| Title : Biochemical and Computational Characterization of Haloalkane Dehalogenase Variants Designed by Generative AI: Accelerating the S(N)2 Step - Gelfand_2025_J.Am.Chem.Soc_147_2747 |
| Author(s) : Gelfand N , Orel V , Cui W , Damborsky J , Li C , Prokop Z , Xie WJ , Warshel A |
| Ref : Journal of the American Chemical Society , 147 :2747 , 2025 |
| Abstract : |
| PubMedSearch : Gelfand_2025_J.Am.Chem.Soc_147_2747 |
| PubMedID: 39792627 |
| Gene_locus related to this paper: xanau-halo1 |
| Title : Functional characterization of luciferase in a brittle star indicates parallel evolution influenced by genomic availability of haloalkane dehalogenase - Lau_2024_bioRxiv__ |
| Author(s) : Lau ES , Majerova M , Hensley NM , Mukherjee A , Vasina M , Pluskal D , Damborsky J , Prokop Z , Delroisse J , Bayaert WS , Parey E , Oliveri P , Marletaz F , Marek M , Oakley TH |
| Ref : Biorxiv , : , 2024 |
| Abstract : |
| PubMedSearch : Lau_2024_bioRxiv__ |
| PubMedID: 39463984 |
| Title : Azobenzene-Based Photoswitchable Substrates for Advanced Mechanistic Studies of Model Haloalkane Dehalogenase Enzyme Family - Slanska_2024_ACS.Catal_14_11635 |
| Author(s) : Slanska M , Stackova L , Marques SM , Stacko P , Martinek M , Jilek L , Toul M , Damborsky J , Bednar D , Klan P , Prokop Z |
| Ref : ACS Catal , 14 :11635 , 2024 |
| Abstract : |
| PubMedSearch : Slanska_2024_ACS.Catal_14_11635 |
| PubMedID: 39114093 |
| Gene_locus related to this paper: 9cyan-q6dnd9 |
| Title : Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyse the Mycotoxin Zearalenone - Fruhauf_2024_ACS.Catal_14_3392 |
| Author(s) : Fruhauf S , Puhringer D , Thamhesl M , Fajtl P , Kunz-Vekiru E , Hobartner-Gussl A , Schatzmayr G , Adam G , Damborsky J , Djinovic-Carugo K , Prokop Z , Moll WD |
| Ref : ACS Catal , 14 :3392 , 2024 |
| Abstract : |
| PubMedSearch : Fruhauf_2024_ACS.Catal_14_3392 |
| PubMedID: 38449531 |
| Gene_locus related to this paper: 9actn-ZenA , 9noca-a0aa46n777 |
| Title : Catalytic mechanism for Renilla-type luciferases - Schenkmayerova_2023_Nat.Catal_6_23 |
| Author(s) : Schenkmayerova A , Toul M , Pluskal D , Baatallah R , Gagnot G , Pinto GP , Santana VT , Stuchla M , Neugebauer P , Chaiyen P , Damborsky J , Bednar D , Janin YL , Prokop Z , Marek M |
| Ref : Nature Catalysis , 6 :23 , 2023 |
| Abstract : |
| PubMedSearch : Schenkmayerova_2023_Nat.Catal_6_23 |
| PubMedID: |
| Gene_locus related to this paper: 9zzzz-AncHLDRLuc2 , renre-luc |
| Title : Advancing Enzyme's Stability and Catalytic Efficiency through Synergy of Force-Field Calculations, Evolutionary Analysis, and Machine Learning - Kunka_2023_ACS.Catal_13_12506 |
| Author(s) : Kunka A , Marques SM , Havlasek M , Vasina M , Velatova N , Cengelova L , Kovar D , Damborsky J , Marek M , Bednar D , Prokop Z |
| Ref : ACS Catal , 13 :12506 , 2023 |
| Abstract : |
| PubMedSearch : Kunka_2023_ACS.Catal_13_12506 |
| PubMedID: 37822856 |
| Gene_locus related to this paper: rhoso-halo1 |
| Title : A catalytic mechanism for Renilla-type bioluminescence - Schenkmayerova_2022_Biorxiv__ |
| Author(s) : Schenkmayerova A , Toul M , Pluskal D , Baatallah R , Gagnot G , Pinto GP , Santana VT , Stuchla M , Neugebauer P , Chaiyen P , Damborsky J , Bednar D , Janin YL , Prokop Z , Marek M |
| Ref : Biorxiv , : , 2022 |
| Abstract : |
| PubMedSearch : Schenkmayerova_2022_Biorxiv__ |
| PubMedID: |
| Gene_locus related to this paper: 9zzzz-AncHLDRLuc2 , renre-luc |
| Title : Advanced database mining of efficient haloalkane dehalogenases by sequence and structure bioinformatics and microfluidics - Vasina_2022_Chem.Catal_2_2704 |
| Author(s) : Vasina M , Vanacek P , Hon J , Kovar D , Faldynova H , Kunka A , Buryska T , Badenhorst CPS , Mazurenko S , Bednar D , Stavrakis S , Bornscheuer UT , deMello A , Damborsky J , Prokop Z |
| Ref : Chem Catalysis , 2 :2704 , 2022 |
| Abstract : |
