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    532 results match your criteria BMC Biochemistry [Journal]

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    Feruloyl esterase immobilization in mesoporous silica particles and characterization in hydrolysis and transesterification.
    BMC Biochem 2018 Feb 2;19(1). Epub 2018 Feb 2.
    Department of Biology and Biological Engineering, Industrial Biotechnology Division, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
    Background: Enzymes display high reactivity and selectivity under natural conditions, but may suffer from decreased efficiency in industrial applications. A strategy to address this limitation is to immobilize the enzyme. Mesoporous silica materials offer unique properties as an immobilization support, such as high surface area and tunable pore size. Read More

    Characterization of sulfhydryl oxidase from Aspergillus tubingensis.
    BMC Biochem 2017 Dec 8;18(1):15. Epub 2017 Dec 8.
    VTT Technical Research Centre of Finland, Ltd., P.O. Box 1000, FI-02044, Espoo, Finland.
    Background: Despite of the presence of sulfhydryl oxidases (SOXs) in the secretomes of industrially relevant organisms and their many potential applications, only few of these enzymes have been biochemically characterized. In addition, basic functions of most of the SOX enzymes reported so far are not fully understood. In particular, the physiological role of secreted fungal SOXs is unclear. Read More

    Glycyl-alanyl-histidine protects PC12 cells against hydrogen peroxide toxicity.
    BMC Biochem 2017 Nov 22;18(1):14. Epub 2017 Nov 22.
    Department of Neurology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka, Urayasu, Chiba, Japan.
    Background: Peptides with cytoprotective functions, including antioxidants and anti-infectives, could be useful therapeutics. Carnosine, β-alanine-histidine, is a dipeptide with anti-oxidant properties. Tripeptides of Ala-His-Lys, Pro-His-His, or Tyr-His-Tyr are also of interest in this respect. Read More

    Antiproliferative factor (APF) binds specifically to sites within the cytoskeleton-associated protein 4 (CKAP4) extracellular domain.
    BMC Biochem 2017 Sep 11;18(1):13. Epub 2017 Sep 11.
    Department of Basic Sciences, Geisinger Commonwealth School of Medicine, 525 Pine Street, Scranton, PA, 18509, USA.
    Background: Antiproliferative factor (APF) is a sialoglycopeptide elevated in the urine of patients with interstitial cystitis-a chronic, painful bladder disease. APF inhibits the proliferation of normal bladder epithelial cells and cancer cells in vitro, presumably by binding to its cellular receptor, cytoskeleton associated-protein 4 (CKAP4); however, the biophysical interaction of APF with CKAP4 has not been characterized previously. In this study, we used surface plasmon resonance (SPR) to explore the binding kinetics of the interaction of APF and as-APF (a desialylated APF analogue with full activity) to CKAP4. Read More

    Use of a special Brazilian red-light emitting railroad worm Luciferase in bioassays of NEK7 protein Kinase and Creatine Kinase.
    BMC Biochem 2017 Jul 19;18(1):12. Epub 2017 Jul 19.
    Instituto de Biologia, Departamento Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, Programa de Pós-gradução em Biologia Molecular e Funcional São Paulo, Rua Monteiro Lobato 255, Campinas, SP, CEP 13083-862, Brazil.
    Background: Luciferases, enzymes that catalyze bioluminescent reactions in different organisms, have been extensively used for bioanalytical purposes. The most well studied bioluminescent system is that of firefly and other beetles, which depends on a luciferase, a benzothiazolic luciferin and ATP, and it is being widely used as a bioanalytical reagent to quantify ATP. Protein kinases are proteins that modify other proteins by transferring phosphate groups from a nucleoside triphosphate, usually ATP. Read More

    Dacin, one metalloproteinase from Deinagkistrodon acutus venom inhibiting contraction of mouse ileum muscle.
    BMC Biochem 2017 Jul 12;18(1):11. Epub 2017 Jul 12.
    Animal Toxin Group, Chongqing Key Laboratory of Animal Biology, Chongqing Engineering Research Center of Bioactive Substance, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, Collaborative Innovation Center of Breeding and Deep Processing of Venomous Snakes, College of Life Science, Chongqing Normal University, Chongqing, 401331, China.
    Background: Mice were bitten by five-pace vipers (Deinagkistrodon acutus), and then envenomed. It was well-known that the snake venom mainly disturbed the blood homeostasis of the envenomed victims. Ocassionally, we found that the venom of D. Read More

