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Enzymology

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https://www.readbyqxmd.com/read/29161251/enzymology-i-want-my-cluster-back
#1
Caitlin Deane
No abstract text is available yet for this article.
November 21, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/29148757/cross-linked-artificial-enzyme-crystals-as-heterogeneous-catalysts-for-oxidation-reactions
#2
Sarah Lopez, Laurianne Rondot, Chloé Leprêtre, Caroline Marchi-Delapierre, Stéphane Ménage, Christine Cavazza
Designing systems that merge the advantages of heterogeneous catalysis, enzymology and molecular catalysis represents the next major goal for sustainable chemistry. Cross-linked enzyme crystals display most of these essential assets (well-designed mesoporous support, protein selectivity, molecular recognition of substrates). Nevertheless, a lack of reaction diversity, particularly in the field of oxidation, remains a constraint for their increased use in the field. Here, thanks to the design of cross-linked artificial non-heme iron oxygenase crystals, we filled this gap by developing bio-based heterogeneous catalysts capable of oxidizing carbon-carbon double bonds...
November 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29143132/thermostable-and-highly-specific-l-aspartate-oxidase-from-thermococcus-litoralis-dsm-5473-cloning-overexpression-and-enzymological-properties
#3
Tsubasa Washio, Tadao Oikawa
We successfully expressed the L-aspartate oxidase homolog gene (accession no: OCC_06611) of Thermococcus litoralis DSM 5473 in the soluble fraction of Escherichia coli BL21 (DE3) using a pET21b vector with 6X His tag at its C-terminus. The gene product (Tl-LASPO) showed L-aspartate oxidase activity in the presence of FAD in vitro, and this report is the first that details an L-aspartate oxidase derived from a Thermococcus species. The homologs of Tl-LASPO existed mainly in archaea, especially in the genus of Thermococcus, Pyrococcus, Sulfolobus, and Halobacteria...
November 15, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29138240/kinetics-of-h2o2-driven-degradation-of-chitin-by-a-bacterial-lytic-polysaccharide-monooxygenase
#4
Silja Kuusk, Bastien Bissaro, Piret Kuusk, Zarah Forsberg, Vincent G H Eijsink, Morten Sørlie, Priit Väljamäe
Lytic polysaccharide monooxygenases (LPMOs) catalyze the oxidative cleavage of glycosidic bonds in recalcitrant polysaccharides, such as cellulose and chitin, and are of interest in biotechnological utilization of these abundant biomaterials. It has recently been shown that LPMOs can use H2O2, instead of O2, as a co-substrate. This peroxygenase-like reaction by a mono-copper enzyme is unprecedented in nature and opens new avenues in chemistry and enzymology. Here, we provide the first detailed kinetic characterization of chitin degradation by the bacterial LPMO chitin-binding protein CBP21 using H2O2 as co-substrate...
November 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29123679/mix-and-diffuse-serial-synchrotron-crystallography
#5
Kenneth R Beyerlein, Dennis Dierksmeyer, Valerio Mariani, Manuela Kuhn, Iosifina Sarrou, Angelica Ottaviano, Salah Awel, Juraj Knoska, Silje Fuglerud, Olof Jönsson, Stephan Stern, Max O Wiedorn, Oleksandr Yefanov, Luigi Adriano, Richard Bean, Anja Burkhardt, Pontus Fischer, Michael Heymann, Daniel A Horke, Katharina E J Jungnickel, Elena Kovaleva, Olga Lorbeer, Markus Metz, Jan Meyer, Andrew Morgan, Kanupriya Pande, Saravanan Panneerselvam, Carolin Seuring, Aleksandra Tolstikova, Julia Lieske, Steve Aplin, Manfred Roessle, Thomas A White, Henry N Chapman, Alke Meents, Dominik Oberthuer
Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29120187/mechanism-of-competitive-inhibition-and-destabilization-of-acidothermus-cellulolyticus-endoglucanase-1-by-ionic-liquids
#6
Samantha R Summers, K G Sprenger, Jim Pfaendtner, Jan Marchant, Michael F Summers, Joel L Kaar
The ability of ionic liquids (ILs) to solubilize cellulose has sparked interest in their use for enzymatic biomass processing. However, this potential is yet to be realized, primarily because ILs inactivate requisite cellulases by mechanisms that are yet to be identified. We used a combination of enzymology, circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular dynamics (MD) methods to investigate the molecular basis for the inactivation of the endocellulase 1 (E1) from Acidothermus cellulolyticus by the imidazolium IL 1-butyl-3-methylimidazolium chloride ([BMIM][Cl])...