| PubMedSearch : Vasina_2022_Chem.Catal_2_2704 |
| PubMedID: |
| Title : CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability - Kunka_2022_Nucleic.Acids.Res__ |
| Author(s) : Kunka A , Lacko D , Stourac J , Damborsky J , Prokop Z , Mazurenko S |
| Ref : Nucleic Acids Research , : , 2022 |
| Abstract : |
| PubMedSearch : Kunka_2022_Nucleic.Acids.Res__ |
| PubMedID: 35580052 |
| Title : Tools for computational design and high-throughput screening of therapeutic enzymes - Vasina_2022_Adv.Drug.Deliv.Rev_183_114143 |
| Author(s) : Vasina M , Velecky J , Planas-Iglesias J , Marques SM , Skarupova J , Damborsky J , Bednar D , Mazurenko S , Prokop Z |
| Ref : Adv Drug Deliv Rev , 183 :114143 , 2022 |
| Abstract : |
| PubMedSearch : Vasina_2022_Adv.Drug.Deliv.Rev_183_114143 |
| PubMedID: 35167900 |
| Title : Engineering the protein dynamics of an ancestral luciferase - Schenkmayerova_2021_Nat.Commun_12_3616 |
| Author(s) : Schenkmayerova A , Pinto GP , Toul M , Marek M , Hernychova L , Planas-Iglesias J , Daniel Liskova V , Pluskal D , Vasina M , Emond S , Dorr M , Chaloupkova R , Bednar D , Prokop Z , Hollfelder F , Bornscheuer UT , Damborsky J |
| Ref : Nat Commun , 12 :3616 , 2021 |
| Abstract : |
| PubMedSearch : Schenkmayerova_2021_Nat.Commun_12_3616 |
| PubMedID: 34127663 |
| Gene_locus related to this paper: renre-luc |
| Title : Substrate inhibition by the blockage of product release and its control by tunnel engineering - Kokkonen_2021_RSC.Chem.Biol_2_645 |
| Author(s) : Kokkonen P , Beier A , Mazurenko S , Damborsky J , Bednar D , Prokop Z |
| Ref : RSC Chemical Biology , 2 :645 , 2021 |
| Abstract : |
| PubMedSearch : Kokkonen_2021_RSC.Chem.Biol_2_645 |
| PubMedID: 34458806 |
| Gene_locus related to this paper: sphpi-linb |
| Title : Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers - Markova_2021_ACS.Catal_11_12864 |
| Author(s) : Markova K , Kunka A , Chmelova K , Havlasek M , Babkova P , Marques SM , Vasina M , Planas-Iglesias J , Chaloupkova R , Bednar D , Prokop Z , Damborsky J , Marek M |
| Ref : ACS Catal , 11 :12864 , 2021 |
| Abstract : |
| PubMedSearch : Markova_2021_ACS.Catal_11_12864 |
| PubMedID: |
| Gene_locus related to this paper: rhoso-halo1 |
| Title : Functional Annotation of an Enzyme Family by Integrated Strategy Combining Bioinformatics with Microanalytical and Microfluidic Technologies - Vanacek_2021_bioRxiv__ |
| Author(s) : Vanacek P , Vasina M , Hon J , Kovar D , Faldynova H , Kunka A , Buryska T , Badenhorst CPS , Mazurenko S , Bednar D , Bornscheuer UT , Damborsky J , Prokop Z |
| Ref : Biorxiv , : , 2021 |
| Abstract : |
| PubMedSearch : Vanacek_2021_bioRxiv__ |
| PubMedID: |
| Title : The impact of tunnel mutations on enzymatic catalysis depends on the tunnel-substrate complementarity and the rate-limiting step - Kokkonen_2020_Comput.Struct.Biotechnol.J_18_805 |
| Author(s) : Kokkonen P , Slanska M , Dockalova V , Pinto GP , Sanchez-Carnerero EM , Damborsky J , Klan P , Prokop Z , Bednar D |
| Ref : Comput Struct Biotechnol J , 18 :805 , 2020 |
| Abstract : |
| PubMedSearch : Kokkonen_2020_Comput.Struct.Biotechnol.J_18_805 |
| PubMedID: 32308927 |
| Title : Engineering Protein Dynamics of Ancestral Luciferase - Schenkmayerova_2020_Chemrxiv__ |
| Author(s) : Schenkmayerova A , Pinto GP , Toul M , Marek M , Hernychova L , Planas-Iglesias J , Liskova V , Pluskal D , Vasina M , Emond S , Dorr M , Chaloupkova R , Bednar D , Prokop Z , Hollfelder F , Bornscheuer UT , Damborsky J |
| Ref : Chemrxiv , : , 2020 |
| Abstract : |
| PubMedSearch : Schenkmayerova_2020_Chemrxiv__ |
| PubMedID: |
| Gene_locus related to this paper: renre-luc |
| Title : A Haloalkane Dehalogenase from Saccharomonospora viridis Strain DSM 43017, a Compost Bacterium with Unusual Catalytic Residues, Unique (S)-Enantiopreference, and High Thermostability - Chmelova_2020_Appl.Environ.Microbiol_86_ |