    Serendipitous discovery of light-induced (In Situ) formation of an Azo-bridged dimeric sulfonated naphthol as a potent PTP1B inhibitor.
    BMC Biochem 2017 May 31;18(1):10. Epub 2017 May 31.
    Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, Concordia University of Wisconsin, Mequon, WI, 53097, USA.
    Background: Protein tyrosine phosphatases (PTPs) like dual specificity phosphatase 5 (DUSP5) and protein tyrosine phosphatase 1B (PTP1B) are drug targets for diseases that include cancer, diabetes, and vascular disorders such as hemangiomas. The PTPs are also known to be notoriously difficult targets for designing inihibitors that become viable drug leads. Therefore, the pipeline for approved drugs in this class is minimal. Read More

    Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase Ldtby biapenem and tebipenem.
    BMC Biochem 2017 May 25;18(1). Epub 2017 May 25.
    Division of Infectious Diseases, Center for Tuberculosis Research, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
    Background: The carbapenem subclass of β-lactams is among the most potent antibiotics available today. Emerging evidence shows that, unlike other subclasses of β-lactams, carbapenems bind to and inhibit non-classical transpeptidases (L,D-transpeptidases) that generate 3 → 3 linkages in bacterial peptidoglycan. The carbapenems biapenem and tebipenem exhibit therapeutically valuable potencies against Mycobacterium tuberculosis (Mtb). Read More

    Chemical and structural characterization of α-N-acetylgalactosaminidase I and II from starfish, asterina amurensis.
    BMC Biochem 2017 May 25;18(1). Epub 2017 May 25.
    Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan.
    Background: The marine invertebrate starfish was found to contain a novel α-N-acetylgalactosaminidase, α-GalNAcase II, which catalyzes removal of terminal α-N-acetylgalactosamine (α-GalNAc), in addition to a typical α-N-acetylgalactosaminidase, α-GalNAcase I, which catalyzes removal of terminal α-N-acetylgalactosamine (α-GalNAc) and, to a lesser extent, galactose. The interrelationship between α-GalNAcase I and α-GalNAcase II and the molecular basis of their differences in substrate specificity remain unknown.

    Results: Chemical and structural comparisons between α-GalNAcase I and II using immunostaining, N-terminal amino acid sequencing and peptide analysis showed high homology to each other and also to other glycoside hydrolase family (GHF) 27 members. Read More

    CrMAPK3 regulates the expression of iron-deficiency-responsive genes in Chlamydomonas reinhardtii.
    BMC Biochem 2017 May 16;18(1). Epub 2017 May 16.
    Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Haikou, 571101, China.
    Background: Under iron-deficient conditions, Chlamydomonas exhibits high affinity for iron absorption. Nevertheless, the response, transmission, and regulation of downstream gene expression in algae cells have not to be investigated. Considering that the MAPK pathway is essential for abiotic stress responses, we determined whether this pathway is involved in iron deficiency signal transduction in Chlamydomonas. Read More

    Structural similarities and functional differences clarify evolutionary relationships between tRNA healing enzymes and the myelin enzyme CNPase.
    BMC Biochem 2017 May 16;18(1). Epub 2017 May 16.
    Centre for Structural Systems Biology - Helmholtz Centre for Infection Research, German Electron Synchrotron (DESY), Hamburg, Germany.
    Background: Eukaryotic tRNA splicing is an essential process in the transformation of a primary tRNA transcript into a mature functional tRNA molecule. 5'-phosphate ligation involves two steps: a healing reaction catalyzed by polynucleotide kinase (PNK) in association with cyclic phosphodiesterase (CPDase), and a sealing reaction catalyzed by an RNA ligase. The enzymes that catalyze tRNA healing in yeast and higher eukaryotes are homologous to the members of the 2H phosphoesterase superfamily, in particular to the vertebrate myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase). Read More