November 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29101705/hematological-hepatic-enzymes-activity-and-oxidative-stress-responses-of-gray-mullet-mugil-cephalus-after-sub-acute-exposure-to-copper-oxide
#7
Paria Akbary, Sahar Sartipi Yarahmadi, Abdolreza Jahanbakhshi
Given the importance of assessing potential toxicity of heavy metals in valuable species of aquatic animals, the goal of the present research was to assess the sub-acute effects of copper oxide on hematological, enzymological, and oxidative stress responses of gray mullet to measure toxicity of copper oxide pollution in this significant fish. The median lethal concentration (LC50) value of copper oxide to gray mullet was detected at 3.15 ± 0.039 mg/L for 96 h, and 25 and 50% of the 96-h LC50 values were selected as sub-acute concentrations...
November 4, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29059321/confronting-the-catalytic-dark-matter-encoded-by-sequenced-genomes
#8
Kenneth W Ellens, Nils Christian, Charandeep Singh, Venkata P Satagopam, Patrick May, Carole L Linster
The post-genomic era has provided researchers with a deluge of protein sequences. However, a significant fraction of the proteins encoded by sequenced genomes remains without an identified function. Here, we aim at determining how many enzymes of uncertain or unknown function are still present in the Saccharomyces cerevisiae and human proteomes. Using information available in the Swiss-Prot, BRENDA and KEGG databases in combination with a Hidden Markov Model-based method, we estimate that >600 yeast and 2000 human proteins (>30% of their proteins of unknown function) are enzymes whose precise function(s) remain(s) to be determined...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29056341/the-human-knockout-gene-clybl-connects-itaconate-to-vitamin-b12
#9
Hongying Shen, Gregory C Campanello, Daniel Flicker, Zenon Grabarek, Junchi Hu, Cheng Luo, Ruma Banerjee, Vamsi K Mootha
CLYBL encodes a ubiquitously expressed mitochondrial enzyme, conserved across all vertebrates, whose cellular activity and pathway assignment are unknown. Its homozygous loss is tolerated in seemingly healthy individuals, with reduced circulating B12 levels being the only and consistent phenotype reported to date. Here, by combining enzymology, structural biology, and activity-based metabolomics, we report that CLYBL operates as a citramalyl-CoA lyase in mammalian cells. Cells lacking CLYBL accumulate citramalyl-CoA, an intermediate in the C5-dicarboxylate metabolic pathway that includes itaconate, a recently identified human anti-microbial metabolite and immunomodulator...
November 2, 2017: Cell
https://www.readbyqxmd.com/read/29048364/protective-effect-of-argan-and-olive-oils-against-lps-induced-oxidative-stress-and-inflammation-in-mice-livers
#10
Soufiane El Kamouni, Riad El Kebbaj, Pierre Andreoletti, Abderrahim El Ktaibi, Issam Rharrassi, Abdelkhalid Essamadi, M'hammed Saïd El Kebbaj, Stéphane Mandard, Norbert Latruffe, Joseph Vamecq, Boubker Nasser, Mustapha Cherkaoui-Malki
Sepsis causes severe dysregulation of organ functions, via the development of oxidative stress and inflammation. These pathophysiological mechanisms are mimicked in mice injected with bacterial lipopolysaccharide (LPS). Here, protective properties of argan oil against LPS-induced oxidative stress and inflammation are explored in the murine model. Mice received standard chow, supplemented with argan oil (AO) or olive oil (OO) for 25 days, before septic shock was provoked with a single intraperitoneal injection of LPS, 16 hours prior to animal sacrifice...