| Author(s) : Chmelova K , Sebestova E , Liskova V , Beier A , Bednar D , Prokop Z , Chaloupkova R , Damborsky J |
| Ref : Applied Environmental Microbiology , 86 : , 2020 |
| Abstract : |
| PubMedSearch : Chmelova_2020_Appl.Environ.Microbiol_86_ |
| PubMedID: 32561584 |
| Gene_locus related to this paper: sacvd-DsvA |
| Title : Exploration of enzyme diversity: High-throughput techniques for protein production and microscale biochemical characterization - Vasina_2020_Methods.Enzymol_643_51 |
| Author(s) : Vasina M , Vanacek P , Damborsky J , Prokop Z |
| Ref : Methods Enzymol , 643 :51 , 2020 |
| Abstract : |
| PubMedSearch : Vasina_2020_Methods.Enzymol_643_51 |
| PubMedID: 32896287 |
| Title : EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities - Hon_2020_Nucleic.Acids.Res__ |
| Author(s) : Hon J , Borko S , Stourac J , Prokop Z , Zendulka J , Bednar D , Martinek T , Damborsky J |
| Ref : Nucleic Acids Research , : , 2020 |
| Abstract : |
| PubMedSearch : Hon_2020_Nucleic.Acids.Res__ |
| PubMedID: 32392342 |
| Title : Fluorescent substrates for haloalkane dehalogenases: Novel probes for mechanistic studies and protein labeling - Dockalova_2020_Comput.Struct.Biotechnol.J_18_922 |
| Author(s) : Dockalova V , Sanchez-Carnerero EM , Dunajova Z , Palao E , Slanska M , Buryska T , Damborsky J , Klan P , Prokop Z |
| Ref : Comput Struct Biotechnol J , 18 :922 , 2020 |
| Abstract : |
| PubMedSearch : Dockalova_2020_Comput.Struct.Biotechnol.J_18_922 |
| PubMedID: 32346465 |
| Title : Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts - Chaloupkova_2019_ACS.Catal_9_48103 |
| Author(s) : Chaloupkova, R , Liskova V , Tool M , Markova K , Sebestova E , Hernychova L , Marek M , Pinto GP , Pluskal D , Waterman J , Prokop Z , Damborsky J |
| Ref : ACS Catal , 9 :4810 , 2019 |
| Abstract : |
| PubMedSearch : Chaloupkova_2019_ACS.Catal_9_48103 |
| PubMedID: |
| Gene_locus related to this paper: 9zzzz-AncHLDRLuc2 , 9zzzz-AncHLDRLuc , renre-luc |
| Title : Transhalogenation Catalysed by Haloalkane Dehalogenases Engineered to Stop Natural Pathway at Intermediate - Beier_2019_Adv.Synth.Catal_361_2438 |
| Author(s) : Beier A , Damborsky J , Prokop Z |
| Ref : Adv Synth Catal , 361 :2438 , 2019 |
| Abstract : |
| PubMedSearch : Beier_2019_Adv.Synth.Catal_361_2438 |
| PubMedID: |
| Gene_locus related to this paper: braja-dhaa , rhoso-halo1 , sphpi-linb |
| Title : Controlled Oil\/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics - Buryska_2019_Anal.Chem_91_10008 |
| Author(s) : Buryska T , Vasina M , Gielen F , Vanacek P , van Vliet L , Jezek J , Pilat Z , Zemanek P , Damborsky J , Hollfelder F , Prokop Z |
| Ref : Analytical Chemistry , 91 :10008 , 2019 |
| Abstract : |
| PubMedSearch : Buryska_2019_Anal.Chem_91_10008 |
| PubMedID: 31240908 |
| Title : Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase - Jindal_2019_Proc.Natl.Acad.Sci.U.S.A_116_389 |
| Author(s) : Jindal G , Slanska K , Kolev V , Damborsky J , Prokop Z , Warshel A |
| Ref : Proc Natl Acad Sci U S A , 116 :389 , 2019 |
| Abstract : |
| PubMedSearch : Jindal_2019_Proc.Natl.Acad.Sci.U.S.A_116_389 |
| PubMedID: 30587585 |
| Gene_locus related to this paper: xanau-halo1 |
| Title : Impact of the access tunnel engineering on catalysis is strictly ligand-specific - Kaushik_2018_FEBS.J_285_1456 |
| Author(s) : Kaushik S , Marques SM , Khirsariya P , Paruch K , Libichova L , Brezovsky J , Prokop Z , Chaloupkova R , Damborsky J |
| Ref : Febs J , 285 :1456 , 2018 |
| Abstract : |
| PubMedSearch : Kaushik_2018_FEBS.J_285_1456 |
| PubMedID: 29478278 |
| Title : Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips - Pilat_2018_Sensors.(Basel)_18_ |
| Author(s) : Pilat Z , Kizovsky M , Jezek J , Kratky S , Sobota J , Siler M , Samek O , Buryska T , Vanacek P , Damborsky J , Prokop Z , Zemanek P |
| Ref : Sensors (Basel) , 18 : , 2018 |
| Abstract : |
| PubMedSearch : Pilat_2018_Sensors.(Basel)_18_ |
