Genomes and Genes
Summary: The facilitation of biochemical reactions with the aid of naturally occurring catalysts such as ENZYMES.
- Mullen N, Price D. Hydrogen peroxide yields mechanistic insights into human mRNA capping enzyme function. PLoS ONE. 2017;12:e0186423 pubmed publisher..Our further characterization of the capping reaction dependence on transcript length and its interaction with the unidentified modulator of capping raises the interesting possibility that the capping reaction could be regulated...
- Rachel N, Toulouse J, Pelletier J. Transglutaminase-Catalyzed Bioconjugation Using One-Pot Metal-Free Bioorthogonal Chemistry. Bioconjug Chem. 2017;28:2518-2523 pubmed publisher..Owing to the breadth of labels that MTG can use as a substrate, our results demonstrate the versatility of this system, with the researcher being able to combine specific protein substrates with a variety of labels...
- Tomita H, Katsuyama Y, Minami H, Ohnishi Y. Identification and characterization of a bacterial cytochrome P450 monooxygenase catalyzing the 3-nitration of tyrosine in rufomycin biosynthesis. J Biol Chem. 2017;292:15859-15869 pubmed publisher..Taken together with the results of an in silico analysis of the ruf cluster, we propose a rufomycin biosynthetic pathway in S. atratus. ..
- Amici A, Grolla A, Del Grosso E, Bellini R, Bianchi M, Travelli C, et al. Synthesis and Degradation of Adenosine 5'-Tetraphosphate by Nicotinamide and Nicotinate Phosphoribosyltransferases. Cell Chem Biol. 2017;24:553-564.e4 pubmed publisher..These results suggest a role of Ap4 in the actions of NAMPT, and prompt to evaluate the role of Ap4 production in the actions of NAMPT inhibitors. ..
- Toliusis P, Zaremba M, Silanskas A, Szczelkun M, Siksnys V. CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction endonucleases. Nucleic Acids Res. 2017;45:8435-8447 pubmed publisher..Our results are consistent with a mechanism of CglI action that is distinct from that of other ATP-dependent restriction-modification enzymes. ..
- Zhu Y, Zhou G, Yu X, Xu Q, Wang K, Xie D, et al. LC-MS-MS quantitative analysis reveals the association between FTO and DNA methylation. PLoS ONE. 2017;12:e0175849 pubmed publisher..In conclusion, our results not only reveal the enzymatic activity of FTO, but also may facilitate the future discovery of proteins involved in epigenetic modification function. ..
- Lilley D. How RNA acts as a nuclease: some mechanistic comparisons in the nucleolytic ribozymes. Biochem Soc Trans. 2017;45:683-691 pubmed publisher..The discovery of several new ribozymes in this class has now allowed comparisons to be made, and the beginnings of mechanistic groupings to emerge. ..
- Han S, Udeshi N, Deerinck T, Svinkina T, Ellisman M, Carr S, et al. Proximity Biotinylation as a Method for Mapping Proteins Associated with mtDNA in Living Cells. Cell Chem Biol. 2017;24:404-414 pubmed publisher..Our study demonstrates that APEX is a powerful tool for mapping macromolecular complexes in living cells, and can identify proteins and pathways that have been missed by traditional approaches. ..
- Xia H, Kitazumi Y, Shirai O, Ozawa H, Onizuka M, Komukai T, et al. Factors affecting the interaction between carbon nanotubes and redox enzymes in direct electron transfer-type bioelectrocatalysis. Bioelectrochemistry. 2017;118:70-74 pubmed publisher..Finally, the electrostatic interaction between an enzyme (especially the portion near the redox active center) and CNTs is proposed as one of the most important factors governing the performance of DET-type bioelectrocatalysis. ..
- Bell K, Cha H, Sindelar C, Cochran J. The yeast kinesin-5 Cin8 interacts with the microtubule in a noncanonical manner. J Biol Chem. 2017;292:14680-14694 pubmed publisher..The novel microtubule-binding mode of Cin8 identified here provides a potential explanation for Cin8 clustering along microtubules and potentially may contribute to the mechanism for direction reversal. ..
