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Biochemical Journal

Cláudio Remedios Frazão, Christopher Topham, Yoann Malbert, Jean Marie François, Thomas Walther
A synthetic pathway for the production of 2,4-dihydroxybutyric acid from homoserine, composed of two consecutive enzymatic reaction steps has been recently reported. An important step in this pathway consists in the reduction of 2-keto-4-hydroxybutyrate (OHB) into (L)-dihydroxybutyrate (DHB), by an enzyme with OHB reductase activity. In this study, we used a rational approach to engineer an OHB reductase by using the cytosolic (L)-malate dehydrogenase from Escherichia coli (Ec-Mdh) as the template enzyme. Structural analysis of (L)-malate dehydrogenase and (L)-lactate dehydrogenase enzymes acting on sterically cognate substrates revealed key residues in the substrate and co-substrate binding sites responsible for substrate discrimination...
November 8, 2018: Biochemical Journal
Ting Ban, Xun Li, Xiaochuan Ma, Hui Yang, Yunpeng Song, Yaping Sun, Michelle Shen, Na Li, Mei-Yun Zhang, Yingli Ma, Wenge Zhong, Mingqiang Zhang, Liaoyuan A Hu
Biased ligands of G protein-coupled receptors (GPCR) may have improved therapeutic benefits and safety profiles. However, the molecular mechanism of GPCR biased signaling remains largely unknown. Using apelin receptor (APJ) as a model, we systematically investigated the potential effects of amino acid residues around the orthosteric binding site on biased signaling. We discovered that a single residue mutation I109A (I1093.32 ) in the transmembrane domain 3 (TM3) located in the deep ligand binding pocket was sufficient to convert a balanced APJ into a G protein signaling biased receptor...
November 8, 2018: Biochemical Journal
Fuyuan Jing, Marna D Yandeau-Nelson, Basil J Nikolau
In plants and bacteria that use a Type II fatty acid synthase (FAS), isozymes of acyl-acyl carrier protein (ACP) thioesterase (TEs) hydrolyze the thioester bond of acyl-ACPs, terminating the process of fatty acid biosynthesis. These TEs are therefore critical in determining the fatty acid profiles produced by these organisms. Past characterizations of a limited number of plant-sourced acyl-ACP TEs have suggested a thiol-based, papain-like catalytic mechanism, involving a triad of Cys, His, and Asn residues...
November 8, 2018: Biochemical Journal
Peter M Fernandes, James R Kinkead, Iain W McNae, Paul A Michels, Malcolm D Walkinshaw
Eukaryotic ATP-dependent phosphofructokinases (PFKs) are often considered unidirectional enzymes  catalysing the transfer of a phospho moiety from ATP to fructose 6-phosphate (F6P) to produce ADP and fructose 1,6-bisphosphate (F16BP). The reverse reaction is not generally considered to occur under normal conditions and has never been demonstrated for any eukaryotic ATP-dependent PFKs, though it does occur in PPi-dependent PFKs and has been experimentally shown for bacterial ATP-dependent PFKs. Evidence is provided via two orthogonal assays that all three human PFK isoforms can catalyse the reverse reaction in vitro , allowing determination of kinetic properties...
November 7, 2018: Biochemical Journal
Craig Steven Robb, Lukas Reisky, Uwe Bornscheuer, Jan-Hendrik Hehemann
Degradation of carbohydrates by bacteria represents a key step in energy metabolism that can be inhibited by methylated sugars. Removal of methyl groups, which is critical for further processing, poses a biocatalytic challenge because enzymes need to overcome a high energy barrier. Our structural and computational analysis revealed how a member of the cytochrome P450 family, evolved to oxidize a carbohydrate ligand. Using structural biology, we ascertained the molecular determinants of substrate specificity and revealed a highly specialized active site complementary to the substrate chemistry...
