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| Title : Exploring new galaxies: Perspectives on the discovery of novel PET-degrading enzymes - Mican_2024_Appl.Catal.B.Environmental_342_123404 |
| Author(s) : Mican J , Jaradat DMM , Liu W , Weber G , Mazurenko S , Bornscheuer UT , Damborsky J , Wei R , Bednar D |
| Ref : Applied Catalysis B: Environmental , 342 :123404 , 2024 |
| Abstract : Mican_2024_Appl.Catal.B.Environmental_342_123404 |
| ESTHER : Mican_2024_Appl.Catal.B.Environmental_342_123404 |
| PubMedSearch : Mican_2024_Appl.Catal.B.Environmental_342_123404 |
| PubMedID: |
| Title : Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum - Snajdarova_2023_Acta.Crystallogr.D.Struct.Biol__ |
| Author(s) : Snajdarova K , Marques SM , Damborsky J , Bednar D , Marek M |
| Ref : Acta Crystallographica D Struct Biol , : , 2023 |
| Abstract : Snajdarova_2023_Acta.Crystallogr.D.Struct.Biol__ |
| ESTHER : Snajdarova_2023_Acta.Crystallogr.D.Struct.Biol__ |
| PubMedSearch : Snajdarova_2023_Acta.Crystallogr.D.Struct.Biol__ |
| PubMedID: 37860958 |
| 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 : Schenkmayerova_2023_Nat.Catal_6_23 |
| ESTHER : Schenkmayerova_2023_Nat.Catal_6_23 |
| 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 : Kunka_2023_ACS.Catal_13_12506 |
| ESTHER : Kunka_2023_ACS.Catal_13_12506 |
| PubMedSearch : Kunka_2023_ACS.Catal_13_12506 |
| PubMedID: 37822856 |
| Gene_locus related to this paper: rhoso-halo1 |
| Title : Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase - Pfaff_2022_ACS.Catalysis_12_9790 |
| Author(s) : Pfaff L , Gao J , Li Z , Jackering A , Weber G , Mican J , Chen Y , Dong W , Han X , Feiler CG , Ao YF , Badenhorst CPS , Bednar D , Palm GJ , Lammers M , Damborsky J , Strodel B , Liu W , Bornscheuer UT , Wei R |
| Ref : ACS Catal , 12 :9790 , 2022 |
| Abstract : Pfaff_2022_ACS.Catalysis_12_9790 |
| ESTHER : Pfaff_2022_ACS.Catalysis_12_9790 |
| PubMedSearch : Pfaff_2022_ACS.Catalysis_12_9790 |
| PubMedID: 35966606 |
| Gene_locus related to this paper: 9firm-PHL7 |
| Title : LoopGrafter: a web tool for transplanting dynamical loops for protein engineering - Planas-Iglesias_2022_Nucleic.Acids.Res__ |
| Author(s) : Planas-Iglesias J , Opaleny F , Ulbrich P , Stourac J , Sanusi Z , Pinto GP , Schenkmayerova A , Byska J , Damborsky J , Kozlikova B , Bednar D |
| Ref : Nucleic Acids Research , : , 2022 |
| Abstract : Planas-Iglesias_2022_Nucleic.Acids.Res__ |
| ESTHER : Planas-Iglesias_2022_Nucleic.Acids.Res__ |
| PubMedSearch : Planas-Iglesias_2022_Nucleic.Acids.Res__ |
| PubMedID: 35438789 |
| 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 : Schenkmayerova_2022_Biorxiv__ |
| ESTHER : Schenkmayerova_2022_Biorxiv__ |
| PubMedSearch : Schenkmayerova_2022_Biorxiv__ |
| PubMedID: |
| Gene_locus related to this paper: 9zzzz-AncHLDRLuc2 , renre-luc |
| 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 : Vasina_2022_Adv.Drug.Deliv.Rev_183_114143 |
