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S Takeshita, T Oda
Alginate-degrading enzyme, alginate lyase, catalyzes the cleavage of glycosidic 1-4 O-linkages between uronic acid residues of alginate by a β-elimination reaction leaving a 4-deoxy-l-erythro-hex-4-ene pyranosyluronate as nonreducing terminal end. The enzymes from a wide variety of sources such as marine molluscs, seaweeds, and marine bacteria have been discovered and studied not only from a point of view of enzymological interest of enzyme itself but also for elucidation of fine chemical structure of alginate, structure-activity relationship of alginate, and biological activities and physicochemical features of the enzymatic digestion products...
2016: Advances in Food and Nutrition Research
Shelley D Minteer
This chapter describes methods for enzyme stabilization using micellar solutions. Micellar solutions have been shown to increase the thermal stability, as well as the pH and solvent tolerance of enzymes. This field is traditionally referred to as micellar enzymology. This chapter details the use of ionic and nonionic micelles for the stabilization of polyphenol oxidase, lipase, and catalase, although this method could be used with any enzymatic system or enzyme cascade system.
2017: Methods in Molecular Biology
Joan B Broderick, James D Moody
The human gut microbiome is the source of not only microbial diversity, but also of interesting chemical reactions and enzymology. An excellent example of this is CutC, an enzyme that makes trimethylamine (TMA). In this issue of Cell Chemical Biology, Bodea et al. (2016) show how CutC uses a glycyl radical to perform C-N bond cleavage needed for TMA production.
October 20, 2016: Cell Chemical Biology
Blake T Riley, Olga Ilyichova, Mauricio G S Costa, Benjamin T Porebski, Simon J de Veer, Joakim E Swedberg, Itamar Kass, Jonathan M Harris, David E Hoke, Ashley M Buckle
The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (~1 Å) resolution, as well as with bound nickel...
October 21, 2016: Scientific Reports
Hafiz Mamoon Rehman, Zahid Hussain Shah, Muhammad Amjad Nawaz, Muhammad Qadir Ahmad, Seung Hwan Yang, Kang Hee Kho, Gyuhwa Chung
This review provides an insight into the beta-cyanoalanine synthase pathway in higher plants for cyanide (CN) detoxification and describes how it contributes to various physiological activities, such as plant growth and development. In higher plants, CN is produced as a natural toxin through the biosynthesis of ethylene and camalexin, the degradation of glucosinolates and cyanogenic glycosides, the oxidation of amino acids, and the metabolism of glyoxylate and hydroxylamine. To maintain cellular homeostasis by maintaining CN at non-toxic levels, plants have evolved four different biochemical pathways: the β-cyanoalanine synthase pathway (beta-CASP), the thiocyanate pathway, the formamide hydrolase pathway, and the natural release of CN through volatilization...
October 15, 2016: Planta
Ilenia Infusino, Erika Frusciante, Federica Braga, Mauro Panteghini
International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) has established reference measurement procedures (RMPs) for the most popular enzymes. Manufacturers should assign values to commercial calibrators traceable to these RMPs to achieve equivalent results in clinical samples, independent of reagent kits, instruments, and laboratory where the measurement is carried out. The situation is, however, far from acceptable. Some manufacturers continue to market assays giving results that are not traceable to internationally accepted RMPs...
October 8, 2016: Clinical Chemistry and Laboratory Medicine: CCLM
Bartholomew P Roland, Todd R Graham
Cellular membranes display a diversity of functions that are conferred by the unique composition and organization of their proteins and lipids. One important aspect of lipid organization is the asymmetric distribution of phospholipids (PLs) across the plasma membrane. The unequal distribution of key PLs between the cytofacial and exofacial leaflets of the bilayer creates physical surface tension that can be used to bend the membrane; and like Ca(2+), a chemical gradient that can be used to transduce biochemical signals...
