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Biochemical Journal

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https://www.readbyqxmd.com/read/28219939/peroxiredoxin-1-prx1-is-a-dual-function-enzyme-by-possessing-cys-independent-catalase-like-activity
#1
Cen-Cen Sun, Wei-Ren Dong, Tong Shao, Jiang-Yuan Li, Jing Zhao, Li Nie, Li-Xin Xiang, Guan Zhu, Jian-Zhong Shao
Peroxiredoxin (Prx) was previously known as a Cys-dependent thioredoxin. However, we unexpected observed that Prx1 from the green spotted puffer fish Tetraodon nigroviridis (TnPrx1) was able to reduce H2O2 in a manner independent on the Cys peroxidation and reductants. This study aimed to validate the novel function for Prx1, delineate the biochemical features and explore its antioxidant role in cells. We have confirmed that Prx1 from the puffer fish and humans truly possesses a catalase-like activity that is independent of Cys residues and reductants, but dependent on iron...
February 20, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28202712/ribeye-b-domain-binds-to-lipid-components-of-synaptic-vesicles-in-an-nad-h-dependent-redox-sensitive-manner
#2
Karin Schwarz, Frank Schmitz
Synaptic ribbons are needed for fast and continuous exocytosis in ribbon synapses. RIBEYE is a main protein component of synaptic ribbons and necessary to build the synaptic ribbon. RIBEYE consists of a unique A-domain and a carboxyterminal B-domain that binds NAD(H). Within the presynaptic terminal, the synaptic ribbons are in physical contact with large numbers of synaptic vesicles. How this physical contact between ribbons and vesicles is established at a molecular level is not well understood. In the present study, we demonstrate that the RIBEYE(B)-domain can directly interact with lipid components of synaptic vesicles using two different sedimentation assays with liposomes of defined chemical composition...
February 15, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28202711/structural-interface-between-lrrk2-and-14-3-3-protein
#3
Loes Stevers, Rens de Vries, Richard Doveston, Lech-Gustav Milroy, Luc Brunsveld, Christian Ottmann
Binding of 14-3-3 proteins to LRRK2 is known to be impaired by a number of Parkinson's disease (PD)-relevant mutations. Abrogation of this interaction is connected to enhanced LRRK2 kinase activity which in turn is implicated in increased ubiquitination of LRRK2, accumulation of LRRK2 into inclusion bodies and reduction of neurite length. Hence, the interaction between 14-3-3 and LRRK2 is of significant interest as a possible drug target for the treatment of PD. However, LRRK2 possesses multiple sites that upon phosphorylation can bind to 14-3-3, thus rendering the interaction relatively complex...
February 15, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28196833/characterization-of-the-activation-of-small-gtpases-by-their-gefs-on-membranes-using-artificial-membrane-tethering
#4
François Peurois, Simon Veyron, Yann Ferrandez, Ilham Ladid, Sarah Benabdi, Mahel Zeghouf, Gérald Peyroche, Jacqueline Cherfils
Attachment of active, GTP-bound small GTPases to membranes by post-translational lipid modifications is pivotal for their ability to process and propagate information in cells. However, generating and manipulating lipidated GTPases has remained difficult, which has limited our quantitative understanding of their activation by GEFs and their termination by GAPs. Here we replaced the lipid modification by a histidine tag in eleven full-length, human small GTPases belonging to the Arf, Rho and Rab families, which allowed to tether them to nickel-lipid containing membranes and characterize the kinetics of their activation by GEFs...
February 14, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28188256/mgdg-pg-and-sqdg-regulate-the-activity-of-light-dependent-protochlorophyllide-oxidoreductase
#5
Michal Gabruk, Beata Myśliwa-Kurdziel, Jerzy Kruk
Light-dependent protochlorophyllide oxidoreductase (POR) is a plant enzyme involved in the chlorophyll biosynthesis pathway. POR reduces one of the double bonds of the protochlorophyllide (Pchlide) using NADPH and light. In the present paper, we found out that PG and SQDG are allosteric regulators of the nucleotide binding, which increase the affinity towards NADPH a hundred fold. Moreover, we showed for the first time that NADH can, like NADPH, form active complexes with Pchlide and POR, however at much higher concentrations...