    Binding of smoothelin-like 1 to tropomyosin and calmodulin is mutually exclusive and regulated by phosphorylation.
    BMC Biochem 2017 Mar 21;18(1). Epub 2017 Mar 21.
    Department of Biochemistry & Molecular Biology, University of Calgary, Cumming School of Medicine, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada.
    Background: The smoothelin-like 1 protein (SMTNL1) can associate with tropomyosin (Tpm) and calmodulin (CaM), two proteins essential to the smooth muscle contractile process. SMTNL1 is phosphorylated at Ser301 by protein kinase A during calcium desensitization in smooth muscle, yet the effect of SMTNL1 phosphorylation on Tpm- and CaM-binding has yet to be investigated.

    Results: Using pull down studies with Tpm-Sepharose and CaM-Sepharose, we examined the interplay between Tpm binding, CaM binding, phosphorylation of SMTNL1 and calcium concentration. Read More

    Increased enzymatic hydrolysis of sugarcane bagasse by a novel glucose- and xylose-stimulated β-glucosidase from Anoxybacillus flavithermus subsp. yunnanensis E13.
    BMC Biochem 2017 Mar 16;18(1). Epub 2017 Mar 16.
    Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis. School of Life Sciences, Anhui University, Hefei, Anhui, China.
    Background: β-Glucosidase is claimed as a key enzyme in cellulose hydrolysis. The cellulosic fibers are usually entrapped with hemicelluloses containing xylose. So there is ongoing interest in searching for glucose- and xylose-stimulated β-glucosidases to increase the efficiency of hydrolysis of cellulosic biomass. Read More

    Interactions of histatin-3 and histatin-5 with actin.
    BMC Biochem 2017 Mar 6;18(1). Epub 2017 Mar 6.
    Institute of Dental Sciences, Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel.
    Background: Histatins are histidine rich polypeptides produced in the parotid and submandibular gland and secreted into the saliva. Histatin-3 and -5 are the most important polycationic histatins. They possess antimicrobial activity against fungi such as Candida albicans. Read More

    Systematic substitutions at BLIP position 50 result in changes in binding specificity for class A β-lactamases.
    BMC Biochem 2017 Mar 6;18(1). Epub 2017 Mar 6.
    Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
    Background: The production of β-lactamases by bacteria is the most common mechanism of resistance to the widely prescribed β-lactam antibiotics. β-lactamase inhibitory protein (BLIP) competitively inhibits class A β-lactamases via two binding loops that occlude the active site. It has been shown that BLIP Tyr50 is a specificity determinant in that substitutions at this position result in large differential changes in the relative affinity of BLIP for class A β-lactamases. Read More

    Copper chelation and interleukin-6 proinflammatory cytokine effects on expression of different proteins involved in iron metabolism in HepG2 cell line.
    BMC Biochem 2017 Jan 24;18(1). Epub 2017 Jan 24.
    Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale F. Stagno D'Alcontres, 31, 98166, Messina, Italy.
    Background: In vertebrates, there is an intimate relationship between copper and iron homeostasis. Copper deficiency, which leads to a defect in ceruloplasmin enzymatic activity, has a strong effect on iron homeostasis resulting in cellular iron retention. Much is known about the mechanisms underlying cellular iron retention under "normal" conditions, however, less is known about the effect of copper deficiency during inflammation. Read More

    Effects of protonation on the hydrolysis of triphosphate in vacuum and the implications for catalysis by nucleotide hydrolyzing enzymes.
    BMC Biochem 2016 Jun 29;17(1):12. Epub 2016 Jun 29.
    Computational Biochemistry, Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, D-69120, Heidelberg, Germany.
    Background: Nucleoside triphosphate (NTP) hydrolysis is a key reaction in biology. It involves breaking two very stable bonds (one P-O bond and one O-H bond of water), in either a concurrent or a sequential way. Here, we systematically examine how protonation of the triphosphate affects the mechanism of hydrolysis. Read More

    Knockdown of GGCT inhibits cell proliferation and induces late apoptosis in human gastric cancer.
    BMC Biochem 2016 Dec 1;17(1):19. Epub 2016 Dec 1.
    Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China.
    Background: Gamma glutamylcyclotransferase (GGCT) has been proved to be involved in various cancers, but the biological function of GGCT in gastric cancer is still largely unknown.

