Genomes and Genes
Summary: Biological molecules that possess catalytic activity. They may occur naturally or be synthetically created. Enzymes are usually proteins, however CATALYTIC RNA and CATALYTIC DNA molecules have also been identified.
Publications426 found, 100 shown here
- Molybdenum cofactors, enzymes and pathwaysGunter Schwarz
Institute of Biochemistry, Department of Chemistry and Centre for Molecular Medicine, University of Cologne, 47 Zuelpicher Street, 50674 Cologne, Germany
Nature 460:839-47. 2009..element molybdenum is essential for nearly all organisms and forms the catalytic centre of a large variety of enzymes such as nitrogenase, nitrate reductases, sulphite oxidase and xanthine oxidoreductases...
- Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1Margret E Berg Miller
Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
PLoS ONE 4:e6650. 2009..gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application in improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels.
- The carbohydrate-active enzymes database (CAZy) in 2013Vincent Lombard
Centre National de la Recherche Scientifique, CNRS UMR 7257, 13288 Marseille, France and Aix Marseille Université, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
Nucleic Acids Res 42:D490-5. 2014The Carbohydrate-Active Enzymes database (CAZy; http://www.cazy...
- Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasmaJohn C Chambers
Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, UK
Nat Genet 43:1131-8. 2011Concentrations of liver enzymes in plasma are widely used as indicators of liver disease...
- The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databasesRon Caspi
SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, USA
Nucleic Acids Res 40:D742-53. 2012..org/) provides a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life...
- CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy databaseByung H Park
Computer Science and Mathematics Division
Glycobiology 20:1574-84. 2010The Carbohydrate-Active Enzyme (CAZy) database provides a rich set of manually annotated enzymes that degrade, modify, or create glycosidic bonds...
- Enzyme-specific profiles for genome annotation: PRIAMClotilde Claudel-Renard
Laboratoire de Genetique Cellulaire, INRA, INRA CNRS, BP27, 31326 Castanet Tolosan Cedex, France
Nucleic Acids Res 31:6633-9. 2003..PRIAM, a method for automated enzyme detection in a fully sequenced genome, based on the classification of enzymes in the ENZYME database...
- ExPASy: The proteomics server for in-depth protein knowledge and analysisElisabeth Gasteiger
Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
Nucleic Acids Res 31:3784-8. 2003..ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community...
- Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymesSergio Bordel
Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
PLoS Comput Biol 6:e1000859. 2010..conditions and comparison of it with the significance of change in gene transcription for the corresponding enzymes. The comparison of flux change and gene expression allows identification of enzymes showing a significant ..
- BRENDA, the enzyme information system in 2011Maurice Scheer
Department for Bioinformatics and Biochemistry, Technische Universitat Braunschweig, Langer Kamp 19 B, 38106 Braunschweig, Germany
Nucleic Acids Res 39:D670-6. 2011The BRENDA (BRaunschweig ENzyme Database, http://www.brenda-enzymes.org) enzyme information system is the main collection of enzyme functional and property data for the scientific community...
- Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic fluxQijun Wang
State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
Science 327:1004-7. 2010..We demonstrated that central metabolism enzymes in Salmonella were acetylated extensively and differentially in response to different carbon sources, ..
- Enzyme promiscuity: a mechanistic and evolutionary perspectiveOlga Khersonsky
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
Annu Rev Biochem 79:471-505. 2010Many, if not most, enzymes can promiscuously catalyze reactions, or act on substrates, other than those for which they evolved...
- The coactivator PGC-1 cooperates with peroxisome proliferator-activated receptor alpha in transcriptional control of nuclear genes encoding mitochondrial fatty acid oxidation enzymesR B Vega
Center for Cardiovascular Research, Departments of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA
Mol Cell Biol 20:1868-76. 2000..plays a key role in the transcriptional control of genes encoding mitochondrial fatty acid beta-oxidation (FAO) enzymes. In this study we sought to determine whether the recently identified PPAR gamma coactivator 1 (PGC-1) is capable ..
- The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymesNicholas Furnham
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Department of Biochemistry and Molecular Genetics, University of Virginia, 1300 Jefferson Park Ave, Charlottesville, VA 22908, USA
Nucleic Acids Res 42:D485-9. 2014..Ontology, which has permitted the transfer of annotations to Mechanism, Annotation and Classification in Enzymes (MACiE) and UniProt Knowledge Base (UniProtKB) resources...
- Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reactionJustin B Siegel
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Science 329:309-13. 2010..No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions...
- Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostabilityC Vieille
Biochemistry Department, Michigan State University, East Lansing, Michigan 48824, USA
Microbiol Mol Biol Rev 65:1-43. 2001b>Enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of > 80 degrees C), also called hyperthermophilic enzymes, are typically thermostable (i.e...
- Metal ions in biological catalysis: from enzyme databases to general principlesClaudia Andreini
Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019, Sesto Fiorentino, Italy
J Biol Inorg Chem 13:1205-18. 2008..In Metal-MACiE, a database of metal-based reaction mechanisms, 116 entries covering 21% of the metal-dependent enzymes and 70% of the types of enzyme-catalysed chemical transformations are annotated according to metal function...
- Zip3 provides a link between recombination enzymes and synaptonemal complex proteinsS Agarwal
Howard Hughes Medical Institute, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
Cell 102:245-55. 2000..We speculate that Zip3 is a component of recombination nodules and serves to link the initiation of synapsis to meiotic recombination...
- Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymesHenri Grosjean
Universite Paris Sud, CNRS, UMR8621, Institut de Génétique et de Microbiologie, Orsay F 91405, France
FEBS Lett 584:252-64. 2010..Many of the modern tRNA modification enzymes acting at position 34 of tRNAs are present only in specific domains and obviously have arisen late during ..
- How protein stability and new functions trade offNobuhiko Tokuriki
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
PLoS Comput Biol 4:e1000002. 2008..by FoldX to analyze the effects of 548 mutations that arose from the directed evolution of 22 different enzymes. The stability effects, location, and type of function-altering mutations were compared to DeltaDeltaG changes ..
- The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome DatabasesRon Caspi
SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA and Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853 USA
Nucleic Acids Res 42:D459-71. 2014..org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life...
- Steroidogenic enzymes and stem cell markers are upregulated during androgen deprivation in prostate cancerMinja J Pfeiffer
Department of Urology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
Mol Med 17:657-64. 2011..To study this hypothesis, we assessed the expression of several steroidogenic enzymes and stem cell markers in clinical PCa samples and cell cultures during androgen depletion...
- The ENZYME database in 2000A Bairoch
Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
Nucleic Acids Res 28:304-5. 2000The ENZYME database is a repository of information related to the nomenclature of enzymes. In recent years it has became an indispensable resource for the development of metabolic databases...