February 10, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28188255/efficiacy-of-safranal-to-cisplatin-induced-nephrotoxicity
#6
Yasemin Karafakıoglu, Mehmet Fatih Bozkurt, Ömer Hazman, Fatih Fidan
The aim of this study was to investigate the effects of safranal on cisplatin-induced nephrotoxicity and oxidative stress in rats. Adult male Sprague-Dawley rats were randomly divided into five groups. The control group received physiological saline; animals in group 2 received only safranal and in group 3 received only cisplatin; 5 days of safranal treatment was performed following administration of cisplatin for the animals in group 4;5 days of safranal pre-treatment was applied to the animals in group 5 before administration of cisplatin...
February 10, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28183985/characterization-of-pph3-mediated-dephosphorylation-of-rad53-during-methyl-methanesulfonate-induced-dna-damage-repair-in-candida-albicans
#7
Guangyin Yao, Junhua Wan, Qizheng Liu, Chunhua Mu, Yue Wang, Jianli Sang
Genotoxic stress causes DNA damage or stalled DNA replication and filamentous growth in the pathogenic fungus Candida albicans The DNA checkpoint kinase Rad53 critically regulates by phosphorylation effectors that execute the stress response. Rad53 itself is activated by phosphorylation and inactivated by dephosphorylation. Previous studies have suggested that the phosphatase Pph3 dephosphorylates Rad53. Here, we used mass spectrometry and mutagenesis to identify Pph3 dephosphorylation sites on Rad53 in C. albicans We found that serine residues 351, 461, and 477, which were dephosphorylated in wild-type cells during the recovery from DNA damage caused by methyl methanesulfonate (MMS), remained phosphorylated in pph3Δ/Δ cells...
February 9, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28167699/modulation-of-the-specific-glutathionylation-of-mitochondrial-proteins-in-the-yeast-saccharomyces-cerevisiae-under-basal-and-stress-conditions
#8
Rachel Gergondey, Camille Garcia, Christophe Marchand, Stephane Lemaire, Jean-Michel Camadro, Françoise Auchere
The potential biological consequences of oxidative stress and changes in glutathione levels include the oxidation of susceptible protein thiols and reversible covalent binding of glutathione to the -SH groups of proteins by S-glutathionylation. Mitochondria are central to the response to oxidative stress and redox signaling. It is therefore crucial to explore the adaptive response to changes in thiol-dependent redox status in these organelles.We optimized the purification protocol of glutathionylated proteins in the yeast S...
February 6, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28167698/adar1-and-pact-contribute-to-efficient-translation-of-transcripts-containing-hiv-1-trans-activating-response-tar-element
#9
Evelyn Chukwurah, Indhira Handy, Rekha C Patel
Human immunodeficiency virus type 1 (HIV-1) has evolved various measures to counter the host cell's innate antiviral response during the course of infection. Interferon (IFN)-stimulated gene products are produced following HIV-1 infection to limit viral replication, but viral proteins and RNAs counteract their effect. One such mechanism is specifically directed against the IFN-induced Protein Kinase R (PKR), which is centrally important to the cellular antiviral response. In the presence of viral RNAs, PKR is activated and phosphorylates the translation initiation factor, eIF2α...
February 6, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28159912/identification-of-tbk1-complexes-required-for-the-phosphorylation-of-irf3-and-the-production-of-interferon-b
#10
Siddharth Bakshi, Jordan Taylor, Sam Strickson, Thomas Macartney, Philip Cohen
The double-stranded RNA mimetic poly(I:C) and LPS activate Toll-like Receptor 3 (TLR3) and TLR4, respectively, triggering the activation of TANK-Binding Kinase 1 (TBK1) complexes, the phosphorylation of Interferon Regulatory Factor 3 (IRF3) and transcription of the Interferon b (IFNb) gene. Here, we demonstrate that the TANK-TBK1 and Optineurin (OPTN)-TBK1 complexes control this pathway. The poly(I:C)- or LPS-stimulated phosphorylation of IRF3 at Ser396 and production of IFNb were greatly reduced in bone-marrow-derived macrophages (BMDM) from TANK knock-out (KO) mice crossed to knock-in mice-expressing the ubiquitin-binding-defective OPTN[D477N] mutant...
