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Enzymology

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https://www.readbyqxmd.com/read/28202539/parps-and-adp-ribosylation-recent-advances-linking-molecular-functions-to-biological-outcomes
#1
REVIEW
Rebecca Gupte, Ziying Liu, W Lee Kraus
The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates...
January 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28163054/on-the-indirect-relationship-between-protein-dynamics-and-enzyme-activity
#2
REVIEW
Qinyi Zhao
The behaviors of simple thermal systems have been well studied in physical chemistry and the principles obtained from such studies have been applied to complex thermal systems, such as proteins and enzymes. But the simple application of such principles is questionable and may lead to mistakes under some circumstances. In enzymology, the transition state theory of chemical reactions has been accepted as a fundamental theory, but the role of protein dynamics in enzyme catalysis is controversial in the context of transition state theory...
February 2, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28151666/enhanced-catalytic-activity-of-%C3%AE-chymotrypsin-in-cationic-surfactant-solutions-the-component-specificity-revisited
#3
Animesh Patra, Nirnay Samanta, Dipak Kumar Das, Rajib Kumar Mitra
Enhanced catalytic activity (super activity) of enzymes in the presence of surfactants is of key importance in "micellar enzymology"; such super activity is not very trivial, it is highly system specific, and the mechanism behind the activity enhancement is not always well apprehended. We report the catalytic activity of α-chymotrypsin (CHT) on ala-ala-phe-7-amido-4-methylcoumarin (AMC) in the presence of cationic surfactants of different hydrophobic chain lengths: dodecyltrimethylammonium bromide (DTAB), cetyltrimethylammonium bromide (CTAB) and octadecyltrimethylammonium bromide (OTAB)...
February 13, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28138099/polysaccharide-utilization-loci-fuelling-microbial-communities
#4
Julie M Grondin, Kazune Tamura, Guillaume Déjean, D Wade Abbott, Harry Brumer
The complex carbohydrates of terrestrial and marine biomass represent a rich nutrient source for free-living and mutualistic microbes alike. The enzymatic saccharification of these diverse substrates is of critical importance for fuelling a variety of complex microbial communities, including marine, soil, ruminant, and monogastric microbiota. Consequently, highly specific carbohydrate-active enzymes, recognition proteins, and transporters are enriched in the genomes of certain species, and are of critical importance in competitive environments...
January 30, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28126738/discovery-and-characterisation-of-the-automethylation-properties-of-prdm9
#5
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/28122367/enzymology-and-ultrastructure-of-the-in-situ-pellicle-in-caries-active-and-caries-inactive-patients
#6
Jasmin Kirsch, Christian Hannig, Sandra Pötschke, Sabine Basche, William H Bowen, Stefan Rupf, Simone Trautmann, Natalia Umanskaya, Matthias Hannig
AIM: The present study aimed to evaluate the impact of caries activity on the key enzymes and the ultrastructure of the in situ pellicle. METHODS: Pellicle formation was performed on bovine enamel slabs. Intraoral exposure (3, 30, and 120 min) was accomplished by 14 caries-active (DMFS: 22.7 ± 12.1) and 13 caries-inactive (DMFS: 1.5 ± 1.8) individuals. The enzyme activities (lysozyme, peroxidase, α-amylase, glycosyltransferase [GTF]) in the in situ pellicle and resting saliva of all participants were analyzed directly after oral exposure...
January 26, 2017: Caries Research
https://www.readbyqxmd.com/read/28073471/biochemistry-and-genetics-of-taste-and-odor-producing-cyanobacteria
#7
REVIEW
Susan B Watson, Paul Monis, Peter Baker, Steven Giglio
Cyanobacteria are one of the principal sources of volatile organic compounds (VOCs) which cause offensive taste and odor (T&O) in drinking and recreational water, fish, shellfish and other seafood. Although non-toxic to humans, these T&O compounds severely undermine public trust in these commodities, resulting in substantial costs in treatment, and lost revenue to drinking water, aquaculture, food and beverage and tourist/hospitality industries. Mitigation and control have been hindered by the complexity of the communities and processes which produce and modify T&O events, making it difficult to source-track the major producer(s) and the factors governing VOC production and fate...