- From genomics to chemical genomics: new developments in KEGGMinoru Kanehisa
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 34:D354-7. 2006..Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps...
- Improving enzymes by using them in organic solventsA M Klibanov
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
Nature 409:241-6. 2001The technological utility of enzymes can be enhanced greatly by using them in organic solvents rather than their natural aqueous reaction media...
- The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural dataCraig T Porter
EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 32:D129-33. 2004The Catalytic Site Atlas (CSA) provides catalytic residue annotation for enzymes in the Protein Data Bank. It is available online at http://www.ebi.ac.uk/thornton-srv/databases/CSA...
- The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sourcesMarion Gremse
Technische Universitat Braunschweig, Institute for Bioinformatics and Biochemistry, Langer Kamp 19 B, 38106 Braunschweig, Germany
Nucleic Acids Res 39:D507-13. 2011BTO, the BRENDA Tissue Ontology (http://www.BTO.brenda-enzymes.org) represents a comprehensive structured encyclopedia of tissue terms...
- PathPred: an enzyme-catalyzed metabolic pathway prediction serverYuki Moriya
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 38:W138-43. 2010..The server provides transformed compounds and reference transformation patterns in each predicted reaction, and displays all predicted multi-step reaction pathways in a tree-shaped graph...
- Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identificationCristina Marino Buslje
Fundacion Instituto Leloir, Buenos Aires, Argentina
PLoS Comput Biol 6:e1000978. 2010....
- Strategy and success for the directed evolution of enzymesPaul A Dalby
Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
Curr Opin Struct Biol 21:473-80. 2011Directed evolution is widely used to improve enzymes, particularly for industrial biocatalytic processes. Molecular biology advances present many new strategies for directed evolution...
- ORENZA: a web resource for studying ORphan ENZyme activitiesOlivier Lespinet
Institut de Genetique et Microbiologie, CNRS UMR 8621, Universite Paris Sud, Batiment 400, 91405 Orsay Cedex, France
BMC Bioinformatics 7:436. 2006..wide gap separating knowledge of biochemical function and sequence information is found for nearly all classes of enzymes. Thus, there is an urgent need to explore these sequence-less EC numbers, in order to progressively close this gap...
- Therapeutic potential and biological role of endogenous antioxidant enzymes in multiple sclerosis pathologyGerty Schreibelt
Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
Brain Res Rev 56:322-30. 2007..Expression of most antioxidant enzymes is regulated through the transcription factor nuclear factor-E2-related factor (Nrf2) and antioxidant response ..
- Enzymes-based resistant mechanism in pyrethroid resistant and susceptible Aedes aegypti strains from northern ThailandPuckavadee Somwang
Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
Parasitol Res 109:531-7. 2011..BNPP), were also added to determine if the resistance is conferred by oxidase or esterase enzymes, respectively. The LC(50) value for PMD-R (25.42 ppb) was ∼25-fold higher than for PMD (1.02 ppb)...
- Antitumour activity of crocetin in accordance to tumor incidence, antioxidant status, drug metabolizing enzymes and histopathological studiesVenkatraman Magesh
Department of Medical Biochemistry, University of Madras, Chennai, India
Mol Cell Biochem 287:127-35. 2006..The level of lipid peroxidation (LPO) and marker enzymes markedly increased in carcinogen administered animals, which was brought back to near normal by crocetin ..
- BKM-react, an integrated biochemical reaction databaseMaren Lang
Department of Bioinformatics and Biochemistry, Institute for Biochemistry and Biotechnology, Technische Universitat Braunschweig, Langer Kamp 19 B, 38106 Braunschweig, Germany
BMC Biochem 12:42. 2011..Since the available databases differ in the number of biochemical reactions and the annotation of the reactions, an integrated knowledge resource would be of great value...
- Mechanistic insights into the regulation of metabolic enzymes by acetylationYue Xiong
Molecular and Cell Biology Laboratory, Institute of Biomedical Sciences, Fudan University, Shanghai 20032, China
J Cell Biol 198:155-64. 2012The activity of metabolic enzymes is controlled by three principle levels: the amount of enzyme, the catalytic activity, and the accessibility of substrates...
- Allosteric mechanisms of signal transductionJean Pierre Changeux
Receptors and Cognition, Institut Pasteur, 75724 Paris Cedex 15, France
Science 308:1424-8. 2005..mechanisms (indirect interactions between distinct sites), used initially to explain feedback-inhibited enzymes, was presented by Monod, Wyman, and Changeux...
- Pyridoxal 5'-phosphate enzymes as targets for therapeutic agentsAlessio Amadasi
Dipartimento di Biochimica e Biologia Molecolare, Universita di Parma, Italy
Curr Med Chem 14:1291-324. 2007The vitamin B(6)-derived pyridoxal 5'-phosphate (PLP) is the cofactor of enzymes catalyzing a large variety of chemical reactions mainly involved in amino acid metabolism...
- Enzymes for chemical synthesisK M Koeller
Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
Nature 409:232-40. 2001..Enzyme-catalysed chemical transformations are now widely recognized as practical alternatives to traditional (non-biological) organic synthesis, and as convenient solutions to certain intractable synthetic problems...
- 'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find itAndrew D Hanson
Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
Biochem J 425:1-11. 2009..that we seek to manipulate remain highly incomplete, due to the dual problem of 'unknown' proteins and 'orphan' enzymes. The former are all the proteins deduced from genome sequence that have no known function, and the latter are all ..
- Defining network topologies that can achieve biochemical adaptationWenzhe Ma
Center for Theoretical Biology, Peking University, Beijing 100871, China
Cell 138:760-73. 2009..These design rules provide a framework for functionally classifying complex natural networks and a manual for engineering networks. For a video summary of this article, see the PaperFlick file with the Supplemental Data available online...
- The Enzyme Function InitiativeJohn A Gerlt
Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
Biochemistry 50:9950-62. 2011..Function Initiative (EFI) was recently established to address the challenge of assigning reliable functions to enzymes discovered in bacterial genome projects; in this Current Topic, we review the structure and operations of the EFI...
- MACiE: exploring the diversity of biochemical reactionsGemma L Holliday
EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 40:D783-9. 2012MACiE (which stands for Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACiE/...
- Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reeseiPamela K Foreman
Genencor International, Inc, Palo Alto, California 94304, USA
J Biol Chem 278:31988-97. 2003The filamentous fungus Trichoderma reesei produces and secretes profuse quantities of enzymes that act synergistically to degrade cellulase and related biomass components. We partially sequenced over 5100 random T. reesei cDNA clones...
- Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerationsAndrew C Eliot
Department of Chemistry University of California, Berkeley, California 94720 3206, USA
Annu Rev Biochem 73:383-415. 2004Pyridoxal phosphate (PLP)-dependent enzymes are unrivaled in the diversity of reactions that they catalyze...
- Protein profiling of plastoglobules in chloroplasts and chromoplasts. A surprising site for differential accumulation of metabolic enzymesA Jimmy Ytterberg
Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA
Plant Physiol 140:984-97. 2006..It is not known whether PGs contain any enzymes or regulatory proteins...
- Targeting epigenetic enzymes for drug discoveryRobert A Copeland
Epizyme Inc, 840 Memorial Drive, Cambridge, MA 02139, United States
Curr Opin Chem Biol 14:505-10. 2010..Many of the enzymes that mediate these epigenetic reactions are dysregulated in human diseases...
- Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymesLena Tasse
Universite de Toulouse, INSA, UPS, INP, LISBP, F 31077 Toulouse, France
Genome Res 20:1605-12. 2010..metabolized in the upper digestive tract, because the human genome does not encode adequate carbohydrate active enzymes (CAZymes)...
- Enzymes of the mevalonate pathway of isoprenoid biosynthesisHenry M Miziorko
University of Missouri Kansas City, 64110, USA
Arch Biochem Biophys 505:131-43. 2011..are different but are situated in active sites that are similar throughout the family of initial condensation enzymes. Both bacterial and animal HMG-CoA reductases have been extensively studied and the contrasts between these ..
- Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP familyIsabelle Callebaut
Systèmes moléculaires et Biologie structurale, LMCP, CNRS UMR 7590, Universités Paris 6 et Paris 7, case 115, 4 place Jussieu, F 75252 Paris Cedex 05, France
Nucleic Acids Res 30:3592-601. 2002A separate family of enzymes within the metallo-beta-lactamase fold comprises several important proteins acting on nucleic acid substrates, involved in DNA repair (Artemis, SNM1 and PSO2) and RNA processing [cleavage and polyadenylation ..
- Directed evolution of industrial enzymes: an updateJoel R Cherry
Novozymes Biotech, Inc, 1445 Drew Avenue, Davis, California, USA
Curr Opin Biotechnol 14:438-43. 2003The use of enzymes in industrial processes can often eliminate the use of high temperatures, organic solvents and extremes of pH, while at the same time offering increased reaction specificity, product purity and reduced environmental ..
- Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymesManfred T Reetz
Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, 45470 Mulheim Ruhr, Germany
Nat Protoc 2:891-903. 2007Iterative saturation mutagenesis (ISM) is a new and efficient method for the directed evolution of functional enzymes. It reduces the necessary molecular biological work and the screening effort drastically...
- Structure and function of enzymes involved in the biosynthesis of phenylpropanoidsJ L Ferrer
Institut de Biologie Structurale, Commissariat a l Energie Atomique, Centre National de la Recherche Scientifique, Universite Joseph Fourier, Groupe Synchrotron, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
Plant Physiol Biochem 46:356-70. 2008..As recently as a decade ago, little was known about the three-dimensional structure of the enzymes involved in these highly branched biosynthetic pathways...
- Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamiliesJ A Gerlt
Departments of Biochemistry and Chemistry, University of Illinois, Urbana, Illinois 61801, USA
Annu Rev Biochem 70:209-46. 2001..Groups of divergently related enzymes whose members catalyze different reactions but share a common partial reaction, intermediate, or transition state ..
- Structure, function, and engineering of enzymes in isoflavonoid biosynthesisXiaoqiang Wang
Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
Funct Integr Genomics 11:13-22. 2011..Structural studies of some key enzymes in the central phenylpropanoid pathway shed light on the early stages of the (iso)flavonoid biosynthetic process...
- HIstome--a relational knowledgebase of human histone proteins and histone modifying enzymesSatyajeet P Khare
Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410210, India
Nucleic Acids Res 40:D337-42. 2012..Several enzymes that catalyze the addition and removal of multiple histone modifications have been discovered in the past decade, ..
- Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighboursTakuji Yamada
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Mol Syst Biol 8:581. 2012Despite the current wealth of sequencing data, one-third of all biochemically characterized metabolic enzymes lack a corresponding gene or protein sequence, and as such can be considered orphan enzymes...
- De novo enzymes by computational designHajo Kries
Laboratory of Organic Chemistry, ETH Zurich, Zurich CH 8093, Switzerland
Curr Opin Chem Biol 17:221-8. 2013..Although the activities of de novo enzymes are typically low, they can be significantly increased by directed evolution...
- Discovery of new enzymes and metabolic pathways by using structure and genome contextSuwen Zhao
1 Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA 2
Nature 502:698-702. 2013..Metabolite docking to multiple binding proteins and enzymes in the same pathway increases the reliability of in silico predictions of substrate specificities because the ..
- Molecular adaptations to cold in psychrophilic enzymesG Feller
Laboratory of Biochemistry, Institute of Chemistry B6, University of Liege, 4000 Liege, Belgium
Cell Mol Life Sci 60:648-62. 2003..To cope with the reduction of chemical reaction rates induced by low temperatures, these organisms synthesize enzymes characterized by a high catalytic activity at low temperatures associated, however, with low thermal stability...
- Aorta of ApoE-deficient mice responds to atherogenic stimuli by a prelesional increase and subsequent decrease in the expression of antioxidant enzymesPeter A C 't Hoen
Division of Biopharmaceutics of the Leiden Amsterdam Center for Drug Research, Leiden, The Netherlands
Circ Res 93:262-9. 2003..relationship between extent of atherosclerotic lesion formation and vascular expression of pro- and antioxidant enzymes in apoE-deficient mice. On normal chow, these mice showed elevated serum cholesterol levels (7.5- to 9...
- An evolutionarily structured universe of protein architectureGustavo Caetano-Anolles
Vital NRG, Knoxville, Tennessee 37919, USA
Genome Res 13:1563-71. 2003..Lastly, we traced the total number of enzymatic functions associated with folds in the trees and show that there is a general link between structure and enzymatic function...
- Novel methods for directed evolution of enzymes: quality, not quantityStefan Lutz
Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
Curr Opin Biotechnol 15:291-7. 2004..Together, these investigations are creating a framework for future engineering projects...
- Enhanced tolerance to oxidative stress in transgenic tobacco plants expressing three antioxidant enzymes in chloroplastsYoung Pyo Lee
Environmental Biotechnology Research Center, KRIBB, Eoeun dong 52, Yuseong Gu, Daejeon, 305 806 Korea
Plant Cell Rep 26:591-8. 2007The effect of simultaneous expression of genes encoding three antioxidant enzymes, copper zinc superoxide dismutase (CuZnSOD, EC 188.8.131.52), ascorbate peroxidase (APX, EC 184.108.40.206), and dehydroascorbate (DHA) reductase (DHAR, EC 1.8.5...
- Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrificationChristopher M Jones
Department of Microbiology, Swedish Agricultural University, Uppsala, Sweden
Mol Biol Evol 25:1955-66. 2008....
- EFICAz2: enzyme function inference by a combined approach enhanced by machine learningAdrian K Arakaki
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
BMC Bioinformatics 10:107. 2009..To improve EFICAz's performance in this regime, we: i) increased the number of predictive components and ii) took advantage of consensual information from the different components to make the final EC number assignment...
- Lipid cubic phase as a membrane mimetic for integral membrane protein enzymesDianfan Li
Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
Proc Natl Acad Sci U S A 108:8639-44. 2011..To date, however, no integral membrane enzymes have yielded to this method, the in meso...
- Interleukin-22 downregulates filaggrin expression and affects expression of profilaggrin processing enzymesD Gutowska-Owsiak
MRC Human Immunology Unit, University of Oxford, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK
Br J Dermatol 165:492-8. 2011..Interleukin (IL)-22 is upregulated in lesional AE tissue, but its effects on filaggrin expression and genes associated with epidermal function have not yet been comprehensively addressed...
- Inhibitors of testosterone biosynthetic and metabolic activation enzymesLeping Ye
The 2nd Affiliated Hospital, Wenzhou Medical College, Wenzhou, Zhejiang 325000, China
Molecules 16:9983-10001. 2011..At least four steroidogenic enzymes are involved in testosterone biosynthesis: Cholesterol side chain cleavage enzyme (CYP11A1) for the conversion of ..
- Chemogenomics of pyridoxal 5'-phosphate dependent enzymesRatna Singh
Department of Biochemistry and Molecular Biology and Laboratory of Molecular Modelling, University of Parma, Parma, Italy
J Enzyme Inhib Med Chem 28:183-94. 2013Pyridoxal 5'-phosphate (PLP) dependent enzymes comprise a large family that plays key roles in amino acid metabolism and are acquiring an increasing interest as drug targets...
- Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystemsJ Kennedy
Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
J Appl Microbiol 111:787-99. 2011..Thus, enzymes isolated from these microbes have the potential to possess quite unique physiological and biochemical properties...
- Nuclear receptors in the multidrug resistance through the regulation of drug-metabolizing enzymes and drug transportersYakun Chen
Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL 62794, United States
Biochem Pharmacol 83:1112-26. 2012..However, its efficacy is limited by multidrug resistant cancer cells. Drug metabolizing enzymes (DMEs) and efflux transporters promote the metabolism, elimination, and detoxification of chemotherapeutic agents...
- Enzymes of glycolysis are functionally associated with the mitochondrion in Arabidopsis cellsPhilippe Giegé
Institut de Biologie Moleculaire des Plantes, Strasbourg 67084, France
Plant Cell 15:2140-51. 2003..Here, we present the unexpected discovery of the presence of the enzymes of glycolysis in a mitochondrial fraction of Arabidopsis cells...
- Cysteine-based redox switches in enzymesChananat Klomsiri
Department of Biochemistry, Wake Forest University School of Medicine, Winston Salem, North Carolina 27157, USA
Antioxid Redox Signal 14:1065-77. 2011The enzymes involved in metabolism and signaling are regulated by posttranslational modifications that influence their catalytic activity, rates of turnover, and targeting to subcellular locations...
- A survey of metabolic databases emphasizing the MetaCyc familyPeter D Karp
Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA
Arch Toxicol 85:1015-33. 2011..These web sites also provide multiple tools for analysis of gene expression and metabolomics data, including visualization of those datasets on metabolic network diagrams and over-representation analysis of gene sets and metabolite sets...
- Nrf2-regulated phase II enzymes are induced by chronic ambient nanoparticle exposure in young mice with age-related impairmentsHongqiao Zhang
Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
Free Radic Biol Med 52:2038-46. 2012Many xenobiotic detoxifying (phase II) enzymes are induced by sublethal doses of environmental toxicants...
- Microbial cellulose utilization: fundamentals and biotechnologyLee R Lynd
Chemical and Biochemical Engineering, Thayer School of Engineering and Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
Microbiol Mol Biol Rev 66:506-77, table of contents. 2002..composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-..
- Electrostatic basis for enzyme catalysisArieh Warshel
Department of Chemistry, University of Southern California, SGM Building 418, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
Chem Rev 106:3210-35. 2006
- Understanding the functional roles of amino acid residues in enzyme catalysisGemma L Holliday
EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
J Mol Biol 390:560-77. 2009..a valuable insight into the functional roles of catalytic amino acid residues, which may have applications in many aspects of enzymology, from the design of novel enzymes to the prediction and validation of enzyme reaction mechanisms.
- Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studiesPieter C A Bruijnincx
Chemical Biology and Organic Chemistry, Department of Chemistry, Debye Institute for NanoMaterials Science, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH Utrecht, The Netherlands
Chem Soc Rev 37:2716-44. 2008Iron-containing enzymes are one of Nature's main means of effecting key biological transformations...
- The enigma of the CLIC proteins: Ion channels, redox proteins, enzymes, scaffolding proteins?Dene R Littler
School of Physics, University of New South Wales, Sydney, NSW 2052, Australia
FEBS Lett 584:2093-101. 2010..The physiological role of CLICs appears to be maintenance of intracellular membranes, which is associated with tubulogenesis but may involve other substructures...
- Structure and function of enzymes in heme biosynthesisGunhild Layer
Institute of Microbiology, Technische Universitat Braunschweig, Braunschweig D 38106, Germany
Protein Sci 19:1137-61. 2010..Further, enzymes such as catalases, peroxidases, or cytochromes P450 rely on heme as essential cofactors...
- Toward mechanistic classification of enzyme functionsDaniel E Almonacid
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, MC 2550, San Francisco, CA 94158, USA
Curr Opin Chem Biol 15:435-42. 2011..Large-scale studies have established that divergently evolved enzymes share conserved elements of structure and common mechanistic steps and that convergently evolved enzymes often ..
- The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parametersArren Bar-Even
Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
Biochemistry 50:4402-10. 2011The kinetic parameters of enzymes are key to understanding the rate and specificity of most biological processes. Although specific trends are frequently studied for individual enzymes, global trends are rarely addressed...
- Cold-adapted enzymesKhawar Sohail Siddiqui
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
Annu Rev Biochem 75:403-33. 2006..Their ability to proliferate in the cold is predicated on a capacity to synthesize cold-adapted enzymes. These enzymes have evolved a range of structural features that confer a high level of flexibility compared to ..