February 3, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28130490/duplication-of-drosophila-melanogaster-mitochondrial-ef-tu-pre-adaptation-to-t-arm-truncation-and-exclusion-of-bulky-aminoacyl-residues
#11
Aya Sato, Takuma Suematsu, Koh-Ki Aihara, Kiyoshi Kita, Tsutomu Suzuki, Kimitsuna Watanabe, Takashi Ohtsuki, Yoh-Ichi Watanabe
Translation elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA to ribosomes in protein synthesis. EF-Tu generally recognizes aminoacyl moieties and acceptor- and T-stems of aminoacyl-tRNAs. However, nematode mitochondrial (mt) tRNAs frequently lack all or part of the T-arm that is recognized by canonical EF-Tu. We previously reported that two distinct EF-Tu species, EF-Tu1 and EF-Tu2, respectively recognize mt tRNAs lacking T-arms and D-arms in the mitochondria of the chromadorean nematode Caenorhabditis elegans C...
January 27, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28126743/superoxide-generation-from-nnos-splice-variants-and-its-potential-involvement-in-redox-signal-regulation
#12
Hideshi Ihara, Atsushi Kitamura, Shingo Kasamatsu, Tomoaki Ida, Kakihana Yuki, Hiroyasu Tsutsuki, Tomohiro Sawa, Yasuo Watanabe, Takaaki Akaike
We previously demonstrated different spacial expression profiles of the neuronal nitric oxide (NO) synthase (nNOS) splice variants nNOS-μ and nNOS-α in the brain; however, their exact functions are not fully understood.  Here, we used electron paramagnetic resonance to compare the electron-uncoupling reactions of recombinant nNOS-μ and nNOS-α that generate reactive oxygen species (ROS), in this case, superoxide.  nNOS-µ generated 44% of the amount of superoxide that nNOS-α generated.  We also evaluated the ROS production in HEK293 cells stably expressing nNOS-α and nNOS-μ by investigating these electron-uncoupling reactions as induced by calcium ionophore, A23187...
January 26, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28126742/binding-of-nadp-triggers-an-open-to-closed-transition-in-a-mycobacterial-fabg-%C3%AE-ketoacyl-acp-reductase
#13
Mickael Blaise, Niel Van Wyk, Francoise Banères-Roquet, Yann Guérardel, Laurent Kremer
The ketoacyl-acyl carrier protein (ACP) reductase FabG catalyzes the NADPH/NADH-dependent reduction of b-ketoacyl-ACP substrates to b-hydroxyacyl-ACP products, the first reductive step in the fatty acid biosynthesis elongation cycle. FabG proteins are ubiquitous in bacteria and are part of the type II fatty acid synthase system (FAS-II). Mining the Mycobacterium smegmatis genome uncovered several putative FabG-like proteins. Among them, we identified MSMEG_6753 whose gene was found adjacent to MSMEG_6754 , encoding a recently characterized enoyl-CoA dehydratase and to MSMEG_6755 , encoding another potential reductase...
January 26, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28126741/mechanism-and-catalytic-strategy-of-the-prokaryotic-specific-gtp-cyclohydrolase-ib
#14
Naduni Paranagama, Shilah A Bonnett, Jonathan Alvarez, Amit Luthra, Boguslaw Stec, Andrew Gustafson, Dirk Iwata-Reuyl, Manal Swairjo
GTP cyclohydrolase I catalyzes the first step in folic acid biosynthesis in bacteria and plants, biopterin biosynthesis in mammals, and the biosynthesis of 7-deazaguanosine modified tRNA nucleosides in bacteria and archaea.  The type IB GTP cyclohydrolase (GCYH-IB) is a prokaryotic-specific enzyme found in a number of pathogens. GCYH-IB is structurally distinct from the canonical type IA GTP cyclohydrolase involved in biopterin biosynthesis in humans and animals, and thus is of interest as a potential antibacterial drug target...
January 26, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28126740/unique-substrate-specificity-of-ornithine-aminotransferase-from-toxoplasma-gondii
#15
Alessandra Astegno, Elena Maresi, Mariarita Bertoldi, Valentina La Verde, Alessandro Paiardini, Paola Dominici
Toxoplasma gondii is a protozoan parasite of medical and veterinary relevance responsible for toxoplasmosis in humans. As an efficacious vaccine remains a challenge, chemotherapy is still the most effective way to combat the disease. In search for novel druggable targets, herein we performed a thorough characterization of the putative pyridoxal 5'-phosphate (PLP)-dependent enzyme ornithine aminotransferase from T. gondii ME49 (TgOAT). We overexpressed the protein in E. coli and analyzed its molecular and kinetic properties by UV-visible absorbance, fluorescence, and CD spectroscopy, in addition to kinetic studies of both the steady state and pre-steady state...