| ESTHER : Vasina_2022_Adv.Drug.Deliv.Rev_183_114143 |
| PubMedSearch : Vasina_2022_Adv.Drug.Deliv.Rev_183_114143 |
| PubMedID: 35167900 |
| Title : Structural Insights into (Tere)phthalate-Ester Hydrolysis by a Carboxylesterase and Its Role in Promoting PET Depolymerization - von Haugwitz_2022_ACS.Catal_12_15259 |
| Author(s) : von Haugwitz G , Han X , Pfaff L , Li Q , Wei H , Gao J , Methling K , Ao Y , Brack Y , Jan Mican J , Feiler CG , Weiss MS , Bednar D , Palm GJ , Lalk M , Lammers M , Damborsky J , Weber G , Liu W , Bornscheuer UT , Wei R |
| Ref : ACS Catal , 12 :15259 , 2022 |
| Abstract : von Haugwitz_2022_ACS.Catal_12_15259 |
| ESTHER : von Haugwitz_2022_ACS.Catal_12_15259 |
| PubMedSearch : von Haugwitz_2022_ACS.Catal_12_15259 |
| PubMedID: 36570084 |
| Gene_locus related to this paper: thefu-1831 |
| Title : Mechanism-Based Design of Efficient PET Hydrolases - Wei_2022_ACS.Catal_12_3382 |
| Author(s) : Wei R , von Haugwitz G , Pfaff L , Mican J , Badenhorst CPS , Liu W , Weber G , Austin HP , Bednar D , Damborsky J , Bornscheuer UT |
| Ref : ACS Catal , 12 :3382 , 2022 |
| Abstract : Wei_2022_ACS.Catal_12_3382 |
| ESTHER : Wei_2022_ACS.Catal_12_3382 |
| PubMedSearch : Wei_2022_ACS.Catal_12_3382 |
| PubMedID: 35368328 |
| Title : Promiscuous Dehalogenase Activity of the Epoxide Hydrolase CorEH from Corynebacterium sp. C12 - Schuiten_2021_ACS.Catal_11_6113 |
| Author(s) : Schuiten ED , Badenhorst CPS , Palm GJ , Berndt L , Lammers M , Mican J , Bednar D , Damborsky J , Bornscheuer UT |
| Ref : ACS Catal , 11 :6113 , 2021 |
| Abstract : Schuiten_2021_ACS.Catal_11_6113 |
| ESTHER : Schuiten_2021_ACS.Catal_11_6113 |
| PubMedSearch : Schuiten_2021_ACS.Catal_11_6113 |
| PubMedID: |
| Gene_locus related to this paper: corsp-cEH |
| 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 : Vanacek_2021_bioRxiv__ |
| ESTHER : Vanacek_2021_bioRxiv__ |
| PubMedSearch : Vanacek_2021_bioRxiv__ |
| PubMedID: |
| 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 : Kokkonen_2021_RSC.Chem.Biol_2_645 |
| ESTHER : Kokkonen_2021_RSC.Chem.Biol_2_645 |
| PubMedSearch : Kokkonen_2021_RSC.Chem.Biol_2_645 |
| PubMedID: 34458806 |
| Gene_locus related to this paper: sphpi-linb |
| 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 : Schenkmayerova_2021_Nat.Commun_12_3616 |
| ESTHER : Schenkmayerova_2021_Nat.Commun_12_3616 |
| PubMedSearch : Schenkmayerova_2021_Nat.Commun_12_3616 |
| PubMedID: 34127663 |
| Gene_locus related to this paper: renre-luc |
| 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 : Markova_2021_ACS.Catal_11_12864 |
| ESTHER : Markova_2021_ACS.Catal_11_12864 |
| PubMedSearch : Markova_2021_ACS.Catal_11_12864 |
| PubMedID: |
| Gene_locus related to this paper: rhoso-halo1 |
| Title : Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst - Markova_2020_Chem.Sci_11_11162 |
| Author(s) : Markova K , Chmelova K , Marques SM , Carpentier P , Bednar D , Damborsky J , Marek M |