- Constructing the wonders of the bacterial world: biosynthesis of complex enzymesFrank Sargent
Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
Microbiology 153:633-51. 2007..Bacterial respiration requires a diverse array of complex, multi-subunit, cofactor-containing redox enzymes, many of which are embedded within, or located on the extracellular side of, the membrane...
- The role of antioxidants and antioxidant-related enzymes in protective responses to environmentally induced oxidative stressJorge Limón-Pacheco
Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Apartado Postal 70 228, 04510, Ciudad Universitaria, Mexico, D F, Mexico
Mutat Res 674:137-47. 2009..We shall review evidence of organ-specific antioxidant responses elicited by environmental pollutants in humans and animal models...
- The conservation and evolutionary modularity of metabolismJose M Peregrin-Alvarez
Program in Molecular Structure and Function, Hospital for Sick Children, College Street, Toronto, ON M5G1L7, Canada
Genome Biol 10:R63. 2009..Here we supplement existing genome and protein resources with partial genome datasets derived from 193 eukaryotes to present a comprehensive survey of the conservation of metabolism across 26 taxa representing the three domains of life...
- Multiple glycolytic enzymes are tightly bound to the fibrous sheath of mouse spermatozoaMichelle Krisfalusi
Laboratory for Reproductive Biology, University of North Carolina School of Medicine, NC 27599, USA
Biol Reprod 75:270-8. 2006..To determine if other glycolytic enzymes are also bound to this cytoskeletal structure, we isolated highly purified fibrous sheath preparations from mouse ..
- Beyond transcription factors: the role of chromatin modifying enzymes in regulating transcription required for memoryRuth M Barrett
Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, California 92697, USA
Learn Mem 15:460-7. 2008..In this review, we will discuss the role of chromatin modifying enzymes in memory processes, as well as how recent studies in yeast genetics and cancer biology may impact the way we ..
- Oral sulforaphane increases Phase II antioxidant enzymes in the human upper airwayMarc A Riedl
The Hart and Louis Laboratory, Clinical Immunology and Allergy, Department of Medicine, UCLA David Geffen School of Medicine, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
Clin Immunol 130:244-51. 2009..Endogenous Phase II enzymes abrogate oxidative stress through the scavenging of reactive oxygen species and metabolism of reactive chemicals.
- Novel mechanisms of natural antioxidant compounds in biological systems: involvement of glutathione and glutathione-related enzymesRoberta Masella
National Centre for Food Quality and Risk Assessment, Istituto Superiore di Sanita, 00161 Rome, Italy
J Nutr Biochem 16:577-86. 2005..that polyphenols can have in biological systems, focusing on their effects on glutathione and its related enzymes. Experimental data indicate that polyhenols may offer an indirect protection by activating endogenous defense ..
- Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage databaseScott C H Pegg
Department of Biopharmaceutical Sciences, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143 2250, USA
Biochemistry 45:2545-55. 2006The study of mechanistically diverse enzyme superfamilies-collections of enzymes that perform different overall reactions but share both a common fold and a distinct mechanistic step performed by key conserved residues-helps elucidate ..
- Identification of novel enzymes with different hydrolytic activities by metagenome expression cloningKatrin Lämmle
Fraunhofer Institute for Interfacial Engineering and Biotechnology, Institute for Interfacial Engineering, University of Stuttgart, Nobelstrasse 12, D 70569 Stuttgart, Germany
J Biotechnol 127:575-92. 2007..A large number of active clones were identified, including lipolytic enzymes, amylases, phosphatases and dioxygenases...
- Enzyme promiscuity: mechanism and applicationsKarl Hult
School of Biotechnology, Department of Biochemistry, Royal Institute of Technology KTH, AlbaNova University Center, SE 106 91 Stockholm, Sweden
Trends Biotechnol 25:231-8. 2007Introductory courses in biochemistry teach that enzymes are specific for their substrates and the reactions they catalyze. Enzymes diverging from this statement are sometimes called promiscuous...
- Structures of ribonucleoprotein particle modification enzymesBo Liang
Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32312, USA
Q Rev Biophys 44:95-122. 2011..nucleolar RNA or Cajal body RNA combined with partner proteins and represent the most complex RNA modification enzymes. Recent advances in structure and function studies have revealed detailed information regarding ribonucleoprotein ..
- Tirandamycin biosynthesis is mediated by co-dependent oxidative enzymesJacob C Carlson
Life Sciences Institute and Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
Nat Chem 3:628-33. 2011..provides important insights into the assembly of potent bioactive molecules, and expands access to unique enzymes able to selectively modify complex substrates...
- FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamiliesNicholas Furnham
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 40:D776-82. 2012..The resource is freely available through a web interface: www.ebi.ac.uk/thorton-srv/databases/FunTree...
- A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes--factors affecting enzymes, conversion and synergyJ S Van Dyk
Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, PO Box 94, Grahamstown, 6140, South Africa
Biotechnol Adv 30:1458-80. 2012Lignocellulose is a complex substrate which requires a variety of enzymes, acting in synergy, for its complete hydrolysis...
- Unusual roles of host metabolic enzymes and housekeeping proteins in plant virus replicationYing Wen Huang
Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
Curr Opin Virol 2:676-82. 2012..Recent studies have revealed that positive-sense RNA [(+)RNA] viruses may adapt regular metabolic enzymes and housekeeping proteins of host plants by exploiting unusual functions to accommodate their need for ..
- Biotinylated Rh(III) complexes in engineered streptavidin for accelerated asymmetric C-H activationTodd K Hyster
Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
Science 338:500-3. 2012b>Enzymes provide an exquisitely tailored chiral environment to foster high catalytic activities and selectivities, but their native structures are optimized for very specific biochemical transformations...
- Discovery metabolite profiling of the prolyl peptidasesAlan Saghatelian; Fiscal Year: 2009..metabolite profiling (DMP), for the assignment of endogenous substrates to the prolyl peptidase family of enzymes. DMP integrates an array of biological and chemical methods, including genetics, pharmacology, and analytical ..
- Variation in M. tuberculosis in response to host selectionSarah Fortune; Fiscal Year: 2009..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
- Serpin Modulation of Inflammatory Vasculitis; Potential for Immunomodulatory TherALEXANDRA ROSE LUCAS; Fiscal Year: 2010..The thrombolytic serine protease enzymes in the clot lysis pathway initiate collagen breakdown and aneurysm formation and serine proteinase inhibitors (..
- CFI Pathogen Inactivation TechnologyTrevor P Castor; Fiscal Year: 2010..CFI pathogen inactivation technology gives pathogens the "bends," inactivating them without damaging proteins and enzymes in medically important transfusion fluids such as human plasma...
