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Biochemistry. Biokhimii︠a︡

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https://www.readbyqxmd.com/read/30482154/cysmotif-searcher-pipeline-for-antimicrobial-peptide-identification-in-plant-transcriptomes
#1
A A Shelenkov, A A Slavokhotova, T I Odintsova
In this paper, we present the new Cysmotif searcher pipeline for identification of various antimicrobial peptides (AMPs), the most important components of innate immunity, in plant transcriptomes. Cysmotif searcher reveals and classifies short cysteine-rich amino acid sequences containing an open reading frame and a signal peptide cleavage site. Due to the combination of various search methods, Cysmotif searcher allows to obtain the most complete repertoire of AMPs for one or more transcriptomes in a short amount of time...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482153/erratum-to-structural-relationships-between-genetically-closely-related-o-antigens-of-escherichia-coli-and-shigella-spp-biochemistry-moscow-81-600-2016
#2
Ya A Knirel, Chengqian Qian, A S Shashkov, O V Sizova, E L Zdorovenko, O I Naumenko, S N Senchenkova, A V Perepelov, Bin Liu
This corrects the article DOI: 10.1134/S0006297916060067.
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482152/aggregation-of-influenza-a-virus-nuclear-export-protein
#3
A O Golovko, O N Koroleva, A P Tolstova, N V Kuz'mina, E V Dubrovin, V L Drutsa
Influenza A virus nuclear export protein (NEP) plays an important role in the viral life cycle. Recombinant NEP proteins containing (His)6 -tag at either N- or C-terminus were obtained by heterologous expression in Escherichia coli cells and their high propensity for aggregation was demonstrated. Dynamic light scattering technique was used to study the kinetics and properties of NEP aggregation in solutions under different conditions (pH, ionic strength, presence of low-molecular-weight additives and organic solvents)...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482151/comprehensive-analysis-of-carbohydrate-active-enzymes-from-the-filamentous-fungus-scytalidium-candidum-3c
#4
I Yu Pavlov, E V Eneyskaya, K S Bobrov, D E Polev, D R Ivanen, A T Kopylov, S N Naryzhny, A A Kulminskaya
Complete enzymatic degradation of plant polysaccharides is a result of combined action of various carbohydrate-active enzymes (CAZymes). In this paper, we demonstrate the potential of the filamentous fungus Scytalidium candidum 3C for processing of plant biomass. Structural annotation of the improved assembly of S. candidum 3C genome and functional annotation of CAZymes revealed putative gene sequences encoding such proteins. A total of 190 CAZyme-encoding genes were identified, including 104 glycoside hydrolases, 52 glycosyltransferases, 28 oxidative enzymes, and 6 carbohydrate esterases...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482150/effect-of-disulfide-bond-incorporation-on-the-structure-and-activity-of-endostatin-peptide
#5
S Ehtesham, R Sariri, A Eidi, S Hosseinkhani
The structure and function of a 27-a.a. fragment of the N-terminal sequence of human endostatin (ES-Zn) were compared to those of the mutant peptide (ES-SSZn) obtained by adding Cys-Pro-Ala to the endostatin N-terminus and substituting Asn16 for Cys ensuring formation of a disulfide bond. Structural comparison of ES-Zn and ES-SSZn by far-UV circular dichroism (CD), intrinsic fluorescence, and molecular dynamics simulation methods revealed significant structural perturbations in ES-SSZn, such as elimination of the β-sheet conformer, modification of the N-terminal loop structure, and reorganization of dynamic properties of the entire peptide backbone...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482149/lymphocyte-phosphatase-associated-phosphoprotein-is-a-substrate-of-protein-kinase-ck2
#6
T D Tsoy, N A Kruglova, A V Filatov