October 4, 2016: Critical Reviews in Biochemistry and Molecular Biology
Becky Tu-Sekine, Hana L Goldschmidt, Daniel M Raben
Diacylglycerol kinases (DGKs) are a family of enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatidic acid (PtdOH). The recognition of the importance of these enzymes has been increasing ever since it was determined that they played a role in the phosphatidylinositol (PtdIns) cycle and a number of excellent reviews have already been written [(see van Blitterswijk and Houssa, 2000; Kanoh et al., 2002; Mérida et al., 2008; Tu-Sekine and Raben, 2009, 2011; Shulga et al...
2016: Frontiers in Cell and Developmental Biology
Dustin Dovala, Christopher M Rath, Qijun Hu, William S Sawyer, Steven Shia, Robert A Elling, Mark S Knapp, Louis E Metzger
Gram-negative bacteria possess a characteristic outer membrane, of which the lipid A constituent elicits a strong host immune response through the Toll-like receptor 4 complex, and acts as a component of the permeability barrier to prevent uptake of bactericidal compounds. Lipid A species comprise the bulk of the outer leaflet of the outer membrane and are produced through a multistep biosynthetic pathway conserved in most Gram-negative bacteria. The final steps in this pathway involve the secondary acylation of lipid A precursors...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Christos S Karamitros, Nikolaos E Labrou
In the present study, we report on the effect of four different soluble additives (sucrose, lactitol, superfloc c577 and dextran sulphate) on the stability of the enzyme glutathione transferase 1 from Zea mays (ZmGSTF1-1) under free and tethered conditions at 4 and 25 °C. Among all additives, the best stabilizing effects observed in case of superfloc c577 and sucrose in both tested temperatures, yet at distinct concentrations at each condition. Those two stabilizing agents were further combined and potential positive synergistic effects were investigated...
September 28, 2016: Biotechnology and Applied Biochemistry
Fanny Sunden, Ishraq AlSadhan, Artem Y Lyubimov, Susanne Ressl, Helen Wiersma-Koch, Jamar Borland, Clayton L Brown, Tory A Johnson, Zorawar Singh, Daniel Herschlag
Naively one might have expected an early division between phosphate monoesterases and diesterases of the Alkaline Phosphatase (AP) superfamily. On the contrary, prior results and our structural and biochemical analyses of phosphate monoesterase PafA, from Chryseobacterium meningosepticum, indicate similarities to a superfamily phosphate diesterase [Xanthomonas citri Nucleotide Pyrophosphatase/Phosphodiesterase (NPP)] and distinct differences from the three metal ion AP superfamily monoesterase, from E. coli AP (EcAP)...
September 26, 2016: Journal of the American Chemical Society
Francesca Di Bartolomeo, Ariane Wagner, Günther Daum
Phosphatidylethanolamine is one of the most abundant phospholipids whose major amounts are formed by phosphatidylserine decarboxylases (PSD). Here we provide a comprehensive description of different types of PSDs in the different kingdoms of life. In eukaryotes, type I PSDs are mitochondrial enzymes, whereas other PSDs are localized to other cellular compartments. We describe the role of mitochondrial Psd1 proteins, their function, enzymology, biogenesis, assembly into mitochondria and their contribution to phospholipid homeostasis in much detail...
September 17, 2016: Biochimica et Biophysica Acta
Paul F Hollenberg
No abstract text is available yet for this article.
September 19, 2016: Chemical Research in Toxicology
Peter Biely, Suren Singh, Vladimír Puchart
Significant progress over the past few years has been achieved in the enzymology of microbial degradation and saccharification of plant xylan, after cellulose being the most abundant natural renewable polysaccharide. Several new types of xylan depolymerizing and debranching enzymes have been described in microorganisms. Despite the increasing variety of known glycoside hydrolases and carbohydrate esterases, some xylan structures still appear quite recalcitrant. This review focuses on the mode of action of different types of depolymerizing endoxylanases and their cooperation with β-xylosidase and accessory enzymes in breakdown of complex highly branched xylan structures...