    Methods: The expression level of GGCT was evaluated by informatics analyses based on the Oncomine database. GGCT gene was then effectively knocked down via lentivirus mediated short hairpin RNA (shRNA) system. Read More

    Identification of replication-dependent and replication-independent linker histone complexes: Tpr specifically promotes replication-dependent linker histone stability.
    BMC Biochem 2016 Oct 1;17(1):18. Epub 2016 Oct 1.
    Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA.
    Background: There are 11 variants of linker histone H1 in mammalian cells. Beyond their shared abilities to stabilize and condense chromatin, the H1 variants have been found to have non-redundant functions, the mechanisms of which are not fully understood. Like core histones, there are both replication-dependent and replication-independent linker histone variants. Read More

    Avoiding false discovery in biomarker research.
    BMC Biochem 2016 Jul 30;17(1):17. Epub 2016 Jul 30.
    Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
    Background: Human tyrosine-protein phosphatase non-receptor type substrate 1α (SIRPA) is a surface marker identified in cardiomyocytes differentiated from human embryonic stem cells. Our objective was to determine if circulating SIRPA levels can serve as a biomarker of cardiac injury in children undergoing open heart surgery.

    Results: Paired pre- and post-operative serum samples from 48 pediatric patients undergoing open heart surgery and from 6 pediatric patients undergoing non-cardiac surgery (controls) were tested for SIRPA protein levels using commercially available SIRPA ELISA kits from two manufacturers. Read More

    Computational studies of human class V alcohol dehydrogenase - the odd sibling.
    BMC Biochem 2016 Jul 25;17(1):16. Epub 2016 Jul 25.
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
    Background: All known attempts to isolate and characterize mammalian class V alcohol dehydrogenase (class V ADH), a member of the large ADH protein family, at the protein level have failed. This indicates that the class V ADH protein is not stable in a non-cellular environment, which is in contrast to all other human ADH enzymes. In this report we present evidence, supported with results from computational analyses performed in combination with earlier in vitro studies, why this ADH behaves in an atypical way. Read More

    Effect of mutations to amino acid A301 and F361 in thermostability and catalytic activity of the β-galactosidase from Bacillus subtilis VTCC-DVN-12-01.
    BMC Biochem 2016 Jul 8;17(1):15. Epub 2016 Jul 8.
    Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Distr. Caugiay, 10600, Hanoi, Vietnam.
    Background: Beta-galactosidase (EC 3.2.1. Read More

    Auto-thiophosphorylation activity of Src tyrosine kinase.
    BMC Biochem 2016 Jul 7;17(1):13. Epub 2016 Jul 7.
    Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA.
    Background: Intermolecular autophosphorylation at Tyr416 is a conserved mechanism of activation among the members of the Src family of nonreceptor tyrosine kinases. Like several other tyrosine kinases, Src can catalyze the thiophosphorylation of peptide and protein substrates using ATPγS as a thiophosphodonor, although the efficiency of the reaction is low.

    Results: Here, we have characterized the ability of Src to auto-thiophosphorylate. Read More

    Sustained activation of mTORC1 in macrophages increases AMPKα-dependent autophagy to maintain cellular homeostasis.
    BMC Biochem 2016 Jul 7;17(1):14. Epub 2016 Jul 7.
    Human Vaccine Institute and Department of Medicine, Duke University, Durham, NC, 27710, USA.
    Background: The mechanistic target of rapamycin complex 1 (mTORC1) is a well-conserved serine/threonine protein kinase that controls autophagy as well as many other processes such as protein synthesis, cell growth, and metabolism. The activity of mTORC1 is stringently and negatively controlled by the tuberous sclerosis proteins 1 and 2 complex (TSC1/2).