October 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29045755/the-triforc-database-a-comprehensive-up-to-date-resource-of-plant-triterpene-biosynthesis
#11
Karel Miettinen, Sabrina Iñigo, Lukasz Kreft, Jacob Pollier, Christof De Bo, Alexander Botzki, Frederik Coppens, S Ren Bak, Alain Goossens
Triterpenes constitute a large and important class of plant natural products with diverse structures and functions. Their biological roles range from membrane structural components over plant hormones to specialized plant defence compounds. Furthermore, triterpenes have great potential for a variety of commercial applications such as vaccine adjuvants, anti-cancer drugs, food supplements and agronomic agents. Their biosynthesis is carried out through complicated, branched pathways by multiple enzyme types that include oxidosqualene cyclases, cytochrome P450s, and UDP-glycosyltransferases...
October 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29044952/protocol-for-computational-enzymatic-reactivity-based-on-geometry-optimisation
#12
Nuno Sousa Cerqueira, Pedro Fernandes, Maria João Ramos
Enzymes play a biologically essential role in performing and controlling an important share of the chemical processes occurring in life. However, despite their critical role in nature, attaining a clear understanding of the way an enzyme acts is still cumbersome. Computational enzymology is playing an increasingly important role in this field of research. It allows to elucidate and present the complete and detailed mechanisms of enzymatic reactions, including the characterization of reaction intermediates and transition states from both structural and energetic points of view, something that no other single experiment can produce alone...
October 16, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/29025876/mevalonate-5-diphosphate-mediates-atp-binding-to-the-mevalonate-diphosphate-decarboxylase-from-the-bacterial-pathogen-enterococcus-faecalis
#13
Chun-Liang Chen, James C Mermoud, Lake N Paul, Calvin Nicklaus Steussy, Cynthia V Stauffacher
The mevalonate pathway produces isopentenyl diphosphate (IPP), a building block for polyisoprenoid synthesis, and is a crucial pathway for growth of the human bacterial pathogen Enterococcus faecalis. The final enzyme in this pathway, mevalonate diphosphate decarboxylase (MDD), acts on mevalonate diphosphate (MVAPP) to produce IPP while consuming ATP. This essential enzyme has been suggested as a therapeutic target for the treatment of drug-resistant bacterial infections. Here we report functional and structural studies on the mevalonate diphosphate decarboxylase from E...
October 12, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29020628/molecular-mechanism-by-which-prominent-human-gut-bacteroidetes-utilize-mixed-linkage-beta-glucans-major-health-promoting-cereal-polysaccharides
#14
Kazune Tamura, Glyn R Hemsworth, Guillaume Déjean, Theresa E Rogers, Nicholas A Pudlo, Karthik Urs, Namrata Jain, Gideon J Davies, Eric C Martens, Harry Brumer
Microbial utilization of complex polysaccharides is a major driving force in shaping the composition of the human gut microbiota. There is a growing appreciation that finely tuned polysaccharide utilization loci enable ubiquitous gut Bacteroidetes to thrive on the plethora of complex polysaccharides that constitute "dietary fiber." Mixed-linkage β(1,3)/β(1,4)-glucans (MLGs) are a key family of plant cell wall polysaccharides with recognized health benefits but whose mechanism of utilization has remained unclear...
October 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28976181/exploring-the-untapped-biosynthetic-potential-of-apicomplexan-parasites
#15
Jack Ganley, Maria Toro-Moreno, Emily R Derbyshire
Apicomplexan parasites encompass a diverse group of eukaryotic intracellular pathogens that infect various animal hosts to cause disease. Intriguingly, apicomplexans possess a unique organelle of algal origin, the apicoplast, which phylogenetically links these parasites to dinoflagellates and photosynthetic, coral-associated organisms. While production of secondary metabolites in closely-related organisms has been thoroughly examined, it remains widely unexplored in apicomplexans. In this perspective, we discuss previous work toward understanding secondary metabolite building block biosynthesis in apicomplexans and highlight the unexplored enzymology and biosynthetic potential of these parasites in the context of evolution...