November 15, 2016: Biotechnology Advances
Josep M Comeron, Jordan Reed, Matthew Christie, Julia S Jacobs, Jason Dierdorff, Daniel F Eberl, J Robert Manak
Accurate and rapid identification or confirmation of single nucleotide polymorphisms (SNPs), point mutations and other human genomic variation facilitates understanding the genetic basis of disease. We have developed a new methodology (called MENA (Mismatch EndoNuclease Array)) pairing DNA mismatch endonuclease enzymology with tiling microarray hybridization in order to genotype both known point mutations (such as SNPs) as well as identify previously undiscovered point mutations and small indels. We show that our assay can rapidly genotype known SNPs in a human genomic DNA sample with 99% accuracy, in addition to identifying novel point mutations and small indels with a false discovery rate as low as 10%...
2016: Microarrays
Shannon L Glisan, Kimberly A Grove, Neela H Yennawar, Joshua D Lambert
Few studies have examined the effect of black tea (Camellia sinensis) theaflavins on obesity-related targets. Pancreatic lipase (PL) plays a central role in fat metabolism and is a validated target for weight loss. We compared the inhibitory efficacy of individual theaflavins and explored the underlying mechanism. Theaflavin-3,3'-digallate (TFdiG), theaflavin-3'-gallate, theaflavin-3-gallate, and theaflavin inhibited PL with IC50 of 1.9, 4.2, 3.0, and >10μmol/L. The presence and location of the galloyl ester moiety were essential for inhibitory potency...
February 1, 2017: Food Chemistry
Michael H Godsey, Omar Davulcu, Jay C Nix, Jack J Skalicky, Rafael P Brüschweiler, Michael S Chapman
Arginine kinase provides a model for functional dynamics, studied through crystallography, enzymology, and nuclear magnetic resonance. Structures are now solved, at ambient temperature, for the transition state analog (TSA) complex. Analysis of quasi-rigid sub-domain displacements show that differences between the two TSA structures average about 5% of changes between substrate-free and TSA forms, and they are nearly co-linear. Small backbone hinge rotations map to sites that also flex on substrate binding...
October 4, 2016: Structure
Hanna Luhavaya, Marcio V B Dias, Simon R Williams, Hui Hong, Luciana G de Oliveira, Peter F Leadlay
Tetrahydropyran rings are a common feature of complex polyketide natural products, but much remains to be learned about the enzymology of their formation. The enzyme SalBIII from the salinomycin biosynthetic pathway resembles other polyether epoxide hydrolases/cyclases of the MonB family, but SalBIII plays no role in the conventional cascade of ring opening/closing. Mutation in the salBIII gene gave a metabolite in which ring A is not formed. Using this metabolite in vitro as a substrate analogue, SalBIII has been shown to form pyran ring A...
November 9, 2015: Angewandte Chemie
Matthew A Deardorff, Nicholas J Porter, David W Christianson
Cornelia de Lange Syndrome (CdLS) encompasses a broad spectrum of phenotypes characterized by distinctive craniofacial abnormalities, limb malformations, growth retardation, and intellectual disability. CdLS spectrum disorders are referred to as cohesinopathies, with ∼70% of patients having a mutation in a gene encoding a core cohesin protein (SMC1A, SMC3, or RAD21) or a cohesin regulatory protein (NIPBL or HDAC8). Notably, the regulatory function of HDAC8 in cohesin biology has only recently been discovered...
August 31, 2016: Protein Science: a Publication of the Protein Society
Zachary D Parsons, Joshua M Bland, Elwood A Mullins, Brandt F Eichman
DNA glycosylases protect genomic integrity by locating and excising aberrant nucleobases. Substrate recognition and excision usually take place in an extrahelical conformation, which is often stabilized by π-stacking interactions between the lesion nucleobase and aromatic side chains in the glycosylase active site. Bacillus cereus AlkD is the only DNA glycosylase known to catalyze base excision without extruding the damaged nucleotide from the DNA helix. Instead of contacting the nucleobase itself, the AlkD active site interacts with the lesion deoxyribose through a series of C-H/π interactions...
September 14, 2016: Journal of the American Chemical Society
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