Lymphocyte phosphatase-associated phosphoprotein (LPAP) is a molecular partner of CD45 phosphatase that plays a key role in the regulation of antigen-specific activation of lymphocytes. The functions of LPAP still remain unknown. We believe that studying LPAP phosphorylation pathways could shed light on its functions. In this work, we studied the phosphorylation of LPAP ectopically expressed in non-lymphoid cells in order to determine the effect of LPAP interaction partners on its phosphorylation. We found that phosphorylation at Ser153 and Ser163 in non-hematopoietic HEK293 cells was conserved, while phosphorylation at Ser99 and Ser172 was almost absent...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482148/contribution-of-eutrema-salsugineum-cold-shock-domain-structure-to-the-interaction-with-rna
#7
V V Taranov, N E Zlobin, K I Evlakov, A O Shamustakimova, A V Babakov
Plant cold shock domain proteins (CSDPs) are DNA/RNA-binding proteins. CSDPs contain the conserved cold shock domain (CSD) in the N-terminal part and a varying number of the CCHC-type zinc finger (ZnF) motifs alternating with glycine-rich regions in the C-terminus. CSDPs exhibit RNA chaperone and RNA-melting activities due to their nonspecific interaction with RNA. At the same time, there are reasons to believe that CSDPs also interact with specific RNA targets. In the present study, we used three recombinant CSDPs from the saltwater cress plant (Eutrema salsugineum) - EsCSDP1, EsCSDP2, EsCSDP3 with 6, 2, and 7 ZnF motifs, respectively, and showed that their nonspecific interaction with RNA is determined by their C-terminal fragments...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482147/exogenous-3-deoxyglucosone-induced-carbonyl-and-oxidative-stress-causes-%C3%AE-cells-dysfunction-by-impairing-gut-permeability-in-rats
#8
L Zhou, X D Song, H Xu, G Q Liang, F Wang, L R Zhang, F Huang, J Cai, G R Jiang
3-Deoxyglucosone (3DG) is a highly reactive dicarbonyl species, and its accumulation evokes carbonyl and oxidative stress. Our recent data reveal the role of 3DG as an independent factor for the development of prediabetes and suggest that intestine could be its novel target tissue. The present study investigated whether exogenous 3DG increases intestinal permeability by triggering carbonyl and oxidative stress, thus contributing to β-cell dysfunction. Rats were administered 3DG for two weeks by gastric gavage...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482146/vitamin-d-in-nature-a-product-of-synthesis-and-or-degradation-of-cell-membrane-components
#9
REVIEW
H Göring
The review discusses the data on vitamin D accumulation in animals, plants, and other organisms. 7-Dehydrocholesterol (7-DHC) and ergosterol are considered to be the only true precursors of vitamin D, although even vitamin D2 (ergocalciferol) is not fully comparable to vitamin D3 (cholecalciferol) in regard to their functions. These precursors are converted by UV radiation into the corresponding D vitamins. There are a few published reports that this reaction can also occur in the dark or under blue light, which is unexpected and requires explanation...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482145/pseudogenes-as-functionally-significant-elements-of-the-genome
#10
REVIEW
T F Kovalenko, L I Patrushev
Pseudogene is a gene copy that has lost its original function. For a long time, pseudogenes have been considered as "junk DNA" that inevitably arises as a result of ongoing evolutionary process. However, experimental data obtained during recent years indicate this understanding of the nature of pseudogenes is not entirely correct, and many pseudogenes perform important genetic functions. In the review, we have addressed classification of pseudogenes, methods of their detection in the genome, and the problem of their evolutionary conservatism and prevalence among species belonging to different taxonomic groups in the light of modern data...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482144/molecular-factors-of-the-maintenance-and-activation-of-the-juvenile-phenotype-of-cellular-sources-for-eye-tissue-regeneration
#11
REVIEW
E N Grigoryan
Modern achievements in the understanding of tissue regeneration, identification of endogenous cell sources for regeneration, and development of approaches for induction and differentiation of pluripotent stem cells have open broad prospects for regenerative medicine. However, application of the obtained information in medicine is hindered by insufficient knowledge on the molecular factors and their combinations capable of regulating the age and fate of cellular sources for eye tissue reparation as well as on the regenerative responses of these cells...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482143/regulation-of-protein-synthesis-in-inactivated-skeletal-muscle-signal-inputs-protein-kinase-cascades-and-ribosome-biogenesis