    Results: In contrast to the previous studies using Tsc1 knockout mouse embryonic fibroblasts (MEF) cells, we demonstrated evidence that TSC1 deficient macrophages exhibited enhanced basal and mycobacterial infection-induced autophagy via AMPKα-dependent phosphorylation of ULK1 (Ser555). Read More

    Molecular characterization of protein kinase C delta (PKCδ)-Smac interactions.
    BMC Biochem 2016 May 23;17(1):11. Epub 2016 May 23.
    Lund University, Translational Cancer Research, Medicon Village, Building 404:C3, SE-22363, Lund, Sweden.
    Background: Protein kinase C δ (PKCδ) is known to be an important regulator of apoptosis, having mainly pro- but also anti-apoptotic effects depending on context. In a previous study, we found that PKCδ interacts with the pro-apoptotic protein Smac. Smac facilitates apoptosis by suppressing inhibitor of apoptosis proteins (IAPs). Read More

    Tubulin is a molecular target of the Wnt-activating chemical probe.
    BMC Biochem 2016 May 20;17(1). Epub 2016 May 20.
    Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 2-26-1, Muraokahigashi, Fujisawa, Kanagawa, Japan.
    Background: In drug discovery research, cell-based phenotypic screening is an essential method for obtaining potential drug candidates. Revealing the mechanism of action is a key step on the path to drug discovery. However, elucidating the target molecules of hit compounds from phenotypic screening campaigns remains a difficult and troublesome process. Read More

    Identification and characterization of the novel nuclease activity of human phospholipid scramblase 1.
    BMC Biochem 2016 May 20;17(1):10. Epub 2016 May 20.
    From the Applied and Industrial Microbiology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India.
    Background: Human phospholipid scramblase 1 (hPLSCR1) was initially identified as a Ca(2+) dependent phospholipid translocator involved in disrupting membrane asymmetry. Recent reports revealed that hPLSCR1 acts as a multifunctional signaling molecule rather than functioning as scramblase. hPLSCR1 is overexpressed in a variety of tumor cells and is known to interact with a number of protein molecules implying diverse functions. Read More

    Altered activity patterns of transcription factors induced by endoplasmic reticulum stress.
    BMC Biochem 2016 Mar 24;17. Epub 2016 Mar 24.
    Signosis Inc., 1700 Wyatt Drive, Suite #10-12, Santa Clara, CA, 95054, USA.
    Background: The endoplasmic-reticulum (ER) responds to the burden of unfolded proteins in its lumen by activating intracellular signal transduction pathways, also known as the unfolded protein response (UPR). Many signal transduction events and transcription factors have been demonstrated to be associated with ER stress. The process in which ER stress affects or interacts with other pathways is still a progressing topic that is not completely understood. Read More

    Conserved motif VIII of murine DNA methyltransferase Dnmt3a is essential for methylation activity.
    BMC Biochem 2016 Mar 22;17. Epub 2016 Mar 22.
    Department of Chemistry, Moscow State University, 119991, Moscow, Russia.
    Background: Dnmt3a is a DNA methyltransferase that establishes de novo DNA methylation in mammals. The structure of the Dnmt3a C-terminal domain is similar to the bacterial M. HhaI enzyme, a well-studied prokaryotic DNA methyltransferase. Read More

    Linalool isomerase, a membrane-anchored enzyme in the anaerobic monoterpene degradation in Thauera linaloolentis 47Lol.
    BMC Biochem 2016 Mar 15;17. Epub 2016 Mar 15.
    Department of Microbiology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.
    Background: Thauera linaloolentis 47Lol uses the tertiary monoterpene alcohol (R,S)-linalool as sole carbon and energy source under denitrifying conditions. The conversion of linalool to geraniol had been observed in carbon-excess cultures, suggesting the presence of a 3,1-hydroxyl-Δ(1)-Δ(2)-mutase (linalool isomerase) as responsible enzyme. To date, only a single enzyme catalyzing such a reaction is described: the linalool dehydratase/isomerase (Ldi) from Castellaniella defragrans 65Phen acting only on (S)-linalool. Read More