- Paolo Fanti; Fiscal Year: 2014..NAC is substrate for the intracellular generation of GSH and the MTh flavonolignans are inducers of many cellular enzymes participating in GSH metabolism, including GSH-reductase (GSH-R), GSH-peroxidase (GSH-Px), GSH-S-transferases (..
- Carole R Mendelson; Fiscal Year: 2016..The histone- and DNA-modifying enzymes that bind to the SP-A promoter in type II cells and mediate developmental-, hormonal- and O2-regulated changes in ..
- Pharmacogenetics of obesity and endocannabinergic modulation (POEM)Russell A Wilke; Fiscal Year: 2012..While 2-AG is degraded by multiple enzymes, recent evidence suggests a primary role for monoacylglycerol lipase (gene name MGLL)...
- VINCENT SCOTT TAGLIABRACCI; Fiscal Year: 2014..However, these enzymes are poorly characterized and their activities have been ascribed to the category of orphan enzymes (enzymes that ..
- Comprehensive biomarker study to capitalize on existing GWAS in 10K South AsiansDanish Saleheen; Fiscal Year: 2010..insulin resistance and adiposity (insulin, C-peptide, adiponectin, leptin, resistin, liver function enzymes);(3) renal function (creatinine, cystatin C, ADMA, uric acid, 25(OH)vitamin D, parathyroid hormone);and (4) ..
- Angiotensin Adrenergic Interactions in the KidneyRoland C Blantz; Fiscal Year: 2013..the increase in GFR that accompanies AII blockade by administration of lysine (A/I + T3) Several molecules and enzymes were overexpressed in the untreated A/I kidney including NADPH oxidase, heme-oxygenase-1 (HO-1),, and ERK 1/2 ..
- FASEB SRC on Lysophospholipd Mediators in Health and DiseaseJulie D Saba; Fiscal Year: 2011..Importantly, lysophospholipids play critical roles in carcinogenesis and cancer progression. Enzymes responsible for catalyzing S1P and LPA formation including autotaxin (the principal enzyme responsible for ..
- Role of SAMe on UBC9 and sumolyation in liver cancer and alcoholic liver injuryMaria Lauda Tomasi; Fiscal Year: 2012..is a multistep process, involving maturation, activation, conjugation and ligation;it is catalyzed by multiple enzymes, including E1, E2 and E3 enzymes...
- Discovery of Small Molecule MBT Domain AntagonistsSTEPHEN VERNON FRYE; Fiscal Year: 2010..Given the wide-spread importance of chromatin regulation to cell biology, the enzymes which produce these modifications (the 'writers'), the proteins that recognize them (the 'readers&..
- Priyabrata Mukherjee; Fiscal Year: 2016..Several factors that cause elevation of plasma Hcy level are;(i) genetic deficiencies/mutations in the enzymes responsible for remethylation/transsulfuration pathway of Hcy;(ii) nutritional deficiencies of the vitamin co-..
- VINCENT COLLINS OFUKA NJAR; Fiscal Year: 2014..Work by our group has identified novel and potent inhibitors of CYP26 enzymes responsible for intracellular catabolism of ATRA into inactive metabolites...
- REGULATION AND FUNCTION OF STE20-RELATED PROTEIN KINASESMelanie H Cobb; Fiscal Year: 2012..WNKs are ubiquitous multipurpose, multifunctional enzymes that have been found in screens to identify proteins required for development and survival, and that affect ..
- Michael Demetriou; Fiscal Year: 2014..In EAE-susceptible PL/J mice, reduced GlcNAc branching is distributed across deficiencies in at least three Golgi enzymes (Mgat1, 2 and 5). Supplementing T cells with hexosamine pathway metabolites (i.e...
- Role of Polyamines in MYCN-Amplified NeuroblastomaANDRE BACHMANN; Fiscal Year: 2009..clinically tested polyamine inhibitors, DFMO and SAM486A, which specifically inhibit the polyamine biosynthetic enzymes ornithine decarboxylase (ODC) and S-adenosylmethionine decarboxylase (AdoMetDC), respectively...
- A Soft Topical Antiandrogenic DrugWei Chu Xu; Fiscal Year: 2013..active topically in androgen-dependent maladies of the skin and scalp, but to be hydrolyzed by plasma or tissue enzymes, thus terminating its systemic action...
- Targeting Inflammation for the Amelioration of Cisplatin-Hearing LossVickram Ramkumar; Fiscal Year: 2011..However, inhibition of caspases, p53, or activation of DNA repair enzymes may promote the development of tumors or promote tumor chemoresistance...
- Retinoid Metabolism and Alcohol Induced DiseaseWilliam S Blaner; Fiscal Year: 2010..involving lecithin:retinol acyltransferase or LRAT) and retinoic acid oxidation (catalyzed by cytochrome enzymes)...
- RODNEY JON SCHLOSSER; Fiscal Year: 2014..Quick degradation of free radicals results in reactive oxygen species (ROS)4-6. Antioxidant enzymes that metabolize ROS, thus serve as potential therapeutic agents...
- Schahram Akbarian; Fiscal Year: 2014..phenotypes resulting from experimental manipulation of other histone modifications and histone modifying enzymes, particularly those defined by a genome-wide enrichment pattern that is highly divergent as compared to ..
- Samuel D Crish; Fiscal Year: 2016..will seek to determine the nature and time course of changes in cytoskeletal proteins within the axon, the enzymes responsible for these changes, and will examine different aspects of axonal transport in two rodent models of ..
- Transgenesis and XenotransplantationJorge A Piedrahita; Fiscal Year: 2013..hepatocytes at multiple levels including expression of mature hepatocyte markers, induction of drug metabolizing enzymes, liver cytoarchitecture and presence/absence of cell fusions...
- Role of the Mammalian Siderophore in Cellular Iron Metabolism and ErythropoiesisLaxminarayana R Devireddy; Fiscal Year: 2012DESCRIPTION (provided by applicant): Iron is an essential co-factor for many enzymes that play a vital role in cellular processes...
- Pathobiology of Cystic Fibrosis-Related Diabetes in a Ferret ModelZoe Stewart; Fiscal Year: 2013..therapy by evaluating ferret growth and nutritional parameters in the presence and absence of PPIs and pancreatic enzymes. Finally, we will evaluate the impact of pancreatic CFTR gene therapy on the progression of early pulmonary ..
- Enzymatic Regulation of S-Glutathionylation : Role in Apoptosis and DiseaseJohn J Mieyal; Fiscal Year: 2012..These enzymes maintain the thiol status of cysteine residues and the corresponding functions of protein intermediates in ..