November 7, 2018: Biochemical Journal
Milan Kožíšek, Václav Navrátil, Kateřina Rojíková, Jana Pokorná, Carlos Berenguer Albiňana, Petr Pachl, Jitka Zemanová, Aleš Machara, Pavel Šácha, Jason Hudlický, Ivana Císařová, Pavlína Řezáčová, Jan Konvalinka
Influenza neuraminidase is responsible for the escape of new viral particles from the infected cell surface. Several neuraminidase inhibitors are used clinically to treat patients or stockpiled for emergencies. However, the increasing development of viral resistance against approved inhibitors has underscored the need for development of new antivirals effective against resistant influenza strains. A facile, sensitive, and inexpensive screening method would help achieve this goal. Recently, we described a multiwell plate-based DNA-linked inhibitor antibody assay (DIANA)...
November 7, 2018: Biochemical Journal
Katsutoshi Yamaguchi, Kiryu Asakura, Masataka Imamura, Gota Kawai, Taiichi Sakamoto, Tomomi Furihata, Robert J Linhardt, Kazuei Igarashi, Toshihiko Toida, Kyohei Higashi
Glycosaminoglycans (GAGs), a group of structurally related acidic polysaccharides, are primarily found as glycan moieties of proteoglycans (PGs).  Among these, chondroitin sulfate (CS) and dermatan sulfate, side chains of PGs, are widely distributed in animal kingdom and show structural variations, such as sulfation patterns and degree of epimerization, which are responsible for their physiological functions through interactions with growth factors, chemokines and adhesion molecules.  However, structural changes in CS, particularly the ratio of 4- O -sulfation to 6- O -sulfation (4S/6S) and CS chain length that occur during the aging process are not fully understood...
November 6, 2018: Biochemical Journal
Davide Gerna, Thomas Roach, Erwann Arc, Wolfgang Markus Stöggl, Margherita Limonta, Patrizia Vaccino, Ilse Kranner
Fast and uniform germination is key to agricultural production and can be achieved by seed "priming" techniques. Here, we characterised the responses of bread wheat ( Triticum aestivum L.) seeds to a hot steam treatment ("BioFlash"), which accelerated water uptake, resulting in faster germination and seedling growth, typical traits of primed seed. Before the completion of germination, metabolite profiling of seeds revealed advanced accumulation of several amino acids (especially cysteine and serine), sugars (ribose, glucose), and organic acids (glycerate, succinate) in hot steam-treated seeds, whereas sugar alcohols (e...
November 6, 2018: Biochemical Journal
Jonathan Rojo-Ruiz, Macarena Rodríguez-Prados, Alba Delrio-Lorenzo, Marìa Teresa Alonso, Javier García-Sancho
Cytosolic Ca2+ signals are often amplified by massive calcium release from the endoplasmic reticulum (ER). This calcium-induced calcium release (CICR) occurs by activation of an ER Ca2+ channel, the ryanodine receptor (RyR), which is facilitated both by cytosolic- and ER- Ca2+ levels. Caffeine sensitizes RyR to Ca2+ and promotes ER Ca2+ release at basal cytosolic Ca2+ levels. This outcome is frequently used as a readout for the presence of CICR. By monitoring ER luminal Ca2+ with the low-affinity genetic Ca2+ probe erGAP3, we find here that application of 50 mM caffeine rapidly reduces the Ca2+ content of the ER in HeLa cells by about 50%...
November 5, 2018: Biochemical Journal
Fangzhen Shan, Kaiqin Ye, Jiahai Zhang, Shanhui Liao, Xuecheng Zhang, Chao Xu, Xiaoming Tu
Centrin is a conserved calcium-binding protein that plays an important role in diverse cellular biological processes such as ciliogenesis, gene expression, DNA repair and signal transduction. In Trypanosoma brucei , TbCentrin4 is mainly localized in basal bodies and bi-lobe structure and is involved in the processes coordinating karyokinesis and cytokinesis. In this study, we solved the solution structure of TbCentrin4 using NMR spectroscopy. TbCentrin4 contains four EF-hand motifs consisting of 8 α-helices...