- Calasso M, Mancini L, de Angelis M, Conte A, Costa C, Del Nobile M, et al. Multiple microbial cell-free extracts improve the microbiological, biochemical and sensory features of ewes' milk cheese. Food Microbiol. 2017;66:129-140 pubmed publisher..05) for internal structure, acid taste and juiciness than CC samples. This study shows the possibility of producing ewes' milk cheese with standardized characteristics and improved flavor intensity in a relatively short time. ..
- Härtl K, Huang F, Giri A, Franz Oberdorf K, Frotscher J, Shao Y, et al. Glucosylation of Smoke-Derived Volatiles in Grapevine (Vitis vinifera) is Catalyzed by a Promiscuous Resveratrol/Guaiacol Glucosyltransferase. J Agric Food Chem. 2017;65:5681-5689 pubmed publisher..This knowledge will help to design strategies for managing the risk of producing smoke-affected wines. ..
- Fujimoto Z, Suzuki N, Kishine N, Ichinose H, Momma M, Kimura A, et al. Carbohydrate-binding architecture of the multi-modular ?-1,6-glucosyltransferase from Paenibacillus sp. 598K, which produces ?-1,6-glucosyl-?-glucosaccharides from starch. Biochem J. 2017;474:2763-2778 pubmed publisher..Ps6TG31A appears to have enhanced transglucosylation activity facilitated by its carbohydrate-binding modules and substrate-binding cleft that positions the substrate and acceptor sugar for the transglucosylation. ..
- Ewing T, Nguyen Q, Allan R, Gygli G, Romero E, Binda C, et al. Two tyrosine residues, Tyr-108 and Tyr-503, are responsible for the deprotonation of phenolic substrates in vanillyl-alcohol oxidase. J Biol Chem. 2017;292:14668-14679 pubmed publisher..These results indicate that Tyr-108 and Tyr-503 are responsible for the activation of substrates in VAO, providing new insights into the catalytic mechanism of VAO and related enzymes that oxidize para-substituted phenols. ..
- Oda T, Hirabayashi H, Shikauchi G, Takamura R, Hiraga K, Minami H, et al. Structural basis of autoinhibition and activation of the DNA-targeting ADP-ribosyltransferase pierisin-1. J Biol Chem. 2017;292:15445-15455 pubmed publisher..Our study provides a structural basis for the DNA-acceptor specificity of pierisin-1 and reveals that a self-regulatory mechanism is required for its activity. ..
- Gu J, Shin D, Pletneva E. Remote Perturbations in Tertiary Contacts Trigger Ligation of Lysine to the Heme Iron in Cytochrome c. Biochemistry. 2017;56:2950-2966 pubmed publisher..The findings emphasize the importance of the hydrogen-bonding network in controlling ligation of the native Met80 to the heme iron. ..
- Xia L, Bai Y, Mu W, Wang J, Xu X, Jin Z. Efficient Synthesis of Glucosyl-?-Cyclodextrin from Maltodextrins by Combined Action of Cyclodextrin Glucosyltransferase and Amyloglucosidase. J Agric Food Chem. 2017;65:6023-6029 pubmed publisher..4% to 24.0% and the side products ?-CD and ?-CD were hydrolyzed because of the coupling activity of ?-CGTase. Thus, this controlled two-step reaction might be an efficient approach for industrial production of pure G1-?-CD. ..
- Maheshwari S, Miller M, O Meally R, Cole R, Amzel L, Gabelli S. Kinetic and structural analyses reveal residues in phosphoinositide 3-kinase ? that are critical for catalysis and substrate recognition. J Biol Chem. 2017;292:13541-13550 pubmed publisher..On the basis of these kinetic and structural analyses, we propose possible mechanistic roles of these critical residues in PI3K? catalysis. ..