| PubMedID: 30249041 |
| Title : Sensitive operation of enzyme-based biodevices by advanced signal processing - Mazurenko_2018_PLoS.One_13_e0198913 |
| Author(s) : Mazurenko S , Bidmanova S , Kotlanova M , Damborsky J , Prokop Z |
| Ref : PLoS ONE , 13 :e0198913 , 2018 |
| Abstract : |
| PubMedSearch : Mazurenko_2018_PLoS.One_13_e0198913 |
| PubMedID: 29912920 |
| Title : Development of fluorescent assay for monitoring of dehalogenase activity - Nevolova_2018_Biotechnol.J__e1800144 |
| Author(s) : Nevolova S , Manaskova E , Mazurenko S , Damborsky J , Prokop Z |
| Ref : Biotechnol J , :e1800144 , 2018 |
| Abstract : |
| PubMedSearch : Nevolova_2018_Biotechnol.J__e1800144 |
| PubMedID: 30052322 |
| Title : A Haloalkane Dehalogenase from a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity - Buryska_2018_Appl.Environ.Microbiol_84_ |
| Author(s) : Buryska T , Babkova P , Vavra O , Damborsky J , Prokop Z |
| Ref : Applied Environmental Microbiology , 84 : , 2018 |
| Abstract : |
| PubMedSearch : Buryska_2018_Appl.Environ.Microbiol_84_ |
| PubMedID: 29101190 |
| Gene_locus related to this paper: 9cyan-q6dnd9 |
| Title : Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization - Beerens_2018_ACS.Catal_8_9420 |
| Author(s) : Beerens K , Mazurenko S , Kunka A , Marques SM , Hansen N , Musil M , Chaloupkova R , Waterman J , Brezovsky J , Bednar D , Prokop Z , Damborsky J |
| Ref : ACS Catal , 8 :9420 , 2018 |
| Abstract : |
| PubMedSearch : Beerens_2018_ACS.Catal_8_9420 |
| PubMedID: |
| Gene_locus related to this paper: rhoso-halo1 |
| Title : Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site - Kokkonen_2018_J.Biol.Chem_293_11505 |
| Author(s) : Kokkonen P , Bednar D , Dockalova V , Prokop Z , Damborsky J |
| Ref : Journal of Biological Chemistry , 293 :11505 , 2018 |
| Abstract : |
| PubMedSearch : Kokkonen_2018_J.Biol.Chem_293_11505 |
| PubMedID: 29858243 |
| Gene_locus related to this paper: xanau-halo1 |
| Title : Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling - Marques_2017_J.Chem.Inf.Model_57_1970 |
| Author(s) : Marques SM , Dunajova Z , Prokop Z , Chaloupkova R , Brezovsky J , Damborsky J |
| Ref : J Chem Inf Model , 57 :1970 , 2017 |
| Abstract : |
| PubMedSearch : Marques_2017_J.Chem.Inf.Model_57_1970 |
| PubMedID: 28696117 |
| Title : Metagenome-derived haloalkane dehalogenases with novel catalytic properties - Kotik_2017_Appl.Microbiol.Biotechnol_101_6385 |
| Author(s) : Kotik M , Vanacek P , Kunka A , Prokop Z , Damborsky J |
| Ref : Applied Microbiology & Biotechnology , 101 :6385 , 2017 |
| Abstract : |
| PubMedSearch : Kotik_2017_Appl.Microbiol.Biotechnol_101_6385 |
| PubMedID: 28674849 |
| Gene_locus related to this paper: 9bact-v5ln96 , 9bact-v5llz5 , 9bact-v5llk8 |
| Title : Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear beta-Haloalkanes: Open-Solvated versus Occluded-Desolvated Active Sites - Liskova_2017_Angew.Chem.Int.Ed.Engl_56_4719 |
| Author(s) : Liskova V , Stepankova V , Bednar D , Brezovsky J , Prokop Z , Chaloupkova R , Damborsky J |
| Ref : Angew Chem Int Ed Engl , 56 :4719 , 2017 |
| Abstract : |
| PubMedSearch : Liskova_2017_Angew.Chem.Int.Ed.Engl_56_4719 |
| PubMedID: 28334478 |
| Title : Kinetics of binding of fluorescent ligands to enzymes with engineered access tunnels - Kaushik_2017_FEBS.J_284_134 |
| Author(s) : Kaushik S , Prokop Z , Damborsky J , Chaloupkova R |
| Ref : Febs J , 284 :134 , 2017 |
| Abstract : |
| PubMedSearch : Kaushik_2017_FEBS.J_284_134 |
| PubMedID: 27863020 |
| Title : Engineering a de novo transport tunnel - Brezovsky_2016_ACS.Catal_6_7597 |
| Author(s) : Brezovsky J , Babkova P , Degtjarik O , Fortova A , Gora A , Iermak I , Rezacova P , Dvorak P , Kuta-Smatanova I , Prokop Z , Chaloupkova R , Damborsky J |
| Ref : ACS Catal , 6 :7597 , 2016 |
| Abstract : |
| PubMedSearch : Brezovsky_2016_ACS.Catal_6_7597 |
| PubMedID: |