- JAMES FRANCIS MCGINNIS; Fiscal Year: 2015..which can be targeted by antioxidants and other molecules which increase the expression of "Phase II" antioxidant enzymes. Our published and preliminary data show that cerium oxide nanoparticles, which catalytically destroy ROS, can ..
- Ethanol Regulation of Serum Glucocorticoid Kinase IBLAIR N COSTIN; Fiscal Year: 2012..determined pharmacologically through the use of drugs, aminoglutethimide, metyrapone, and RU-486, which inhibit enzymes involved in glucocorticoid synthesis or block the glucocorticoid receptor...
- Protein Nitration in the PlacentaLeslie Myatt; Fiscal Year: 2012..The involvement of the mtNOS, eNOS and iNOS isoforms, NOX enzymes and manganese superoxide dismutase in nitration and the role of hypoxia and hypoxia/reoxygenation on protein ..
- A novel peroxidase in vascular endothelium and the development of atherosclerosisGuangjie Cheng; Fiscal Year: 2012..Peroxidases are enzymes that catalyze hydrogen peroxide reduction and play important roles in physiology, immunology and pathology such ..
- Lai Hua Xie; Fiscal Year: 2015..Our preliminary studies also showed up-regulation of antioxidant enzymes, e.g., MnSOD and lower levels of CaMKII activity (oxidized form) in woodchuck hearts in winter than in summer...
- Sirtuin/FOXO Signaling in the Regulation of Bone MassStavroula Kousteni; Fiscal Year: 2012..Oxidative stress increases FOXO1-mediated transcription of anti-oxidant enzymes;and attenuates both the anti-osteoclastogenic and the osteoblastogenic effects of [unreadable]-catenin-mediated ..
- ALTERED CARDIAC MYOCYTE SIGNALING IN DIABETIC MYOCARDIUM AND FUNCTIONAL SEQUELAEANTHONY JUSTIN MUSLIN; Fiscal Year: 2010..When insulin travels to different tissues and binds to cells, it activates a cascade of enzymes inside of cells, called signaling proteins, leading to the increased ability of cells to take up glucose from the ..
- Novel diagnostic and safety biomarkers of liver injury and hepatotoxicityStanislav I Svetlov; Fiscal Year: 2010..For the last 30 years, two enzymes, serum ALT and AST have been used in hepatic function panels to assess liver health...
- Gonadal Steroid Receptors and the Hypothalamo-Pituitary-Adrenal AxisRobert J Handa; Fiscal Year: 2013..Five specific aims are proposed. Aim 1 will identify the location and regulation of steroid metabolizing enzymes in neurons of the PVN that allow synthesis of 32-Diol...
- Donald B Jump; Fiscal Year: 2015..Aim 3 will establish the requirement for HMOX1 and other anti-oxidant enzymes in the Elovl5 control of FoxO1, GNG, ATGL, CGI58 and TAG...
- Chemical modulators of Tet-family proteinsAnjana Rao; Fiscal Year: 2010..these studies should identify small molecules that modulate the functions of this new and interesting class of enzymes, and may be used as reagents to investigate their biological functions in cells and in organisms...
- Therapeutic Effect of a Novel Antioxidant on Degenerative Eye DisordersNuran Ercal; Fiscal Year: 2012..Lens and retinal cells combat oxidative stress by generating sufficient antioxidant enzymes or small molecular weight antioxidants like glutathione (GSH)...
- Role of Mitochondria in the Regulation of Iron metabolism by AlcoholDUYGU DEE DEE HARRISON-FINDIK; Fiscal Year: 2012..We will employ transgenic mouse models deficient in mitochondrial antioxidant enzymes, adenine nucleotide transport, cytochrome c oxidase activity or the dimerization of hypoxia-inducible ..
- Ceramide Metabolism and Photoreceptor HomeostasisUsha R Acharya; Fiscal Year: 2013..They are a large group of inherited diseases caused by defects in enzymes of sphingolipid metabolism and are associated with retinal impairment...
- Arsenic Trioxide and Acute Myeloid LeukemiaYongkui Jing; Fiscal Year: 2012..physiological conditions ROS generated as a byproduct of mitochondrial respiration are detoxified by glutathione-enzymes, glutathione peroxidase (GPx), glutathione-s-transferase ? (GST?) and glutathione reductase (GR)...
- HUIPING ROSE ZHOU; Fiscal Year: 2015..They have been shown to regulate the expression of numerous genes encoding enzymes/proteins involved in the metabolism/synthesis of bile acids, glucose, fatty acids, and lipoproteins as well as ..
- Cell signaling as a leukemia biomarkerJAMES WILLIAM JACOBBERGER; Fiscal Year: 2013..Additionally, since the enzymes of these pathways are focus of targeted therapy, this approach provides information with therapeutic implications...
- Nitric Oxide in Hemodialysis AV Fistula MaturationRichard A Cohen; Fiscal Year: 2010..3) To determine whether impaired NO responsiveness can be restored by over- expression of antioxidant enzymes, down-regulation of oxidant producing enzymes, or over- expression of SERCA...
- Peter Sarnow; Fiscal Year: 2015..miR-122 protects the 5'end sequences of the HCV RNA from degradation by ribonucleases or RNA modification enzymes, or aids in the avoidance of activation of double-stranded RNA sensors such as the retinoic acid inducible gene I...
- MECHANISM-BASED DRUG SELECTION AND DESIGN: NUCLEOTIDE SABuddy Ullman; Fiscal Year: 2003..of the proposed studies is to integrate genetic, biochemical, and structural studies on key transporters and enzymes of the pyrimidine and purine salvage pathways in Toxoplasma gondii and related apicomplexan parasites, including ..
- Aldosterone Action In The Brain, Hypertension and InflammationELISE PEERY GOMEZ-SANCHEZ; Fiscal Year: 2012..MR are abundantly expressed in neurons in specific brain areas and in the heart, however the enzymes that confer MR selectivity for aldo over the more abundant glucocorticoids with similar MR affinity, are limited ..
- Prevention of Inherited Retinal Diseases by Therapeutic Rare Earth NanoparticlesJAMES FRANCIS MCGINNIS; Fiscal Year: 2010..Antioxidants and over-expression of antioxidant enzymes have been shown to inhibit the progression of many retinal diseases...
- Robert W Burgess; Fiscal Year: 2016..These enzymes are well characterized for their function in charging amino acids onto their cognate tRNAs for translation...
- Tumor Microenvironment Interactions in Brain TumorsEric C Holland; Fiscal Year: 2010..that stromal cells, particularly macrophages and endothelial cells, provide key factors, such as matrix-degrading enzymes, which are co-opted by the tumor to promote its own growth and invasion...
