About: Evolution of substrate specificity in enzymes acting on xenobiotic compounds

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Attributes	Values
rdf:type	http://linked.opendata.cz/ontology/domain/vavai/Projekt
rdfs:seeAlso	http://www.isvav.cz/projectDetail.do?rowId=IAA401630901
Description	The main objective of this project is to study evolution of substrate specificity in microbial enzymes acting on xenobiotic compounds. Selected model system, haloalkane dehalogenases, is suitable for this purpose since these enzymes act on recalcitrant compounds which have not been available in the biosphere until industrial revolution. Evolution will be studied recursively by quantitative characterization of the substrate specificity of modern haloalkane dehalogenases and their comparison with ancestral enzymes designed by phylogenetic inference and constructed by gene synthesis. The ultimate goal will be estimation of the level of functional overlap of individual protein subfamilies and dissecting molecular events leading to specialization of enzymes for efficient catalysis of their xenobiotic substrates. Various theoretical and experimental approaches will be employed to obtain appropriate biological material and collect data for testing of alternative evolutionary hypotheses. (en) Hlavním cílem projektu je studium evoluce substrátové specifity mikrobiálních enzymů aktivních s xenobiotickými sloučeninami. Zvolený modelovým systém, halogenalkandehalogenasy, je vhodný k tomuto účelu vzhledem k aktivitě dehalogenas enzymů s biologicky špatně rozložitelnými sloučeninami, které se v biosféře nevyskytovaly před průmyslovou revolucí. Evoluce bude studována rekurzivně kvantitativním popisem substrátové specifity moderních halogenalkandehalogenas a srovnáním se specifitou předků těchto enzymů navržených fylogenetickou dedukcí a konstruovaných genovou syntézou. Konečným výsledkem této analýzy bude ohodnocení funkčního přesahu jednotlivých podrodin a podrobný popis molekulárních událostí vedoucích ke specializaci těchto enzumů umožňující účinný rozklad xenobiotických substrátů. Různé teoretické a experimentální přístupy budou použity k přípravě biologického materiálu a ke sběru dat nezbytných k testování alternativních evolučních hypotéz.
Title	Evolution of substrate specificity in enzymes acting on xenobiotic compounds (en) Evoluce substrátové specifity u enzymů aktivních s xenobiotickými látkami
skos:notation	IAA401630901
http://linked.open...avai/cep/aktivita	Grants of distinctly investigative character focused on the sphere of research pursued at present particularly in the Academy of Sciences of the Czech Republic
http://linked.open...kovaStatniPodpora	http://linked.opendata.cz/resource/domain/vavai/projekt/IAA401630901/celkovaStatniPodpora
http://linked.open...ep/celkoveNaklady	http://linked.opendata.cz/resource/domain/vavai/projekt/IAA401630901/celkoveNaklady
http://linked.open...datumDodatniDoRIV	2014-04-14 (xsd:date)
http://linked.open...i/cep/druhSouteze	VS - Veřejná soutěž ve výzkumu a vývoji
http://linked.open...ep/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open.../cep/fazeProjektu	100738400
http://linked.open...ai/cep/hlavniObor	CE - Biochemie
http://linked.open...hodnoceniProjektu	V - Vynikající výsledky (s mezinárodním významem apod.). Zároveň byly splněny cíle a předpokládané výsledky uvedené ve smlouvě / rozhodnutí o poskytnutí podpory.
http://linked.open...vai/cep/kategorie	ZV - Základní výzkum
http://linked.open.../cep/klicovaSlova	evolution; enzymes; dehalogenation; multivariate statistics; substrate specificity; molecular modelling; virtual screening; QSAR and 3D QSAR (en)
http://linked.open...ep/partnetrHlavni	Přírodovědecká fakulta
http://linked.open...inujicichPrijemcu	0 (xsd:int)
http://linked.open...cep/pocetPrijemcu	1 (xsd:int)
http://linked.open...ocetSpoluPrijemcu	0 (xsd:int)
http://linked.open.../pocetVysledkuRIV	66 (xsd:int)
http://linked.open...enychVysledkuVRIV	66 (xsd:int)
http://linked.open...lneniVMinulemRoce	2013-02-27 (xsd:date)
http://linked.open.../prideleniPodpory	http://linked.opendata.cz/resource/domain/vavai/cep/prideleniPodpory/IAA401630901
http://linked.open...iciPoslednihoRoku	2013
http://linked.open...atUdajeProjZameru	2014
http://linked.open.../vavai/cep/soutez	SAV02009-A
http://linked.open...usZobrazovaneFaze	DUU
http://linked.open...ai/cep/typPojektu	P - Projekt výzkumu a vývoje financovaný ze státního rozpočtu
http://linked.open...ep/ukonceniReseni	2013-12-31 (xsd:date)
http://linked.open.../cep/vedlejsiObor	EB - Genetika a molekulární biologie EE - Mikrobiologie, virologie
http://linked.open...ep/zahajeniReseni	2009-01-01 (xsd:date)
http://linked.open...jektu+dodavatelem	Six modern and five ancestral haloalkane dehalogenases were characterized. The ancestors showed highly improved thermostability and good activity. A novel system for quantitative classification of enzymes based on their specificity was established. (en) Bylo charakterizováno šest moderních a pět předků halogenalkandehalogenas. Předci vykazovali významně zvýšenou termální stabilitu a dobrou katalytickou aktivitu. Byl zaveden nový systém kvantitativní klasifikace enzymů podle jejich specifity. (cs)