| Gene_locus related to this paper: sphpi-linb |
| Title : Fluorescence-based biosensor for monitoring of environmental pollutants: From concept to field application - Bidmanova_2016_Biosens.Bioelectron_84_97 |
| Author(s) : Bidmanova S , Kotlanova M , Rataj T , Damborsky J , Trtilek M , Prokop Z |
| Ref : Biosensors & Bioelectronics , 84 :97 , 2016 |
| Abstract : |
| PubMedSearch : Bidmanova_2016_Biosens.Bioelectron_84_97 |
| PubMedID: 26725215 |
| Title : Regio- and Enantioselective Sequential Dehalogenation of rac-1,3-Dibromobutane by Haloalkane Dehalogenase LinB - Gross_2016_Chembiochem_17_1437 |
| Author(s) : Gross J , Prokop Z , Janssen D , Faber K , Hall M |
| Ref : Chembiochem , 17 :1437 , 2016 |
| Abstract : |
| PubMedSearch : Gross_2016_Chembiochem_17_1437 |
| PubMedID: 27223496 |
| Title : Discovery of Novel Haloalkane Dehalogenase Inhibitors - Buryska_2016_Appl.Environ.Microbiol_82_1958 |
| Author(s) : Buryska T , Daniel L , Kunka A , Brezovsky J , Damborsky J , Prokop Z |
| Ref : Applied Environmental Microbiology , 82 :1958 , 2016 |
| Abstract : |
| PubMedSearch : Buryska_2016_Appl.Environ.Microbiol_82_1958 |
| PubMedID: 26773086 |
| Title : Mechanism-based discovery of novel substrates of haloalkane dehalogenases using in silico screening - Daniel_2015_J.Chem.Inf.Model_55_54 |
| Author(s) : Daniel L , Buryska T , Prokop Z , Damborsky J , Brezovsky J |
| Ref : J Chem Inf Model , 55 :54 , 2015 |
| Abstract : |
| PubMedSearch : Daniel_2015_J.Chem.Inf.Model_55_54 |
| PubMedID: 25495415 |
| Title : FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants - Bednar_2015_PLoS.Comput.Biol_11_e1004556 |
| Author(s) : Bednar D , Beerens K , Sebestova E , Bendl J , Khare S , Chaloupkova R , Prokop Z , Brezovsky J , Baker D , Damborsky J |
| Ref : PLoS Comput Biol , 11 :e1004556 , 2015 |
| Abstract : |
| PubMedSearch : Bednar_2015_PLoS.Comput.Biol_11_e1004556 |
| PubMedID: 26529612 |
| Gene_locus related to this paper: rhoso-halo1 |
| Title : Dynamics and hydration explain failed functional transformation in dehalogenase design - Sykora_2014_Nat.Chem.Biol_10_428 |
| Author(s) : Sykora J , Brezovsky J , Koudelakova T , Lahoda M , Fortova A , Chernovets T , Chaloupkova R , Stepankova V , Prokop Z , Smatanova IK , Hof M , Damborsky J |
| Ref : Nat Chemical Biology , 10 :428 , 2014 |
| Abstract : |
| PubMedSearch : Sykora_2014_Nat.Chem.Biol_10_428 |
| PubMedID: 24727901 |
| Gene_locus related to this paper: rhoso-halo1 |
| Title : Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites - Chaloupkova_2014_Acta.Crystallogr.D.Biol.Crystallogr_70_1884 |
| Author(s) : Chaloupkova R , Prudnikova T , Rezacova P , Prokop Z , Koudelakova T , Daniel L , Brezovsky J , Ikeda-Ohtsubo W4 , Sato Y , Kuty M , Nagata Y , Kuta Smatanova I , Damborsky J |
| Ref : Acta Crystallographica D Biol Crystallogr , 70 :1884 , 2014 |
| Abstract : |
| PubMedSearch : Chaloupkova_2014_Acta.Crystallogr.D.Biol.Crystallogr_70_1884 |
| PubMedID: 25004965 |
| Gene_locus related to this paper: brael-e2rv62 |
| Title : Stepwise enhancement of catalytic performance of haloalkane dehalogenase LinB towards beta-hexachlorocyclohexane - Moriuchi_2014_AMB.Express_4_72 |
| Author(s) : Moriuchi R , Tanaka H , Nikawadori Y , Ishitsuka M , Ito M , Ohtsubo Y , Tsuda M , Damborsky J , Prokop Z , Nagata Y |
| Ref : AMB Express , 4 :72 , 2014 |
| Abstract : |
| PubMedSearch : Moriuchi_2014_AMB.Express_4_72 |
| PubMedID: 25401073 |
| Title : Microscopic monitoring provides information on structure and properties during biocatalyst immobilization - Bidmanova_2014_Biotechnol.J_9_852 |
| Author(s) : Bidmanova S , Hrdlickova E , Jaros J , Ilkovics L , Hampl A , Damborsky J , Prokop Z |
| Ref : Biotechnol J , 9 :852 , 2014 |
| Abstract : |
| PubMedSearch : Bidmanova_2014_Biotechnol.J_9_852 |
| PubMedID: 24639415 |