January 26, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28126739/structure-based-mutational-studies-of-o-acetylserine-sulfhydrylase-reveal-the-reason-for-the-loss-of-cysteine-synthase-complex-formation-in-brucella-abortus
#16
Sudhaker Dharavath, Isha Raj, Samudrala Gourinath
Cysteine biosynthesis takes place via a two-step pathway in bacteria, fungi, plants and protozoan parasites, but not in humans, and hence the machinery of cysteine biosynthesis is an opportune target for therapeutics. The decameric cysteine synthase complex (CSC) is formed when the C-terminal tail of serine acetyl transferase (SAT) binds in the active site of O-acetyl serine sulfydrylase (OASS), playing a role in the regulation of this pathway. Here we show that OASS from Brucella abortus (BaOASS) does not interact with its cognate SAT C-terminal tail...
January 26, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28126738/discovery-and-characterisation-of-the-automethylation-properties-of-prdm9
#17
Xiaoying Koh-Stenta, Anders Poulsen, Rong Li, John Liang Kuan Wee, Perlyn Zekui Kwek, Sin Yin Chew, Jianhe Peng, Liling Wu, Ernesto Guccione, Joma Joy, Jeffrey Hill
We have previously characterised the histone lysine methyltransferase properties of PRDM9, a member of the PRDM family of putative transcriptional regulators. PRDM9 displays broad substrate recognition and methylates a range of histone substrates including octamers, core histone proteins, and peptides. In this study, we show that PRDM9 performs intramolecular automethylation on multiple lysine residues localised to a lysine-rich region on the post-SET domain. PRDM9 automethylation is abolished by a single active site mutation, C321P, also known to disrupt interactions with SAM...
January 26, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28108640/bonds-broken-and-formed-during-the-mixed-linkage-glucan-xyloglucan-endotransglucosylase-reaction-catalysed-by-equisetum-hetero-trans-%C3%AE-glucanase
#18
Thomas J Simmons, Stephen C Fry
Mixed-linkage glucan : xyloglucan endotransglucosylase (MXE) is one of the three activities of the recently characterised hetero-trans-β-glucanase (HTG), which among land-plants is known only from Equisetum species. The biochemical details of the MXE reaction were incompletely understood - details that would promote understanding of MXE's role in vivo and enable its full technological exploitation. We investigated HTG's site of attack on one of its donor substrates, mixed-linkage (1→3),(1→4)-β-D-glucan (MLG), with radioactive oligosaccharides of xyloglucan as acceptor substrate...
January 20, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28104757/analysis-and-identification-of-the-grem2-heparin-heparan-sulfate-binding-motif
#19
Chandramohan Kattamuri, Kristof Nolan, Thomas B Thompson
Bone Morphogenetic Proteins (BMP) are regulated by extracellular antagonists of the DAN (differential screening selected gene aberrative in neuroblastoma) family. Similar to the BMP ligands, certain DAN family members have been shown to interact with heparin and heparan sulfate (HS). Structural studies of DAN family members Gremlin-1 and Gremlin-2 have revealed a dimeric growth-factor like fold where a series of lysine residues cluster along one face of the protein. In this study, we used mutagenesis, heparin binding measurements, and cell surface binding analysis to identify lysine residues that are important for heparin/HS binding in Gremlin-2...
January 19, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28104756/sugar-nucleotide-quantification-by-liquid-chromatography-tandem-mass-spectrometry-reveals-a-distinct-profile-in-plasmodium-falciparum-sexual-stage-parasites
#20
Borja López-Gutiérrez, Rhoel R Dinglasan, Luis Izquierdo
The obligate intracellular lifestyle of Plasmodium falciparum and the difficulties to obtain sufficient amounts of biological material has hampered the study of specific metabolic pathways in the malaria parasite. Thus, for example, the pools of sugar nucleotides required to fuel glycosylation reactions have never been studied in-depth in well-synchronized asexual parasites or in other stages of its life cycle. These metabolites are of critical importance, especially considering the renewed interest in the presence of N -, O - and other glycans in key parasite proteins...
January 19, 2017: Biochemical Journal
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