#12
REVIEW
T M Mirzoev, B S Shenkman
Disuse atrophy of skeletal muscles is characterized by a significant decrease in the mass and size of muscle fibers. Disuse atrophy develops as a result of prolonged reduction in the muscle functional activity caused by bed rest, limb immobilization, and real or simulated microgravity. Disuse atrophy is associated with the downregulation of protein biosynthesis and simultaneous activation of protein degradation. This review is focused on the key molecular mechanisms regulating the rate of protein synthesis in mammalian skeletal muscles during functional unloading...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30482142/regulation-of-tumor-suppressor-gene-cdkn2a-and-encoded-p16-ink4a-protein-by-covalent-modifications
#13
REVIEW
Yang Jiao, Yunpeng Feng, Xiuli Wang
CDKN2A is one of the most studied tumor suppressor genes. It encodes the p16-INK4a protein that plays a critical role in the cell cycle progression, differentiation, senescence, and apoptosis. Mutations in CDKN2A or dysregulation of its functional activity are frequently associated with various types of human cancer. As a cyclin-dependent kinase inhibitor, p16-INK4a forms a complex with cyclin-dependent kinases 4/6 (CDK4/6) thereby competing with cyclin D. It is believed that the helix-turn-helix structures in the content of tandem ankyrin repeats in p16-INK4a are required for the protein interaction with CDK4...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30472964/inhibition-of-cannabinoid-receptor-1-can-influence-the-lipid-metabolism-in-mice-with-diet-induced-obesity
#14
L W Wei, Z Q Yuan, M D Zhao, C W Gu, J H Han, L Fu
A growing number of evidences accumulated about critical metabolic role of cannabinoid type 1 receptor (CB1), carnitine palmitoyltransferase-1 (CPT1) and peroxisome proliferator-activated receptors (PPARs) in some peripheral tissues, including adipose tissue, liver, skeletal muscle and heart. To better understand the interactions of CB1, CPT1 and PPARs in these tissues, 30 diet-induced obese (DIO) C57BL/6J male mice were obtained, weight-matched and divided into two groups (15 in each group): (i) DIO/vehicle mice (D-Veh) and (ii) DIO/SR141716 mice (D-SR) treated with SR141716 (or rimonabant, a selective CB1 receptor blocker) administered orally (10 mg/kg daily)...
October 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30472963/does-oxidation-of-mitochondrial-cardiolipin-trigger-a-chain-of-antiapoptotic-reactions
#15
A Y Mulkidjanian, D N Shalaeva, K G Lyamzaev, B V Chernyak
Oxidative stress causes selective oxidation of cardiolipin (CL), a four-tail lipid specific for the inner mitochondrial membrane. Interaction with oxidized CL transforms cytochrome c into peroxidase capable of oxidizing even more CL molecules. Ultimately, this chain of events leads to the pore formation in the outer mitochondrial membrane and release of mitochondrial proteins, including cytochrome c, into the cytoplasm. In the cytoplasm, cytochrome c promotes apoptosome assembly that triggers apoptosis (programmed cell death)...
October 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30472962/the-expression-of-matryoshka-gene-encoding-a-homologue-of-kunitz-peptidase-inhibitor-is-regulated-both-at-the-level-of-transcription-and-translation
#16
E V Sheshukova, T V Komarova, N M Ershova, A M Bronstein, Y L Dorokhov
The gene for Kunitz peptidase inhibitor-like protein (KPILP) contains nested alternative open reading frame (aORF) that controls expression of the maternal mRNA. The content of NbKPILP mRNA in intact leaves of Nicotiana benthamiana plant is low but increases significantly upon extended dark exposure or when foreign nucleic acid is overexpressed in the cells. The NbKPILP gene promoter along with the expressed nested aORF are likely to play an important role in maintaining the levels of NbKPILP mRNA. To elucidate the role of NbKPILP promoter, we isolated a fragment of N...