    1,2-Dichlorobenzene affects the formation of the phosphoenzyme stage during the catalytic cycle of the Ca(2+)-ATPase from sarcoplasmic reticulum.
    BMC Biochem 2016 Mar 11;17. Epub 2016 Mar 11.
    Departamento de Ciencias Químico Biológicas, Laboratorio de Biología Molecular y Bioquímica (Edif. T-216), Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Plutarco Elías Calles #1210 Fovissste Chamizal, Ciudad Juárez, Chihuahua, C.P. 32310, Mexico.
    Background: 1,2-Dichlorobenzene (1,2-DCB) is a benzene-derived molecule with two Cl atoms that is commonly utilized in the synthesis of pesticides. 1,2-DCB can be absorbed by living creatures and its effects on naturally-occurring enzymatic systems, including the effects on Ca(2+)-ATPases, have been poorly studied. Therefore, we aimed to study the effect of 1,2-DCB on the Ca(2+)-ATPase from sarcoplasmic reticulum (SERCA), a critical regulator of intracellular Ca(2+) concentration. Read More

    Substrate specificity and function of acetylpolyamine amidohydrolases from Pseudomonas aeruginosa.
    BMC Biochem 2016 Mar 9;17. Epub 2016 Mar 9.
    Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Haardtring 100, 64295, Darmstadt, Germany.
    Background: Pseudomonas aeruginosa, a Gram-negative, aerobic coccobacillus bacterium is an opportunistic human pathogen and worldwide the fourth most common cause of hospital-acquired infections which are often high mortality such as ventilator-associated pneumoniae. The polyamine metabolism of P. aeruginosa and particularly the deacetylation of acetylpolyamines has been little studied up to now. Read More

    Characterization of a cold-active and salt tolerant esterase identified by functional screening of Arctic metagenomic libraries.
    BMC Biochem 2016 Jan 19;17. Epub 2016 Jan 19.
    NorStruct, Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway.
    Background: The use of metagenomics in enzyme discovery constitutes a powerful approach to access to genomes of unculturable community of microorganisms and isolate novel valuable biocatalysts for use in a wide range of biotechnological and pharmaceutical fields.

    Results: Here we present a novel esterase gene (lip3) identified by functional screening of three fosmid metagenomic libraries, constructed from three marine sediment samples. The sequenced positive fosmid revealed an enzyme of 281 amino acids with similarity to class 3 lipases. Read More

    A comparison of the enzymatic properties of three recombinant isoforms of thrombolytic and antibacterial protein--Destabilase-Lysozyme from medicinal leech.
    BMC Biochem 2015 Nov 21;16:27. Epub 2015 Nov 21.
    Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russia.
    Background: Destabilase-Lysozyme (mlDL) is a multifunctional i-type enzyme that has been found in the secretions from the salivary glands of medicinal leeches. mlDL has been shown to exhibit isopeptidase, muramidase and antibacterial activity. This enzyme attracts interest because it expresses thrombolytic activity through isopeptidolysis of the ε-(γ-Glu)-Lys bonds that cross-link polypeptide chains in stabilised fibrin. Read More

    The GH5 1,4-β-mannanase from Bifidobacterium animalis subsp. lactis Bl-04 possesses a low-affinity mannan-binding module and highlights the diversity of mannanolytic enzymes.
    BMC Biochem 2015 Nov 11;16:26. Epub 2015 Nov 11.
    Enzyme and Protein Chemistry (EPC), Department of Systems Biology, Technical University of Denmark (DTU), Søltofts Plads, building 224, DK-2800, Kgs Lyngby, Denmark.
    Background: β-Mannans are abundant and diverse plant structural and storage polysaccharides. Certain human gut microbiota members including health-promoting Bifidobacterium spp. catabolize dietary mannans. Read More

    The eukaryotic translation initiation factor 3f (eIF3f) interacts physically with the alpha 1B-adrenergic receptor and stimulates adrenoceptor activity.
    BMC Biochem 2015 Oct 23;16:25. Epub 2015 Oct 23.
    Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B-3 Ciudad Universitaria Avenida Francisco J. Múgica S/N, Morelia, Michoacán, 58030, México.
    Background: eIF3f is a multifunctional protein capable of interacting with proteins involved in different cellular processes, such as protein synthesis, DNA repair, and viral mRNA edition. In human cells, eIF3f is related to cell cycle and proliferation, and its deregulation compromises cell viability.