October 4, 2017: Biochemistry
https://www.readbyqxmd.com/read/28959952/deubiquitylating-enzymes-and-drug-discovery-emerging-opportunities
#16
REVIEW
Jeanine A Harrigan, Xavier Jacq, Niall M Martin, Stephen P Jackson
More than a decade after a Nobel Prize was awarded for the discovery of the ubiquitin-proteasome system and clinical approval of proteasome and ubiquitin E3 ligase inhibitors, first-generation deubiquitylating enzyme (DUB) inhibitors are now approaching clinical trials. However, although our knowledge of the physiological and pathophysiological roles of DUBs has evolved tremendously, the clinical development of selective DUB inhibitors has been challenging. In this Review, we discuss these issues and highlight recent advances in our understanding of DUB enzymology and biology as well as technological improvements that have contributed to the current interest in DUBs as therapeutic targets in diseases ranging from oncology to neurodegeneration...
September 29, 2017: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/28956599/first-biochemical-characterization-of-a-methylcitric-acid-cycle-from-bacillus-subtilis-strain-168
#17
Jason J Reddick, Sherona Sirkisoon, Rejwi Acharya Dahal, Grant Hardesty, Natalie E Hage, William T Booth, Amy L Quattlebaum, Suzette N Mills, Victoria G Meadows, Sydney L H Adams, Jennifer S Doyle, Brittany E Kiel
The genome of Bacillus subtilis strain 168 contains the mother cell metabolic gene (mmg) operon that encodes homologues from the methylcitric acid cycle. We showed that the three genes, mmgDE and yqiQ(mmgF), provide three of the five steps of the methylcitric acid cycle. We also showed that the fourth step can be supplied by citB (aconitase), and we suggest that the fifth missing step, the propionyl-CoA synthetase, is probably skipped because the β-oxidation of methyl-branched fatty acids by the enzymes encoded by mmgABC should produce propionyl-CoA...
October 24, 2017: Biochemistry
https://www.readbyqxmd.com/read/28956339/phosphodiesterase-1-a-unique-drug-target-for-degenerative-diseases-and-cognitive-dysfunction
#18
Lawrence P Wennogle, Helen Hoxie, Youyi Peng, Joseph P Hendrick
The focus of this chapter is on the cyclic nucleotide phosphodiesterase 1 (PDE1) family. PDE1 is one member of the 11 PDE families (PDE 1-11). It is the only phosphodiesterase family that is calcium/calmodulin activated. As a result, whereas other families of PDEs 2-11 play a dominant role controlling basal levels of cyclic nucleotides, PDE1 is involved when intra-cellular calcium levels are elevated and, thus, has an "on demand" or activity-dependent involvement in the control of cyclic nucleotides in excitatory cells including neurons, cardiomyocytes and smooth muscle...
2017: Advances in Neurobiology
https://www.readbyqxmd.com/read/28943461/the-importance-of-sourcing-enzymes-from-non-conventional-fungi-for-metabolic-engineering-and-biomass-breakdown
#19
REVIEW
Susanna Seppälä, St Elmo Wilken, Doriv Knop, Kevin V Solomon, Michelle A O'Malley
A wealth of fungal enzymes has been identified from nature, which continue to drive strain engineering and bioprocessing for a range of industries. However, while a number of clades have been investigated, the vast majority of the fungal kingdom remains unexplored for industrial applications. Here, we discuss selected classes of fungal enzymes that are currently in biotechnological use, and explore more basal, non-conventional fungi and their underexploited biomass-degrading mechanisms as promising agents in the transition towards a bio-based society...
September 21, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28940509/morphological-and-transcript-changes-in-the-biosynthesis-of-lignin-in-oil-palm-elaeis-guineensis-during-ganoderma-boninense-infections-in-vitro
#20
Goh Kar Mun, Matthew Dickinson, Christina V Supramaniam
Lignification of the plant cell wall could serve as the first line of defence against pathogen attack, but the molecular mechanisms of virulence and disease between oil palm and Ganoderma boninense is poorly understood. This study presents the biochemical, histochemical, enzymology and gene expression evidences of enhanced lignin biosynthesis in young oil palm as a response to G. boninense (GBLS strain). Comparative studies with control (T1), wounded (T2) and infected (T3) oil palm plantlets showed significant accumulation of total lignin content and monolignol derivatives (syringaldehyde and vanillin)...
September 20, 2017: Physiologia Plantarum
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