October 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30472961/skq1-controls-casp3-gene-expression-and-caspase-3-like-activity-in-the-brain-of-rats-under-oxidative-stress
#17
S B Panina, O I Gutsenko, N P Milyutina, I V Kornienko, A A Ananyan, D Yu Gvaldin, A A Plotnikov, V V Vnukov
Here, we studied the effect of the mitochondria-targeted antioxidant SkQ1 (plastoquinone cationic derivative) on the CASP3 gene expression and caspase-3 activity in rat cerebral cortex and brain mitochondria under normal conditions and in oxidative stress induced by hyperbaric oxygenation (HBO). Under physiological conditions, SkQ1 administration (50 nmol/kg, 5 days) did not affect the CASP3 gene expression and caspase-3-like activity in the cortical cells, as well as caspase-3-like activity in brain mitochondria, but caused a moderate decrease in the content of primary products of lipid peroxidation (LPO) and an increase in the reduced glutathione (GSH) level...
October 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30472960/thermodynamic-study-of-interactions-of-distamycin-a-with-chromatin-in-rat-liver-nuclei-in-the-presence-of-polyamines
#18
A N Prusov, T A Smirnova, G Ya Kolomijtseva
We studied the thermodynamics of melting of isolated rat liver nuclei with different degrees of chromatin condensation determined by the concentration of polyamines (PA) and the solution ionic strength, as well as the effect of the antibiotic distamycin A (DM) on melting. Differential scanning calorimetry (DSC) profiles of nuclear preparations contained three peaks that reflected melting of three main chromatin domains. The number of peaks did not depend on the degree of condensation; however, nuclei with more condensed chromatin had a higher total enthalpy...
October 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30472959/hydrophobic-derivatives-of-glycopeptide-antibiotics-as-inhibitors-of-protein-kinases
#19
G Cozza, M Fortuna, F Meggio, S Sarno, M H G Kubbutat, F Totzke, C Schaechtele, L A Pinna, E N Olsufyeva, M N Preobrazhenskaya
As key regulators of cell signaling, protein kinases (PKs) are attractive targets for therapeutic intervention in a variety of diseases. Herein, we report for the first time the inhibitory activity of polycyclic peptides, particularly, derivatives of glycopeptide antibiotics teicoplanin and eremomycin, against a panel of 12 recombinant human protein kinases and two protein kinases (CK1 and CK2) isolated from rat liver. Several of the investigated compounds inhibited various PKs with IC50 values below 10 μM and caused >90% suppression of the enzyme activity at 10 µM concentration...
October 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30472958/synthesis-in-escherichia-coli-and-characterization-of-human-recombinant-erythropoietin-with-additional-heparin-binding-domain
#20
A S Karyagina, T M Grunina, M S Poponova, P A Orlova, V N Manskikh, A V Demidenko, N V Strukova, M S Manukhina, K E Nikitin, A M Lyaschuk, Z M Galushkina, S A Cherepushkin, N B Polyakov, A I Solovyev, V G Zhukhovitsky, D A Tretyak, I S Boksha, A V Gromov, V G Lunin
Recombinant human erythropoietin (EPO) with additional N-terminal heparin-binding protein domain (HBD) from bone morphogenetic protein 2 was synthesized in Escherichia coli cells. A procedure for HBD-EPO purification and refolding was developed for obtaining highly-purified HBD-EPO. The structure of recombinant HBD-EPO was close to that of the native EPO protein. HBD-EPO contained two disulfide bonds, as shown by MALDI-TOF mass spectrometry. The protein demonstrated in vitro biological activity in the proliferation of human erythroleukemia TF-1 cell test and in vivo activity in animal models...
October 2018: Biochemistry. Biokhimii︠a︡
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