| Title : Release of halide ions from the buried active site of the haloalkane dehalogenase LinB revealed by stopped-flow fluorescence analysis and free energy calculations - Hladilkova_2013_J.Phys.Chem.B_117_14329 |
| Author(s) : Hladilkova J , Prokop Z , Chaloupkova R , Damborsky J , Jungwirth P |
| Ref : J Phys Chem B , 117 :14329 , 2013 |
| Abstract : |
| PubMedSearch : Hladilkova_2013_J.Phys.Chem.B_117_14329 |
| PubMedID: 24151979 |
| Title : Engineering enzyme stability and resistance to an organic cosolvent by modification of residues in the access tunnel - Koudelakova_2013_Angew.Chem.Int.Ed.Engl_52_1959 |
| Author(s) : Koudelakova T , Chaloupkova R , Brezovsky J , Prokop Z , Sebestova E , Hesseler M , Khabiri M , Plevaka M , Kulik D , Kuta Smatanova I , Rezacova P , Ettrich R , Bornscheuer UT , Damborsky J |
| Ref : Angew Chem Int Ed Engl , 52 :1959 , 2013 |
| Abstract : |
| PubMedSearch : Koudelakova_2013_Angew.Chem.Int.Ed.Engl_52_1959 |
| PubMedID: 23303607 |
| Gene_locus related to this paper: rhoso-halo1 |
| Title : Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents - Stepankova_2013_Chembiochem_14_890 |
| Author(s) : Stepankova V , Khabiri M , Brezovsky J , Pavelka A , Sykora J , Amaro M , Minofar B , Prokop Z , Hof M , Ettrich R , Chaloupkova R , Damborsky J |
| Ref : Chembiochem , 14 :890 , 2013 |
| Abstract : |
| PubMedSearch : Stepankova_2013_Chembiochem_14_890 |
| PubMedID: 23564727 |
| Gene_locus related to this paper: rhoso-halo1 |
| Title : Haloalkane dehalogenases: Biotechnological applications - Koudelakova_2013_Biotechnol.J_8_32 |
| Author(s) : Koudelakova T , Bidmanova S , Dvorak P , Pavelka A , Chaloupkova R , Prokop Z , Damborsky J |
| Ref : Biotechnol J , 8 :32 , 2013 |
| Abstract : |
| PubMedSearch : Koudelakova_2013_Biotechnol.J_8_32 |
| PubMedID: 22965918 |
| Title : The effect of a unique halide-stabilizing residue on the catalytic properties of haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 - Hasan_2013_FEBS.J_280_3149 |
| Author(s) : Hasan K , Gora A , Brezovsky J , Chaloupkova R , Moskalikova H , Fortova A , Nagata Y , Damborsky J , Prokop Z |
| Ref : Febs J , 280 :3149 , 2013 |
| Abstract : |
| PubMedSearch : Hasan_2013_FEBS.J_280_3149 |
| PubMedID: 23490078 |
| Title : Strategies for Stabilization of Enzymes in Organic Solvents - Stepankova_2013_ACS.Catal_3_2823 |
| Author(s) : Stepankova V , Bidmanova S , Koudelakova T , Prokop Z , Chaloupkova R , Damborsky J |
| Ref : ACS Catal , 3 :2823 , 2013 |
| Abstract : |
| PubMedSearch : Stepankova_2013_ACS.Catal_3_2823 |
| PubMedID: |
| Title : A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB - Biedermannova_2012_J.Biol.Chem_287_29062 |
| Author(s) : Biedermannova L , Prokop Z , Gora A , Chovancova E , Kovacs M , Damborsky J , Wade RC |
| Ref : Journal of Biological Chemistry , 287 :29062 , 2012 |
| Abstract : |
| PubMedSearch : Biedermannova_2012_J.Biol.Chem_287_29062 |
| PubMedID: 22745119 |
| Title : Stereoselectivity and conformational stability of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110: the effect of pH and temperature - Chaloupkova_2011_FEBS.J_278_2728 |
| Author(s) : Chaloupkova R , Prokop Z , Sato Y , Nagata Y , Damborsky J |
| Ref : Febs J , 278 :2728 , 2011 |
| Abstract : |
| PubMedSearch : Chaloupkova_2011_FEBS.J_278_2728 |
| PubMedID: 21635695 |
| Title : Biochemical characteristics of the novel haloalkane dehalogenase DatA, isolated from the plant pathogen Agrobacterium tumefaciens C58 - Hasan_2011_Appl.Environ.Microbiol_77_1881 |
| Author(s) : Hasan K , Fortova A , Koudelakova T , Chaloupkova R , Ishitsuka M , Nagata Y , Damborsky J , Prokop Z |
| Ref : Applied Environmental Microbiology , 77 :1881 , 2011 |
| Abstract : |
| PubMedSearch : Hasan_2011_Appl.Environ.Microbiol_77_1881 |
| PubMedID: 21193677 |
| Title : Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering - |
| Author(s) : Prokop Z , Sato Y , Brezovsky J , Mozga T , Chaloupkova R , Koudelakova T , Jerabek P , Stepankova V , Natsume R , van Leeuwen JG , Janssen DB , Florian J , Nagata Y , Senda T , Damborsky J |
| Ref : Angew Chem Int Ed Engl , 49 :6111 , 2010 |
| PubMedID: 20645368 |
| Gene_locus related to this paper: braja-dhaa |
| Title : Development of an enzymatic fiber-optic biosensor for detection of halogenated hydrocarbons - Bidmanova_2010_Anal.Bioanal.Chem_398_1891 |
| Author(s) : Bidmanova S , Chaloupkova R , Damborsky J , Prokop Z |
| Ref : Anal Bioanal Chem , 398 :1891 , 2010 |
| Abstract : |
| PubMedSearch : Bidmanova_2010_Anal.Bioanal.Chem_398_1891 |
| PubMedID: 20721539 |
| Title : Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations - Klvana_2009_J.Mol.Biol_392_1339 |
| Author(s) : Klvana M , Pavlova M , Koudelakova T , Chaloupkova R , Dvorak P , Prokop Z , Stsiapanava A , Kuty M , Kuta-Smatanova I , Dohnalek J , Kulhanek P , Wade RC , Damborsky J |
| Ref : Journal of Molecular Biology , 392 :1339 , 2009 |
| Abstract : |
| PubMedSearch : Klvana_2009_J.Mol.Biol_392_1339 |
| PubMedID: 19577578 |
| Gene_locus related to this paper: rhoso-halo1 |
| Title : Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate - Pavlova_2009_Nat.Chem.Biol_5_727 |
| Author(s) : Pavlova M , Klvana M , Prokop Z , Chaloupkova R , Banas P , Otyepka M , Wade RC , Tsuda M , Nagata Y , Damborsky J |
| Ref : Nat Chemical Biology , 5 :727 , 2009 |
| Abstract : |
| PubMedSearch : Pavlova_2009_Nat.Chem.Biol_5_727 |
| PubMedID: 19701186 |
| Title : Biochemical characterization of haloalkane dehalogenases DrbA and DmbC, Representatives of a Novel Subfamily - Jesenska_2009_Appl.Environ.Microbiol_75_5157 |
| Author(s) : Jesenska A , Monincova M , Koudelakova T , Hasan K , Chaloupkova R , Prokop Z , Geerlof A , Damborsky J |
| Ref : Applied Environmental Microbiology , 75 :5157 , 2009 |
| Abstract : |
| PubMedSearch : Jesenska_2009_Appl.Environ.Microbiol_75_5157 |
| PubMedID: 19502442 |
| Gene_locus related to this paper: myctu-Rv1833c |
| Title : Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from gamma-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205 - Ito_2007_Arch.Microbiol_188_313 |
| Author(s) : Ito M , Prokop Z , Klvana M , Otsubo Y , Tsuda M , Damborsky J , Nagata Y |
| Ref : Arch Microbiol , 188 :313 , 2007 |
| Abstract : |
| PubMedSearch : Ito_2007_Arch.Microbiol_188_313 |
| PubMedID: 17516046 |
| Gene_locus related to this paper: sphpi-linb |
| Title : Weak activity of haloalkane dehalogenase LinB with 1,2,3-trichloropropane revealed by X-Ray crystallography and microcalorimetry - Monincova_2007_Appl.Environ.Microbiol_73_2005 |
| Author(s) : Monincova M , Prokop Z , Vevodova J , Nagata Y , Damborsky J |
| Ref : Applied Environmental Microbiology , 73 :2005 , 2007 |
| Abstract : |
| PubMedSearch : Monincova_2007_Appl.Environ.Microbiol_73_2005 |
| PubMedID: 17259360 |
| Gene_locus related to this paper: sphpi-linb |
| Title : The identification of catalytic pentad in the haloalkane dehalogenase DhmA from Mycobacterium avium N85: reaction mechanism and molecular evolution - Pavlova_2007_J.Struct.Biol_157_384 |
| Author(s) : Pavlova M , Klvana M , Jesenska A , Prokop Z , Konecna H , Sato T , Tsuda M , Nagata Y , Damborsky J |
| Ref : J Struct Biol , 157 :384 , 2007 |
| Abstract : |
| PubMedSearch : Pavlova_2007_J.Struct.Biol_157_384 |
| PubMedID: 17084094 |
| Title : Expression of glycosylated haloalkane dehalogenase LinB in Pichia pastoris - Nakamura_2006_Protein.Expr.Purif_46_85 |
| Author(s) : Nakamura T , Zamocky M , Zdrahal Z , Chaloupkova R , Monincova M , Prokop Z , Nagata Y , Damborsky J |
| Ref : Protein Expr Purif , 46 :85 , 2006 |
| Abstract : |
| PubMedSearch : Nakamura_2006_Protein.Expr.Purif_46_85 |
| PubMedID: 16216524 |
| Title : Enzymes fight chemical weapons - |
| Author(s) : Prokop Z , Oplustil F , DeFrank J , Damborsky J |
| Ref : Biotechnol J , 1 :1370 , 2006 |