- Pressman A, Moretti J, Campbell G, MULLER U, Chen I. Analysis of in vitro evolution reveals the underlying distribution of catalytic activity among random sequences. Nucleic Acids Res. 2017;45:8167-8179 pubmed publisher..The frequency distribution of rate constants appears to be log-normal, with a surprisingly steep dropoff at higher activity, consistent with a mechanism for the emergence of activity as the product of many independent contributions. ..
- Jung Y, Lee B, Yoo S. Physical structure and absorption properties of tailor-made porous starch granules produced by selected amylolytic enzymes. PLoS ONE. 2017;12:e0181372 pubmed publisher..This biocatalytic approach could contribute to develop tailor-made PSGs with distinct internal structure for specific uses in wide range of food, pharmaceutical and other industrial applications. ..
- Williams I, Chib S, Nuthakki V, Gatchie L, Joshi P, Narkhede N, et al. Biotransformation of Chrysin to Baicalein: Selective C6-Hydroxylation of 5,7-Dihydroxyflavone Using Whole Yeast Cells Stably Expressing Human CYP1A1 Enzyme. J Agric Food Chem. 2017;65:7440-7446 pubmed publisher..Similar CYP-expressing yeast cell based systems are likely to have wider applications in the syntheses of medicinally important polyphenolic compounds. ..
- Li X, Li M, Liu J, Ji N, Liang C, Sun Q, et al. Preparation of Hollow Biopolymer Nanospheres Employing Starch Nanoparticle Templates for Enhancement of Phenolic Acid Antioxidant Activities. J Agric Food Chem. 2017;65:3868-3882 pubmed publisher..Furthermore, they can be used as nanoreactors to immobilize phenolic acids, enhance their antioxidative activities, and improve their stability when exposed to high salt concentrations, UV light, or heat treatments. ..
- Li P, Jiang H, Zhang W, Li Y, Zhao M, Zhou W, et al. Synthesis of carbazole derivatives containing chalcone analogs as non-intercalative topoisomerase II catalytic inhibitors and apoptosis inducers. Eur J Med Chem. 2018;145:498-510 pubmed publisher..It was further confirmed by Annexin-V-FITC binding assay. Western blot analysis revealed that compound 3h induces apoptosis likely through the activation of caspase proteins. ..
- Iwamoto S, Kasahara Y, Yoshimura Y, Seko A, Takeda Y, Ito Y, et al. Endo-?-Mannosidase-Catalyzed Transglycosylation. Chembiochem. 2017;18:1376-1378 pubmed publisher..The synthetic utility of the enzyme was demonstrated by generation of a high-mannose-type undecasaccharide (Glc1 Man9 GlcNAc2 ). ..
- Dautant A, Meyer P, Georgescauld F. Hydrogen/Deuterium Exchange Mass Spectrometry Reveals Mechanistic Details of Activation of Nucleoside Diphosphate Kinases by Oligomerization. Biochemistry. 2017;56:2886-2896 pubmed publisher..Further HDX-MS studies are necessary to establish the general activation mechanism for other homo-oligomers. ..
- Yan Y, Hu Y, Simpson D, Ganzle M. Enzymatic Synthesis and Purification of Galactosylated Chitosan Oligosaccharides Reducing Adhesion of Enterotoxigenic Escherichia coli K88. J Agric Food Chem. 2017;65:5142-5150 pubmed publisher..Galactosylation of COS produces oligosaccharides which reduce ETEC K88 adhesion; moreover, resulting oligosaccharides match the composition of human milk oligosaccharides, which prevent adhesion of multiple pathogens. ..
- Jennings S, Chenevert M, Liu L, Mottamal M, Wojcik E, Huckaba T. Characterization of kinesin switch I mutations that cause hereditary spastic paraplegia. PLoS ONE. 2017;12:e0180353 pubmed publisher..This work provides mechanistic insight into the cause of HSP in patients with these mutations and points to future experiments to further dissect the root cause of this disease. ..