    Results: We here report that, in native conditions, eIF3f physically interacts with the alpha 1B-adrenergic receptor, a plasma membrane protein considered as a proto-oncogene, and involved in vasoconstriction and cell proliferation. Read More

    The laforin/malin E3-ubiquitin ligase complex ubiquitinates pyruvate kinase M1/M2.
    BMC Biochem 2015 Oct 23;16:24. Epub 2015 Oct 23.
    Instituto de Biomedicina de Valencia, CSIC, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Jaime Roig 11, 46010, Valencia, Spain.
    Background: Lafora disease (LD, OMIM 254780) is a fatal neurodegenerative disorder produced mainly by mutations in two genes: EPM2A, encoding the dual specificity phosphatase laforin, and EPM2B, encoding the E3-ubiquitin ligase malin. Although it is known that laforin and malin may form a functional complex, the underlying molecular mechanisms of this pathology are still far from being understood.

    Methods: In order to gain information about the substrates of the laforin/malin complex, we have carried out a yeast substrate-trapping screening, originally designed to identify substrates of protein tyrosine phosphatases. Read More

    Evaluating the role of a trypsin inhibitor from soap nut (Sapindus trifoliatus L. Var. Emarginatus) seeds against larval gut proteases, its purification and characterization.
    BMC Biochem 2015 Oct 22;16:23. Epub 2015 Oct 22.
    Department of Biotechnology, Institute of Science, GITAM University, Rushikonda, Visakhapatnam, 530045, Andhra Pradesh, India.
    Background: The defensive capacities of plant protease Inhibitors (PI) rely on inhibition of proteases in insect guts or those secreted by microorganisms; and also prevent uncontrolled proteolysis and offer protection against proteolytic enzymes of pathogens.

    Methods: An array of chromatographic techniques were employed for purification, homogeneity was assessed by electrophoresis. Specificity, Ki value, nature of inhibition, complex formation was carried out by standard protocols. Read More

    Respiration and substrate transport rates as well as reactive oxygen species production distinguish mitochondria from brain and liver.
    BMC Biochem 2015 Sep 10;16:22. Epub 2015 Sep 10.
    Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida College of Medicine, Gainesville, FL, 32610, USA.
    Background: Aberrant mitochondrial function, including excessive reactive oxygen species (ROS) production, has been implicated in the pathogenesis of human diseases. The use of mitochondrial inhibitors to ascertain the sites in the electron transport chain (ETC) resulting in altered ROS production can be an important tool. However, the response of mouse mitochondria to ETC inhibitors has not been thoroughly assessed. Read More

    Purification and characterization of a cytochrome c with novel caspase-3 activation activity from the pathogenic fungus Rhizopus arrhizus.
    BMC Biochem 2015 Sep 3;16:21. Epub 2015 Sep 3.
    Department of Chemistry, University of Puerto Rico, Rio Piedras Campus, P.O. Box 70377, San Juan, PR, 00936-837, USA.
    Background: Members of Rhizopus species are the most common cause of mucormycosis, a rare but often fatal fungal infection. Host induced pathogen apoptosis and pathogen induced host cell apoptosis are often involved in fungal infections. In many organisms, the release of mitochondrial cytochrome c can trigger apoptosis by activating caspase proteases, but the role of fungal cytochrome c in apoptosis remains unknown. Read More

    Complex kinetics and residual structure in the thermal unfolding of yeast triosephosphate isomerase.
    BMC Biochem 2015 Sep 3;16:20. Epub 2015 Sep 3.
    Área de Biofisicoquímica, Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Iztapalapa, D.F. 09340, Mexico.
    Background: Saccharomyces cerevisiae triosephosphate isomerase (yTIM) is a dimeric protein that shows noncoincident unfolding and refolding transitions (hysteresis) in temperature scans, a phenomenon indicative of the slow forward and backward reactions of the native-unfolded process. Thermal unfolding scans suggest that no stable intermediates appear in the unfolding of yTIM. However, reported evidence points to the presence of residual structure in the denatured monomer at high temperature. Read More

    Identification of inhibitors that target dual-specificity phosphatase 5 provide new insights into the binding requirements for the two phosphate pockets.
    BMC Biochem 2015 Aug 19;16:19. Epub 2015 Aug 19.
    Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA.
    Background: Dual-specificity phosphatase-5 (DUSP5) plays a central role in vascular development and disease. We present a p-nitrophenol phosphate (pNPP) based enzymatic assay to screen for inhibitors of the phosphatase domain of DUSP5.