April 2016: Harmful Algae
https://www.readbyqxmd.com/read/28065271/signal-peptidase-enzymology-and-substrate-specificity-profiling
#8
R E Dalbey, D Pei, Ö D Ekici
Signal peptidases are membrane proteases that play crucial roles in the protein transport pathway of bacteria. They cleave off the signal peptide from precursor proteins that are membrane inserted by the SecYEG or Tat translocons. Signal peptide cleavage releases the translocated protein from the inner membrane allowing the protein to be exported to the periplasm, outer membrane, or secreted into the medium. Signal peptidases are very important proteins to study. They are unique serine proteases with a Ser-Lys dyad, catalyze cleavage at the membrane surface, and are promising potential antibacterial drug targets...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28031352/phosphoribosyl-diphosphate-prpp-biosynthesis-enzymology-utilization-and-metabolic-significance
#9
REVIEW
Bjarne Hove-Jensen, Kasper R Andersen, Mogens Kilstrup, Jan Martinussen, Robert L Switzer, Martin Willemoës
Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics...
March 2017: Microbiology and Molecular Biology Reviews: MMBR
https://www.readbyqxmd.com/read/28028852/structural-investigation-on-wlarg-from-campylobacter-jejuni-a-sugar-aminotransferase
#10
Garrett T Dow, Michel Gilbert, James B Thoden, Hazel M Holden
Campylobacter jejuni is a Gram-negative bacterium that represents a leading cause of human gastroenteritis worldwide. Of particular concern is the link between C. jejuni infections and the subsequent development of Guillain-Barré syndrome, an acquired autoimmune disorder leading to paralysis. All Gram-negative bacteria contain complex glycoconjugates anchored to their outer membranes, but in most strains of C. jejuni, this lipoglycan lacks the O-antigen repeating units. Recent mass spectrometry analyses indicate that the C...
December 28, 2016: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28011149/chromatin-associated-mechanisms-in-base-excision-repair-nucleosome-remodeling-and-dna-transcription-two-key-players
#11
Hervé Menoni, Paolo Di Mascio, Jean Cadet, Stefan Dimitrov, Dimitar Angelov
Genomic DNA is prone to a large number of insults by a myriad of endogenous and exogenous agents. The base excision repair (BER) is the major mechanism used by cells for the removal of various DNA lesions spontaneously or environmentally induced and the maintenance of genome integrity. The presence of persistent DNA damage is not compatible with life, since abrogation of BER leads to early embryonic lethality in mice. There are several lines of evidences showing existence of a link between deficient BER, cancer proneness and ageing, thus illustrating the importance of this DNA repair pathway in human health...
December 20, 2016: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28007654/archaeal-phospholipids-structural-properties-and-biosynthesis
#12
REVIEW
Antonella Caforio, Arnold J M Driessen
Phospholipids are major components of the cellular membranes present in all living organisms. They typically form a lipid bilayer that embroiders the cell or cellular organelles, constitute a barrier for ions and small solutes and form a matrix that supports the function of membrane proteins. The chemical composition of the membrane phospholipids present in the two prokaryotic domains Archaea and Bacteria are vastly different. Archaeal lipids are composed of highly-methylated isoprenoid chains that are ether-linked to a glycerol-1-phosphate backbone while bacterial phospholipids consist of straight fatty acids bound by ester bonds to the enantiomeric glycerol-3-phosphate backbone...
December 20, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27995398/a-slc39a8-variant-causes-manganese-deficiency-and-glycosylation-and-mitochondrial-disorders
#13
Lisa G Riley, Mark J Cowley, Velimir Gayevskiy, Tony Roscioli, David R Thorburn, Kristina Prelog, Melanie Bahlo, Carolyn M Sue, Shanti Balasubramaniam, John Christodoulou
SLC39A8 variants have recently been reported to cause a type II congenital disorder of glycosylation (CDG) in patients with intellectual disability and cerebellar atrophy. Here we report a novel SLC39A8 variant in siblings with features of Leigh-like mitochondrial disease. Two sisters born to consanguineous Lebanese parents had profound developmental delay, dystonia, seizures and failure to thrive. Brain MRI of both siblings identified bilateral basal ganglia hyperintensities on T2-weighted imaging and cerebral atrophy...
December 19, 2016: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/27993553/screening-ubiquitin-specific-protease-activities-using-chemically-synthesized-ubiquitin-and-ubiquitinated-peptides
#14
Marine Bacchi, Benjamin Fould, Magali Jullian, Aude Kreiter, Amélie Maurras, Olivier Nosjean, Thibault Coursindel, Karine Puget, Gilles Ferry, Jean A Boutin
Ubiquitin, a 76 amino acid protein, is a key component that contributes to cellular protein homeostasis. The specificity of this modification is due to a series of enzymes: ligases, attaching the ubiquitin to a lysine, and deubiquitinases, which remove it. More than a hundred of such proteins are implicated in the regulation of protein turnover. Their specificities are only partially understood. We chemically synthesized ubiquitin, attached it to lysines belonging to the protein sequences known to be ubiquitinated...
