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BMC Biochemistry

Pei Zhang, Owen E Branson, Michael A Freitas, Mark R Parthun
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. The histone chaperones and other factors that regulate linker histone dynamics in the cell are largely unknown. In particular, it is not known whether replication-dependent and replication-independent linker histones interact with distinct or common sets of proteins...
October 1, 2016: BMC Biochemistry
Pranali Patel, Uros Kuzmanov, Seema Mital
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...
2016: BMC Biochemistry
Linus J Östberg, Bengt Persson, Jan-Olov Höög
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...
2016: BMC Biochemistry
Thao Thi Nguyen, Hanh Van Vu, Nhung Thi Hong Nguyen, Tuyen Thi Do, Thanh Sy Le Nguyen
BACKGROUND: Beta-galactosidase (EC, a commercially important enzyme, catalyses the hydrolysis of β-1,3- and β-1,4-galactosyl bonds of polymer or oligosaccharidesas well as transglycosylation of β-galactopyranosides. Due to catalytic properties; β-galactosidase might be useful in the milk industry to hydrolyze lactose and produce prebiotic GOS. The purpose of this study is to characterize β-galactosidase mutants from B. subtilis. RESULTS: Using error prone rolling circle amplification (epRCA) to characterize some random mutants of the β-galactosidase (LacA) from B...
2016: BMC Biochemistry
M Zulema Cabail, Emily I Chen, Antonius Koller, W Todd Miller
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. Auto-thiophosphorylation of Src at Tyr416 in the activation loop proceeds efficiently in the presence of Ni(2+), resulting in kinase activation...
2016: BMC Biochemistry
Hongjie Pan, Xiao-Ping Zhong, Sunhee Lee
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)...
2016: BMC Biochemistry
Christian Holmgren, Louise Cornmark, Gry Kalstad Lønne, Katarzyna Chmielarska Masoumi, Christer Larsson
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). We previously established that the PKCδ-Smac complex dissociates during induction of apoptosis indicating a functional importance. Because the knowledge on the molecular determinants of the interaction is limited, we aimed at characterizing the interactions between PKCδ and Smac...
2016: BMC Biochemistry
Yasunori Fukuda, Osamu Sano, Kenichi Kazetani, Koji Yamamoto, Hidehisa Iwata, Junji Matsui
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. Simple and efficient methods for identifying the target molecules are essential. RESULTS: 2-Amino-4-(3,4-(methylenedioxy)benzylamino)-6-(3-methoxyphenyl)pyrimidine (AMBMP) was identified as a senescence inducer from a phenotypic screening campaign...
2016: BMC Biochemistry
Ulaganathan Sivagnanam, Shweta Narayana Murthy, Sathyanarayana N Gummadi
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. RESULTS: In this study, the nuclease activity of recombinant hPLSCR1 and its biochemical properties have been determined...
2016: BMC Biochemistry
Sheena Jiang, Eric Zhang, Rachel Zhang, Xianqiang Li
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. Identifying new transcription factors associated with ER stress pathways provides a platform to comprehensively characterize mechanism and functionality of ER...
2016: BMC Biochemistry
Olga V Lukashevich, Natalia A Cherepanova, Renata Z Jurkovska, Albert Jeltsch, Elizaveta S Gromova
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. No X-ray structure is available for the complex of Dnmt3a with DNA and the mechanistic details of DNA recognition and catalysis by mammalian Dnmts are not completely understood. RESULTS: Mutant variants of the catalytic domain of the murine Dnmt3a carrying substitutions of highly conserved N167, R200, and R202 have been generated by site directed mutagenesis and purified...
2016: BMC Biochemistry
Robert Marmulla, Barbara Šafarić, Stephanie Markert, Thomas Schweder, Jens Harder
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...
2016: BMC Biochemistry
Javier Vargas-Medrano, Jorge A Sierra-Fonseca, Luis F Plenge-Tellechea
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. RESULTS: Concentrations of 0...
2016: BMC Biochemistry
Andreas Krämer, Jan Herzer, Joerg Overhage, Franz-Josef Meyer-Almes
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. Results with other bacterial pathogens e.g., Y. pestis suggest that polyamines may be involved in the formation of biofilms or confer resistance against certain antibiotics...
2016: BMC Biochemistry
Manoj Saxena, Rohit Kumar Sharma, Josell Ramirez-Paz, Arthur D Tinoco, Kai Griebenow
No abstract text is available yet for this article.
2016: BMC Biochemistry
Concetta De Santi, Bjørn Altermark, Marcin Miroslaw Pierechod, Luca Ambrosino, Donatella de Pascale, Nils-Peder Willassen
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...
2016: BMC Biochemistry
Alexey S Kurdyumov, Valentin A Manuvera, Isolda P Baskova, Vassili N Lazarev
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. To date, three isoforms of mlDL have been identified. The enzymatic properties of pure mlDL isoforms have not yet been described because only destabilase complexes containing other proteins could be isolated from the salivary gland secretion and because low product yield from the generation of recombinant proteins has made comprehensive testing difficult...
2015: BMC Biochemistry
Johan Morrill, Evelina Kulcinskaja, Anna Maria Sulewska, Sampo Lahtinen, Henrik Stålbrand, Birte Svensson, Maher Abou Hachem
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. Little insight is available on the enzymology of mannan deconstruction in the gut ecological niche. Here, we report the biochemical properties of the first family 5 subfamily 8 glycoside hydrolase (GH5_8) mannanase from the probiotic bacterium Bifidobacterium animalis subsp. lactis Bl-04 (BlMan5_8)...
2015: BMC Biochemistry
Mario Javier Gutiérrez-Fernández, Ana Edith Higareda-Mendoza, César Adrián Gómez-Correa, Marco Aurelio Pardo-Galván
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...
2015: BMC Biochemistry
Rosa Viana, Pablo Lujan, Pascual Sanz
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...
2015: BMC Biochemistry
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