    Methods: pNPP is a mimic of the phosphorylated tyrosine on the ERK2 substrate (pERK2) and binds the DUSP5 phosphatase domain with a Km of 7. Read More

    Design of symmetric TIM barrel proteins from first principles.
    BMC Biochem 2015 Aug 12;16:18. Epub 2015 Aug 12.
    Biochemistry Department, Indian Institute of Science, Bangalore, India.
    Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Read More

    Structural plasticity of green fluorescent protein to amino acid deletions and fluorescence rescue by folding-enhancing mutations.
    BMC Biochem 2015 Jul 25;16:17. Epub 2015 Jul 25.
    Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
    Background: Green fluorescent protein (GFP) and its derivative fluorescent proteins (FPs) are among the most commonly used reporter systems for studying gene expression and protein interaction in biomedical research. Most commercially available FPs have been optimized for their oligomerization state to prevent potential structural constraints that may interfere with the native function of fused proteins. Other approach to reducing structural constraints may include minimizing the structure of GFPs. Read More

    Kv1.3 contains an alternative C-terminal ER exit motif and is recruited into COPII vesicles by Sec24a.
    BMC Biochem 2015 Jul 10;16:16. Epub 2015 Jul 10.
    Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL, 32306, USA.
    Background: Potassium channels play a fundamental role in resetting the resting membrane potential of excitable cells. Determining the intracellular trafficking and localization mechanisms of potassium channels provides a platform to fully characterize their maturation and functionality. Previous investigations have discovered residues or motifs that exist in their primary structure, which directly promote anterograde trafficking of nascent potassium channels. Read More

    Enzyme assays for synthesis and degradation of 2-5As and other 2'-5' oligonucleotides.
    BMC Biochem 2015 Jun 26;16:15. Epub 2015 Jun 26.
    Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, DK-8000, Aarhus C, Denmark.
    Background: The 5'-triphosphorylated, 2'-5'-linked oligoadenylate polyribonucleotides (2-5As) are central to the interferon-induced antiviral 2-5A system. The 2-5As bind and activate the RNase L, an endoRNase degrading viral and cellular RNA leading to inhibition of viral replication. The 2-5A system is tightly controlled by synthesis and degradation of 2-5As. Read More

    Human POLD1 modulates cell cycle progression and DNA damage repair.
    BMC Biochem 2015 Jun 19;16:14. Epub 2015 Jun 19.
    Department of Clinical Laboratory, Xuanwu Hospital Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing, 100053, China.
    Background: The activity of eukaryotic DNA polymerase delta (Pol δ) plays an essential role in genome stability through its effects on DNA replication and repair. The p125 catalytic subunit of Pol δ is encoded by POLD1 gene in human cells. To clarify biological functions of POLD1, we investigated the effects of POLD1 overexpression or downregulation on cell proliferation, cell cycle progression, DNA synthesis and oxidative DNA damage induced by H2O2. Read More

    The androgen receptor plays a suppressive role in epithelial- mesenchymal transition of human prostate cancer stem progenitor cells.
    BMC Biochem 2015 May 6;16:13. Epub 2015 May 6.
    Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, 030001, China.
    Background: To investigate the roles of androgen receptor (AR) in epithelial- mesenchymal transition (EMT) in human prostate cancer stem progenitor (S/P) cells isolated from LNCaP cell line.

    Methods: The S/P cells were obtained from LNCaP cell line through florescence-activated cell sorting (FACS). AR was overexpressed in S/P cells through lentivirus. Read More

    Alternative divalent cations (Zn²⁺, Co²⁺, and Mn²⁺) are not mutagenic at conditions optimal for HIV-1 reverse transcriptase activity.
    BMC Biochem 2015 May 3;16:12. Epub 2015 May 3.
    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
    Background: Fidelity of DNA polymerases can be influenced by cation co-factors. Physiologically, Mg(2+) is used as a co-factor by HIV reverse transcriptase (RT) to perform catalysis; however, alternative cations including Mn(2+), Co(2+), and Zn(2+) can also support catalysis. Although Zn(2+) supports DNA synthesis, it inhibits HIV RT by significantly modifying RT catalysis. Read More

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