February 15, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/27976889/trends-in-food-enzymology
#15
Holger Zorn, Qing X Li
No abstract text is available yet for this article.
December 15, 2016: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/27966844/intellectual-property-rights-standards-and-data-exchange-in-systems-biology-reflections-from-the-ip-expert-meeting-at-the-university-of-luxembourg-8-9-october-2015-erasysapp-era-net-for-systems-biology-applications
#16
Esther van Zimmeren, Berthold Rutz, Timo Minssen
Intellectual property rights (IPRs) have become a key concern for researchers and industry in basically all high-tech sectors. IPRs regularly figure prominently in scientific journals and at scientific conferences and lead to dedicated workshops to increase the awareness and "IPR savviness" of scientists. In 2015, Biotechnology Journal published a report from an expert meeting on "Synthetic Biology & Intellectual Property Rights" organized by the Danish Agency for Science, Technology and Innovation sponsored by the European Research Area Network (ERA-Net) in Synthetic Biology (ERASynBio), in which we provided a number of recommendations for a variety of stakeholders [1]...
December 2016: Biotechnology Journal
https://www.readbyqxmd.com/read/27933102/a-polysaccharide-utilization-locus-from-flavobacterium-johnsoniae-enables-conversion-of-recalcitrant-chitin
#17
Johan Larsbrink, Yongtao Zhu, Sampada S Kharade, Kurt J Kwiatkowski, Vincent G H Eijsink, Nicole M Koropatkin, Mark J McBride, Phillip B Pope
BACKGROUND: Chitin is the second most abundant polysaccharide on earth and as such a great target for bioconversion applications. The phylum Bacteroidetes is one of nature's most ubiquitous bacterial lineages and is essential in the global carbon cycle with many members being highly efficient degraders of complex carbohydrates. However, despite their specialist reputation in carbohydrate conversion, mechanisms for degrading recalcitrant crystalline polysaccharides such as chitin and cellulose are hitherto unknown...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27929431/internet-databases-of-the-properties-enzymatic-reactions-and-metabolism-of-small-molecules-search-options-and-applications-in-food-science
#18
REVIEW
Piotr Minkiewicz, Małgorzata Darewicz, Anna Iwaniak, Justyna Bucholska, Piotr Starowicz, Emilia Czyrko
Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software...
December 6, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27917381/arachidonoyl-specific-diacylglycerol-kinase-%C3%AE%C2%B5-and-the-endoplasmic-reticulum
#19
REVIEW
Tomoyuki Nakano, Hirooki Matsui, Toshiaki Tanaka, Yasukazu Hozumi, Ken Iseki, Kaneyuki Kawamae, Kaoru Goto
The endoplasmic reticulum (ER) comprises an interconnected membrane network, which is made up of lipid bilayer and associated proteins. This organelle plays a central role in the protein synthesis and sorting. In addition, it represents the synthetic machinery of phospholipids, the major constituents of the biological membrane. In this process, phosphatidic acid (PA) serves as a precursor of all phospholipids, suggesting that PA synthetic activity is closely associated with the ER function. One enzyme responsible for PA synthesis is diacylglycerol kinase (DGK) that phosphorylates diacylglycerol (DG) to PA...
2016: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/27894770/activity-based-targeting-of-secretory-phospholipase-a2-enzymes-a-fatty-acid-binding-protein-assisted-approach
#20
Amir Keshavarz, Ligia Zelaya, Jasmeet Singh, Radha Ranganathan, Joseph Hajdu
Syntheses and enzymological characterization of fluorogenic substrate probes targeting secretory phospholipase A2 (sPLA2) for detection and quantitative assays are presented. Three fluorogenic phosphatidylcholine analogs PC-1, PC-2, and PC-3 each containing the duo of 7-mercapto-4-methyl-coumarin fluorophore and 2,4-dinitroanaline quencher on either tail were synthesized from (R)-3-amino-1,2-propanediol and R-(-)-2,2-dimethyl-1,3-dioxolane-4-methanol. These small reporter groups are advantageous in preserving natural membrane integrity...
January 2017: Chemistry and Physics of Lipids
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