November 2, 2018: Biochemical Journal
Lionel Tarrago, Sandrine Grosse, Marina I Siponen, David Lemaire, Béatrice Alonso, Guylaine Miotello, Jean Armengaud, Pascal Arnoux, David Pignol, Monique Sabaty
Methionine (Met) is prone to oxidation and can be converted to Met sulfoxide (MetO), which exists as R - and S -diastereomers. MetO can be reduced back to Met by the ubiquitous methionine sulfoxide reductase (Msr) enzymes. Canonical MsrA and MsrB were shown to be absolutely stereospecific for the reduction of S ‑ and R‑ diastereomer, respectively. Recently, a new enzymatic system, MsrQ/MsrP which is conserved in all gram‑negative bacteria, was identified as a key actor in the reduction of oxidized periplasmic proteins...
November 2, 2018: Biochemical Journal
Alvin Gomez, Christian Bindesbøll, Venkata Satheesh Somisetty, Giulia Grimaldi, David Hutin, Laura MacPherson, Shaimaa Ahmed, Laura Tamblyn, Tiffany Cho, Hilde Irene Nebb, Anders Moen, Jan Haug Anonsen, Denis M Grant, Jason Matthews
Here we report the biochemical characterization of the mono-ADP-ribosyltransferase 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) poly-ADP-ribose-polymerase (TIPARP/ARTD14/PARP7), which is known to repress aryl hydrocarbon receptor (AHR)-dependent transcription. We found that the nuclear localization of TIPARP was dependent on a short N-terminal sequence and its zinc finger domain. Deletion and in vitro ADP-ribosylation studies identified amino acids 400-657 as the minimum catalytically active region, which retained its ability to mono-ADP-ribosylate AHR...
October 29, 2018: Biochemical Journal
Weibing Dong, Xin Zhu, Xuan Zhou, Ying Yang, Xin Yan, Li Sun, Dejing Shang
Antimicrobial peptides have broad-spectrum killing activity against bacteria, enveloped viruses, fungi and several parasites via cell membrane permeation and exhibit primarily immunomodulatory and anti-infective functions in their interactions with host cells. However, the mechanism underlying their anti-inflammatory activity remains to be elucidated. L-K6, a analog of temporin-1CEb isolated from the skin secretion of Rana chensinensis has been demonstrated a wide range of antimicrobial activity against gram-negative and -positive bacteria...
October 29, 2018: Biochemical Journal
Béatrice Vallée, Hélène Cuberos, Michel Doudeau, Fabienne Godin, David Gosset, Patrick Vourc'h, Christian R Andres, Hélène Bénédetti
LIMK1 and LIMK2 (LIMKs) are kinases that play a crucial role in cytoskeleton dynamics by independently regulating both actin filament and microtubule remodeling. LIMK1, and more recently LIMK2, have been shown to be involved in cancer development and metastasis, resistance of cancer cells to microtubule targeted treatments, neurological diseases, and viral infection. LIMKs have thus recently emerged as new therapeutic targets. Databanks describe three isoforms of human LIMK2: LIMK2a, LIMK2b, and LIMK2-1. Evidence suggests that they may not have completely overlapping functions...
October 29, 2018: Biochemical Journal
Fozia Ahmed, Kalina Hristova
Receptor tyrosine kinases (RTKs) are cell surface receptors which control cell growth and differentiation, and play important roles in tumorigenesis. Despite decades of RTK research, the mechanism of RTK activation in response to their ligands is still under debate. Here we investigate the interactions that control the activation of the tropomyosin receptor kinase (Trk) family of RTKs in the plasma membrane, using a FRET-based methodology. The Trk receptors are expressed in neuronal tissues, and they guide the development of the central and peripheral nervous systems during development...