- Wang S, Zhang Y, Ren H, Wang Y, Jiang W, Fang B. Strategies and perspectives of assembling multi-enzyme systems. Crit Rev Biotechnol. 2017;37:1024-1037 pubmed publisher..This review summarizes advances and progresses employing these strategies. Furthermore, challenges and perspectives in designing multi-enzyme systems are highlighted. ..
- Appadurai R, Senapati S. How Mutations Can Resist Drug Binding yet Keep HIV-1 Protease Functional. Biochemistry. 2017;56:2907-2920 pubmed publisher..These findings in combination with the identified protease flap and active site residues that contribute to ligand recognition and strong binding can help in the design of future resistance-evading HIV-1 protease inhibitors. ..
- Palomo J. Semisynthetic Enzymes by Protein-Peptide Site-Directed Covalent Conjugation: Methods and Applications. Methods Enzymol. 2017;590:305-316 pubmed publisher..The new enzyme also exhibited excellent enantioselectivity in the desymmetrization reaction with enantiomeric excess (ee) of >99% when compared to that of the unmodified enzyme (ee=78%). ..
- Littlechild J. Improving the 'tool box' for robust industrial enzymes. J Ind Microbiol Biotechnol. 2017;44:711-720 pubmed publisher..It will highlight specific hydrolase enzymes and recent case studies which have been carried out within our group in Exeter. ..
- Wagner G, Bhatt D, O Connell T, Thompson J, DuBois L, Backos D, et al. A Class of Reactive Acyl-CoA Species Reveals the Non-enzymatic Origins of Protein Acylation. Cell Metab. 2017;25:823-837.e8 pubmed publisher..These data uncover a fundamental relationship between reactive acyl-CoA species and proteins and define a new regulatory paradigm in metabolism. ..
- Christenson J, Robinson S, Engel T, Richman J, Kim A, Wackett L. OleB from Bacterial Hydrocarbon Biosynthesis Is a ?-Lactone Decarboxylase That Shares Key Features with Haloalkane Dehalogenases. Biochemistry. 2017;56:5278-5287 pubmed publisher..This work defines a previously unrecognized reaction in nature, functionally identifies some HLD-III enzymes as ?-lactone decarboxylases, and posits an enzymatic mechanism of ?-lactone decarboxylation...
- Quifer Rada P, Martínez Huelamo M, Lamuela Raventos R. Is enzymatic hydrolysis a reliable analytical strategy to quantify glucuronidated and sulfated polyphenol metabolites in human fluids?. Food Funct. 2017;8:2419-2424 pubmed publisher..Thus, enzymatic hydrolysis does not seem an ideal analytical strategy to quantify glucuronidated and sulfated polyphenol metabolites. ..
- Agmon I. Sequence complementarity at the ribosomal Peptidyl Transferase Centre implies self-replicating origin. FEBS Lett. 2017;591:3252-3258 pubmed publisher..Furthermore, it indicates a simple and efficient replication mode; the strand of each monomer could have acted as a template for the synthesis of its counterpart, forming a self-replicating ribozyme. ..
- Mahmoud M, Schechter A, Alnajjar K, Huang J, Towle Weicksel J, Eckenroth B, et al. Defective Nucleotide Release by DNA Polymerase Î² Mutator Variant E288K Is the Basis of Its Low Fidelity. Biochemistry. 2017;56:5550-5559 pubmed publisher..Structural modeling implies that this inherent defect is due to interaction of E288K with DNA, resulting in a stable closed enzyme structure. ..
- Wu X, Kwon S, Kim J, Kane R, Dordick J. Biocatalytic Nanocomposites for Combating Bacterial Pathogens. Annu Rev Chem Biomol Eng. 2017;8:87-113 pubmed publisher..Here, we highlight the use of enzymes as antimicrobial agents, including applications that may prove effective in new therapeutics and through control of key societal infrastructures. ..