have shown that the degree oftrans-inactivation of theUAS-eGFP reporter gene in adult flies depen...
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

Structural Organization and Dynamic Characteristics of the Binding Site for Conformational Rearrangement Inhibitors in Hemagglutinins from H3N2 and H7N9 Influenza Viruses
AbstractComputer models of hemagglutinins from the H3N2 and H7N9 influenza viruses were developed to study structural organization and dynamic characteristics of the binding site for the conformational rearrangement inhibitors. The metadynamics was used to map the binding site free energy and to define the volume of its most energetically favorable states. It was demonstrated by simulation of the umifenovir (Arbidol) interaction with hemagglutinin that ligand binding requires an increase in the binding site volume and deformation of its most energetically favorable state. We also identified amino acid residues directly inv...
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

Catalytic Subunit of PKA as a Prototype of the Eukaryotic Protein Kinase Family
AbstractThe catalytic subunit of protein kinase A (PKAc) is conserved in all eukaryotic protein kinases. PKAc consists of two lobes that form the catalytic cleft containing the ATP-binding, peptide-binding site, and catalytic sites. During folding, PKAc secondary structures organize so that the non-polar regions form a globular core, while mobile loops and tails are exposed and can act as regulatory elements.De novo synthesized PKAc is phosphorylated at the T-loop, resulting in the formation of the active center capable of high-affinity binding of co-substrates. The ATP-molecule “sticks” the two lobes together,...
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

Substrate Diversity of L-Threonic Acid Dehydrogenase Homologs
AbstractDespite physiological importance of aldonic sugar acids for living organisms, little is known about metabolic pathways of these compounds. Here, we investigated the functional diversity of homologs of L-threonic acid dehydrogenase (ThrDH; UniProt ID: Q0KBC7), an enzyme composed of two NAD-binding domains (PF14833 and PF03446). Ten ThrDH homologs with different genomic context were studied; seven new enzymatic activities were identified, such as (R)-pantoate dehydrogenase, L-altronic acid dehydrogenase, 6-deoxy-L-talonate dehydrogenase, L-idonic acid dehydrogenase, D-xylonic acid dehydrogenase, D-gluconic acid dehyd...
Source: Biochemistry (Moscow) - April 1, 2020 Category: Biochemistry Source Type: research

Effect of Human XRCC1 Protein Oxidation on the Functional Activity of Its Complexes with the Key Enzymes of DNA Base Excision Repair
In this study, we demonstrated for the first timein vitro formation of the ternary XRCC1 complex with the key enzymes of SP BER — DNA polymerase β (Polβ) and DNA ligase IIIa (LiglIIa) — using the fluorescence-based technique. It was found that Polβ directly interacts with LiglIIa, but their complex is less stable than the XRCC1—Polβ and XRCC1—LigIIIa complexes. The effect of XRCC1 oxidation and composition of the multiprotein complex on the efficiency of DNA synthesis and DNA ligation during DNA repair has been explored. We found that formation of the disulfide bond between Cys12...
Source: Biochemistry (Moscow) - March 1, 2020 Category: Biochemistry Source Type: research

Effect of Structure Variations in the Inter-subunit Contact Zone on the Activity and Allosteric Regulation of Inorganic Pyrophosphatase from Mycobacterium tuberculosis
AbstractHexameric inorganic pyrophosphatase fromMycobacterium tuberculosis (Mt-PPase) has a number of structural and functional features that distinguish it from homologous enzymes widely occurring in living organisms. In particular, it has unusual zones of inter-subunit contacts and lacks theN-terminal region common for other PPases. In this work, we constructed two mutant forms of the enzyme, Ec-Mt-PPase and R14Q-Mt-PPase. In Ec-Mt-PPase, the missing part of the polypeptide chain was compensated with a fragment of PPase fromEscherichia coli (Ec-PPase). In R14Q-Mt-PPase, a point mutation was introduced to the contact inte...
Source: Biochemistry (Moscow) - March 1, 2020 Category: Biochemistry Source Type: research

Thiamine Mono- and Diphosphate Phosphatases in Bovine Brain Synaptosomes
AbstractNeurodegenerative diseases are accompanied by changes in the activity of thiamine mono- and diphosphate phosphatases, but molecular identification of these mammalian enzymes is incomplete. In this work, the protein fraction of bovine brain synaptosomes displaying phosphatase activity toward thiamine derivatives was subjected to affinity chromatography on thiamine-Sepharose. Protein fractions eluted with thiamine (pH 7.4 or 5.6), NaCl, and urea were assayed for the phosphatase activity against thiamine monophosphate (ThMP), thiamine diphosphate (ThDP), and structurally similar purine nucleotides. Proteins in each fr...
Source: Biochemistry (Moscow) - March 1, 2020 Category: Biochemistry Source Type: research

Alternative Naphthalene Metabolic Pathway Includes Formation of ortho -Phthalic Acid and Cinnamic Acid Derivatives in the Rhodococcus opacus Strain 3D
In this study, we investigated the ability ofRhodococcus opacus strain 3D to utilize naphthalene as a sole carbon and energy source. The characteristic feature of this strain is the inability to grow in the mineral medium supplemented with salicylate (typical intermediate of naphthalene degradation in Gram-negative bacteria). The absence of salicylate hydroxylase activity and salicylate accumulation in the course ofR. opacus 3D cultivation in the mineral medium supplemented with naphthalene indicated existence of an alternative pathway of naphthalene oxidation. At the same time,R. opacus 3D was able to use monoaromatic com...
Source: Biochemistry (Moscow) - March 1, 2020 Category: Biochemistry Source Type: research

Neuroprotective Effects of Peptides in the Brain: Transcriptome Approach
AbstractThe importance of studying the action mechanisms of drugs based on natural regulatory peptides is commonly recognized. Particular attention is paid to the peptide drugs that contribute to the restoration of brain functions after acute cerebrovascular accidents (stroke), which for many years continues to be one of the main problems and threats to human health. However, molecular genetic changes in the brain in response to ischemia, as well as the mechanisms of protective effects of peptides, have not been sufficiently studied. This limits the use of neuroprotective peptides and makes it difficult to develop new, mor...
Source: Biochemistry (Moscow) - March 1, 2020 Category: Biochemistry Source Type: research