October 26, 2018: Biochemical Journal
Rebecca A Dewhirst, Stephen C Fry
l-Ascorbate, dehydro-l-ascorbic acid (DHA) and 2,3-diketo-l-gulonate (DKG) can all quench reactive oxygen species (ROS) in plants and animals. The vitamin C oxidation products thereby formed are investigated here. DHA and DKG were incubated aerobically at pH 4.7 with peroxide (H2 O2 ), 'superoxide' (a ~50:50 mixture of O2 • - and HO2 • ), hydroxyl radicals (• OH, formed in Fenton mixtures), and illuminated riboflavin (generating singlet oxygen, 1 O2 ). Products were monitored electrophoretically. DHA quenched H2 O2 far more effectively than superoxide, but the main products in both cases were 4- O -oxalyl-l-threonate (4-OxT) and smaller amounts of 3-OxT and OxA + threonate...
October 22, 2018: Biochemical Journal
Alexander K H Weiss, Andreas Naschberger, Johannes R Loeffler, Hubert Gstach, Matthew W Bowler, Max Holzknecht, Elia Cappuccio, Annabella Pittl, Solmaz Etemad, Theresia Dunzendorfer-Matt, Klaus Scheffzek, Klaus R Liedl, Pidder Jansen-Dürr
Whereas enzymes in the fumarylacetoacetate hydrolase (FAH) superfamily catalyze several distinct chemical reactions, the structural basis for their multi-functionality remains elusive. As a well-studied example, human FAH domain containing protein 1 (FAHD1) is a mitochondrial protein displaying both acylpyruvate hydrolase (ApH), and oxaloacetate decarboxylase (ODx) activity. As mitochondrial ODx, FAHD1 acts antagonistically to pyruvate carboxylase, a key metabolic enzyme. Despite its importance for mitochondrial function, very little is known about the catalytic mechanisms underlying FAHD1 enzymatic activities, and the architecture of its ligated active site is currently ill defined...
October 22, 2018: Biochemical Journal
Anthony Fullam, Lili Gu, Yvette Höhn, Martina Schröder
DDX3 is a DEAD-box RNA helicase that we and others have previously implicated in anti-viral immune signalling pathways leading to type I interferon (IFN) induction. We previously demonstrated that it directly interacts with the kinase IKKε, enhances it activation, and then facilitates phosphorylation of the transcription factor IRF3 by IKKε. However, the TLR7/9-mediated pathway, one of the most physiologically relevant IFN induction pathways, proceeds independently of IKKε or the related kinase TBK1. This pathway induces type I IFN production via the kinases NIK and IKKα and is activated when plasmacytoid Dendritic Cells (pDCs) sense viral nucleic acids...
October 19, 2018: Biochemical Journal
Yubao Liu, Rui Zou, Zhen Wang, Chuanyang Wen, Fan Zhang, Fuqing Lin
This study was designed to explore whether exosomal lncRNA-KLF3-AS1 derived from human mesenchymal stem cells (hMSCs) can serve as a positive treatment for osteoarthritis (OA). hMSCs and MSC-derived exosomes (MSC-exo) were prepared for morphological observation and identification by transmission electron microscopy (TEM) and flow cytometry. IL-1β-induced OA chondrocytes and collagenase-induced rat model of OA were established for the further experiments. Lentivirus mediated siRNA targeting KLF3-AS1 was transfected into MSCs for silencing KLF3-AS1...
October 19, 2018: Biochemical Journal
Jonathan Dorival, Sophie Ruppert, Melissa Gunnoo, Adam Orłowski, Maylis Chapelais-Baron, Jérôme Dabin, Aurore Labourel, Damien Thompson, Gurvan Michel, Mirjam Czjzek, Sabine Genicot
Cell walls of marine macroalgae are composed of diverse polysaccharides that provide abundant carbon sources for marine heterotrophic bacteria. Among them, Zobellia galactanivorans is considered as a model for studying algae-bacteria interactions. The degradation of typical algal polysaccharides, such as agars or alginate, has been intensively studied in this bacterium, but the catabolism of plant-like polysaccharides is essentially uncharacterized. Here we identify a polysaccharide utilization locus in the genome of Z...
October 19, 2018: Biochemical Journal
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