http://linked.open...tniCyklusProjektu	ZBBBKU
http://linked.open.../cep/klicoveSlovo	evolution dehalogenation enzymes molecular modelling multivariate statistics substrate specificity virtual screening
is http://linked.open...vavai/riv/projekt of	.: Keyhole-Lock-Key Model: Engineering of Tunnels in Proteins with Buried Active Sites Are Time-Dependent Fluorescence Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore? The Effect of a Unique Halide-Stabilising Residue on the Catalytic Properties of Haloalkane Dehalogenase DatA from Agrobacterium tumefaciens C58 Interaction of Organic Solvents with Protein Structures at Protein-Solvent Interface Organic Co-solvents Affect Activity, Stability and Enantioselectivity of Haloalkane Dehalogenases Engineering Robust and Efficient Protein Catalysts In vitro protein and metabolic engineering of a biodegradation pathway Molecular mechanisms of the effects of organic solvents on activity of haloalkane dehalogenases Stereoselectivity and conformational stability of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110: the effect of pH and temperature Sphingobium czechense LL01 sp. nov Sphingobium baderi LL03 sp. nov A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures Biochemical Characterization of a Novel Haloalkane Dehalogenase from a Cold-Adapted Bacterium Effect of organic solvents on structure and function of haloalkane dehalogenases Construction of pollutant-degrading bacteria by protein and metabolic engineering Computer-Assisted Enzyme Engineering by Modification of Tunnels, Channels and Gates. Crystallization and structural analysis of DhaA31 from Rhodococcus rhodochrous Crystallization and Preliminary Crystallographic Analysis of Rhodococcus rhodochrous Wild-type DhAa Protein and its Variant DhaA13 Complexed with Different Ligands Crystallization and crystallographic analysis of the Rhodococcus rhodochrous NCIMB 13064 DhaA mutant DhaA31 and its complex with 1,2,3-trichloropropane Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands Development of a Crystallization Protocol for the DbeA1 Variant of Novel Haloalkane Dehalogenase from Bradyrhizobium elkani USDA94 DspA from Strongylocentrotus purpuratus: the First Biochemically Characterized Haloalkane Dehalogenase of Non-Microbial Origin. E. coli degWT upravená bakterie degradující toxické environmentální polutanty. E. coli degWT-opt- upravená bakterie degradující toxické environmentální polutanty. E. coli deg90R upravená bakterie degradující toxické environmentální polutanty. E. coli deg90R-opt upravená bakterie degradující toxické environmentální polutanty. E. coli deg31 upravená bakterie degradující toxické environmentální polutanty. Engineered bacterium degrading toxic environmental pollutant E. coli deg31-opt Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents. Immobilization of Haloalkane Dehalogenase LinB from Sphingobium japonicum UT26 for Biotechnological Applications HotSpot Wizard: a Web Server for Identification of Hot Spots in Protein Engineering. Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations. Chiral Aliphatic Hydroxy Compounds in Nature: a Review of Biological Functions and Practical Applications. Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering Development of an enzymatic fiber-optic biosensor for detection of halogenated hydrocarbons. Systems biology at work Substrate Specificity of Haloalkane Dehalogenases Recombinant enzyme haloalkane dehalogenase DatA Recombinant enzyme haloalkane dehalogenase DspA. Software tools for identification, visualization and analysis of protein tunnels and channels Sphingobium czechense sp nov., isolated from a hexachlorocyclohexane dump site Sphingobium baderi sp nov., isolated from a hexachlorocyclohexane dump site Miniaturized portable fluorimeter Biosenzory k včasné detekci otravných látek Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate Biochemical and structural characterization of novel haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94 possesing two halide binding sites Engineering of Biocatalysts by Modification of Access Tunnels HOTSPOT WIZARD: TOOL FOR ENGINEERING OF ENZYMES Increasing activity of bacterial biocatalyst with toxic anthropogenic substrate using methods of protein engineering. Study of water molecule dynamics at the tunnel openings of haloalkane dehalogenase Study of water molecule dynamics at the tunnel openings of haloalkane dehalogenase Biology and Bioinformatics Biochemical Characteristics of the Novel Haloalkane Dehalogenase DatA Isolated from the Plant Pathogen Agrobacterium tumefaciens C58. Biodegradation of 1,2,3-Trichloropropane

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