| PubMedID: 17136732 |
| Title : Cloning, biochemical properties, and distribution of mycobacterial haloalkane dehalogenases - Jesenska_2005_Appl.Environ.Microbiol_71_6736 |
| Author(s) : Jesenska A , Pavlova M , Strouhal M , Chaloupkova R , Tesinska I , Monincova M , Prokop Z , Bartos M , Pavlik I , Rychlik I , Mobius P , Nagata Y , Damborsky J |
| Ref : Applied Environmental Microbiology , 71 :6736 , 2005 |
| Abstract : |
| PubMedSearch : Jesenska_2005_Appl.Environ.Microbiol_71_6736 |
| PubMedID: 16269704 |
| Gene_locus related to this paper: myctu-linb |
| Title : Degradation of beta-Hexachlorocyclohexane by Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 - Nagata_2005_Appl.Environ.Microbiol_71_2183 |
| Author(s) : Nagata Y , Prokop Z , Sato Y , Jerabek P , Kumar A , Ohtsubo Y , Tsuda M , Damborsky J |
| Ref : Applied Environmental Microbiology , 71 :2183 , 2005 |
| Abstract : |
| PubMedSearch : Nagata_2005_Appl.Environ.Microbiol_71_2183 |
| PubMedID: 15812056 |
| Title : Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, encode haloalkane dehalogenases with novel structures and substrate specificities - Sato_2005_Appl.Environ.Microbiol_71_4372 |
| Author(s) : Sato Y , Monincova M , Chaloupkova R , Prokop Z , Ohtsubo Y , Minamisawa K , Tsuda M , Damborsky J , Nagata Y |
| Ref : Applied Environmental Microbiology , 71 :4372 , 2005 |
| Abstract : |
| PubMedSearch : Sato_2005_Appl.Environ.Microbiol_71_4372 |
| PubMedID: 16085827 |
| Title : Reconstruction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB - Nagata_2003_Appl.Environ.Microbiol_69_2349 |
| Author(s) : Nagata Y , Prokop Z , Marvanova S , Sykorova J , Monincova M , Tsuda M , Damborsky J |
| Ref : Applied Environmental Microbiology , 69 :2349 , 2003 |
| Abstract : |
| PubMedSearch : Nagata_2003_Appl.Environ.Microbiol_69_2349 |
| PubMedID: 12676719 |
| Title : Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel - Chaloupkova_2003_J.Biol.Chem_278_52622 |
| Author(s) : Chaloupkova R , Sykorova J , Prokop Z , Jesenska A , Monincova M , Pavlova M , Tsuda M , Nagata Y , Damborsky J |
| Ref : Journal of Biological Chemistry , 278 :52622 , 2003 |
| Abstract : |
| PubMedSearch : Chaloupkova_2003_J.Biol.Chem_278_52622 |
| PubMedID: 14525993 |
| Title : Catalytic mechanism of the maloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 - Prokop_2003_J.Biol.Chem_278_45094 |
| Author(s) : Prokop Z , Monincova M , Chaloupkova R , Klvana M , Nagata Y , Janssen DB , Damborsky J |
| Ref : Journal of Biological Chemistry , 278 :45094 , 2003 |
| Abstract : |
| PubMedSearch : Prokop_2003_J.Biol.Chem_278_45094 |
| PubMedID: 12952988 |
| Gene_locus related to this paper: sphpi-linb |
| Title : Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates - Streltsov_2003_Biochemistry_42_10104 |
| Author(s) : Streltsov VA , Prokop Z , Damborsky J , Nagata Y , Oakley A , Wilce MC |
| Ref : Biochemistry , 42 :10104 , 2003 |
| Abstract : |
| PubMedSearch : Streltsov_2003_Biochemistry_42_10104 |
| PubMedID: 12939138 |
| Gene_locus related to this paper: sphpi-linb |
| Title : Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis - Bohac_2002_Biochemistry_41_14272 |
| Author(s) : Bohac M , Nagata Y , Prokop Z , Prokop M , Monincova M , Tsuda M , Koca J , Damborsky J |
| Ref : Biochemistry , 41 :14272 , 2002 |
| Abstract : |
| PubMedSearch : Bohac_2002_Biochemistry_41_14272 |
| PubMedID: 12450392 |
| Gene_locus related to this paper: sphpi-linb |
| Title : Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition - Oakley_2002_Biochemistry_41_4847 |
| Author(s) : Oakley AJ , Prokop Z , Bohac M , Kmunicek J , Jedlicka T , Monincova M , Kuta-Smatanova I , Nagata Y , Damborsky J , Wilce MC |
| Ref : Biochemistry , 41 :4847 , 2002 |
| Abstract : |
| PubMedSearch : Oakley_2002_Biochemistry_41_4847 |
| PubMedID: 11939779 |
| Gene_locus related to this paper: sphpi-linb |