- Mechanisms of Heme Transport in MacrophagesCARINE CARINE WHITE; Fiscal Year: 2012..Once transported out of the phagolysosome, heme is either degraded by the heme oxygenase family of enzymes for the recycling of iron or incorporated in toto into cellular hemoproteins...
- Complex I: Role of L Subunit in Proton TranslocationSteven B Vik; Fiscal Year: 2011..from NADH is used to reduce ubiquinone to ubiquinol, which then functions as an electron carrier to downstream enzymes. This reduction is coupled to the translocation of protons across the membrane, by an unknown mechanism...
- FASEB SUMMER CONFERENCE ON PHOSPHOLIPASESAlex Brown; Fiscal Year: 2010..These widely expressed enzymes hydrolyze ester and phosphodiester bonds in membrane phospholipids to generate bioactive lipids and lipid-derived ..
- Clifford A Lowell; Fiscal Year: 2016..Binding of the pathogen molecules to these receptors activates intracellular enzymes that initiate intracellular signaling pathways that lead to immune cell activation to eliminate the pathogen...
- Md Mizanur Rahman; Fiscal Year: 2014..energy absorptiometry (DXA) to determine muscle mass;analyze fiber types, fat content, iron content, antioxidant enzymes and oxidative damage levels of muscle to determine muscle quality;analyze mitochondrial functions by measuring ..
- Lucy A Waskell; Fiscal Year: 2014..PUBLIC HEALTH RELEVANCE: The proposed investigation of how the human enzymes responsible for drug metabolism, drug-drug interactions, blood clotting, and cholesterol levels function at a ..
- Protection of Brain Injury from Cyanide Poisoning by Carnosic AcidStuart A Lipton; Fiscal Year: 2013..rosemary extract, which crosses the blood-brain-barrier to exert effects by up-regulating endogenous anti-oxidant enzymes via the Nrf2 transcriptional pathway...
- Metabolic Adapation and Control of Lactation in HumansMorey W Haymond; Fiscal Year: 2010..of alpha-Iactalbumin mRNA and GLUT 1 and GLUT-3 transporters mRNAs but not those of PEPCK, key gluconeogenic enzymes. 5...
- Fanyin Meng; Fiscal Year: 2016..Instead, these ncRNAs can act as enzymes, signaling molecules and transcriptional factors...
- Disease chronicity in juvenile dermatomyositis (JDM): Epigenetic cluesLauren M Pachman; Fiscal Year: 2013..In treating JDM, the accepted guide to therapy is serum levels of muscle enzymes, which normalize rapidly, leaving a void...
- N-Acetylcysteine and Milk Thistle for Treatment of Diabetic NephropathyPaolo Fanti; Fiscal Year: 2011..NAC is substrate for the intracellular generation of GSH and the MTh flavonolignans are inducers of many cellular enzymes participating in GSH metabolism, including GSH-reductase (GSH-R), GSH-peroxidase (GSH-Px), GSH-S-transferases (..
- Genistein and Prostate CancerRajvir Dahiya; Fiscal Year: 2010..5). Alterations in mRNA expression of genes that encode enzymes participating in DNA methylation and histone acetylation including DNMTs, demethylases, HATs, HDACs using RT-PCR ..
- Biochemical Characterization of Cytochrome b5 Reductase in Candida albicansMARY JOLENE PATRICIA HOLLOWAY; Fiscal Year: 2010..Emerging drug resistance is a major problem in Candida, contributed by enzymes involved in the detoxification of xenobiotics and pharmacological agents...
- Potential Mechanisms of Glucagon-like peptide-1 in Fatty Liver DiseaseFrank A Anania; Fiscal Year: 2010..with GLP-1, which favors hepatocyte fatty acid depletion, is reversed;and, to measure the effect of GLP-1 on key enzymes involved with hepatic fatty acid metabolism...
- ADENOSINE AND ANTIOXIDANT ENZYMESVickram Ramkumar; Fiscal Year: 1999..An antioxidant defense system provides protection of the cell from free radicals and comprises enzymes such as superoxide dismutase (SOD), catalase CAT), glutathione peroxidase (GSH...
- Analogs of GTP as novel inhibitors of bacterial c-di-GMP-synthesizing enzymesGeorge E Wright; Fiscal Year: 2010..enteric and S. aureus. The biosynthesis of c-di-GMP from two molecules of GTP is catalyzed by highly conserved enzymes known as diguanylate cyclases (DGCs)...
- Bacteriolytic phage enzymes as novel antibacterials against Yersinia pestisIan Molineux; Fiscal Year: 2009..Phage-encoded bacteriolytic enzymes are promising reagents to treat a wide range of bacterial infections because their mechanisms of action are ..
- A novel transgenic silkworm system for recombinant glycoprotein productionDonald L Jarvis; Fiscal Year: 2010..approach will be to use the piggyBac vector system to isolate transgenic silkworms encoding (1) higher eukaryotic enzymes needed to humanize the native silk gland protein N-glycosylation pathway and (2) a recombinant human N-..
- Histone Deacetylases and reversible acetylation in signaling and diseaseJOHN DENU; Fiscal Year: 2009..With the first cloning (~10 years ago) of histone acetyltransferase (HATs) and deacetylase (HDACs) enzymes, there has been an explosion of research in the field...
- ACROSOMAL ENZYMES AND THEIR ROLE IN FERTILIZATIONPRAKASH SRIVASTAVA; Fiscal Year: 1993..Capacitated rabbit sperm undergo the acrosome reaction during the passage through the cumulus. Enzymes released following the acrosome reaction or enzymes still bound to the vesicles composed of the plasma (PM) and ..
- High throughput screening assays to identify small molecules that target the ClpXCarolyn K Suzuki; Fiscal Year: 2010DESCRIPTION (provided by applicant): ATP-dependent roteases are a unique family of proteolytic enzymes that require energy to unfold protein substrates prior to peptide bond hydrolysis...
- Cloning and Engineering of Nicking enzymesShuang yong Xu; Fiscal Year: 2004This proposal is aimed towards cloning, expression and engineering of DNA nicking enzymes. Two nicking enzymes CviNY2A and CviNYSI have been found in Chlorella-like algae virus strains NY2A and NYSI with three-nucleotide recognition ..
- Human Cathepsin G: Expression, C-Terminal Processing and Dual SpecificityDavid Johnson; Fiscal Year: 2007..Both serine proteases are stored as active enzymes in cytoplasmic granules...
- EICOSANOID OXIDATION BY LIVER AND KIDNEY P450 ENZYMESJerome Lasker; Fiscal Year: 2006DESCRIPTION (provided by applicant): It is now evident that P450 enzymes metabolize key cellular constituents, including long-chain fatty acid such as arachidonic acid (AA), leukotrienes (LT) such as LTB4, and other eicosanoids...