| Ref : Chem Sci , 11 :11162 , 2020 |
| Abstract : Markova_2020_Chem.Sci_11_11162 |
| ESTHER : Markova_2020_Chem.Sci_11_11162 |
| PubMedSearch : Markova_2020_Chem.Sci_11_11162 |
| PubMedID: 34094357 |
| Gene_locus related to this paper: rhoso-halo1 |
| 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 : Chmelova_2020_Appl.Environ.Microbiol_86_ |
| ESTHER : Chmelova_2020_Appl.Environ.Microbiol_86_ |
| PubMedSearch : Chmelova_2020_Appl.Environ.Microbiol_86_ |
| PubMedID: 32561584 |
| Gene_locus related to this paper: sacvd-DsvA |
| Title : Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics - Babkova_2020_Comput.Struct.Biotechnol.J_18_1497 |
| Author(s) : Babkova P , Dunajova Z , Chaloupkova R , Damborsky J , Bednar D , Marek M |
| Ref : Comput Struct Biotechnol J , 18 :1497 , 2020 |
| Abstract : Babkova_2020_Comput.Struct.Biotechnol.J_18_1497 |
| ESTHER : Babkova_2020_Comput.Struct.Biotechnol.J_18_1497 |
| PubMedSearch : Babkova_2020_Comput.Struct.Biotechnol.J_18_1497 |
| PubMedID: 32637047 |
| Gene_locus related to this paper: 9bact-AncHLD3 , 9bact-AncHLD2 , 9bact-AncHLD5 |
| 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 : Kokkonen_2020_Comput.Struct.Biotechnol.J_18_805 |
| ESTHER : Kokkonen_2020_Comput.Struct.Biotechnol.J_18_805 |
| 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 : Schenkmayerova_2020_Chemrxiv__ |
| ESTHER : Schenkmayerova_2020_Chemrxiv__ |
| PubMedSearch : Schenkmayerova_2020_Chemrxiv__ |
| PubMedID: |
| Gene_locus related to this paper: renre-luc |
| 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 : Hon_2020_Nucleic.Acids.Res__ |
| ESTHER : Hon_2020_Nucleic.Acids.Res__ |
| PubMedSearch : Hon_2020_Nucleic.Acids.Res__ |
| PubMedID: 32392342 |
| Title : Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17 - Chrast_2019_Microorganisms_7_ |
| Author(s) : Chrast L , Tratsiak K , Planas-Iglesias J , Daniel L , Prudnikova T , Brezovsky J , Bednar D , Kuta Smatanova I , Chaloupkova R , Damborsky J |
| Ref : Microorganisms , 7 : , 2019 |
| Abstract : Chrast_2019_Microorganisms_7_ |
| ESTHER : Chrast_2019_Microorganisms_7_ |
| PubMedSearch : Chrast_2019_Microorganisms_7_ |
| PubMedID: 31661858 |
| Gene_locus related to this paper: 9alte-a3jb27 |
| Title : Computational Study of Protein-Ligand Unbinding for Enzyme Engineering - Marques_2018_Front.Chem_6_650 |
| Author(s) : Marques SM , Bednar D , Damborsky J |
| Ref : Front Chem , 6 :650 , 2018 |
| Abstract : Marques_2018_Front.Chem_6_650 |
| ESTHER : Marques_2018_Front.Chem_6_650 |
| PubMedSearch : Marques_2018_Front.Chem_6_650 |
| PubMedID: 30671430 |
| 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 : Kokkonen_2018_J.Biol.Chem_293_11505 |
| ESTHER : Kokkonen_2018_J.Biol.Chem_293_11505 |
| PubMedSearch : Kokkonen_2018_J.Biol.Chem_293_11505 |
| PubMedID: 29858243 |
| Gene_locus related to this paper: xanau-halo1 |
| 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 : Liskova_2017_Angew.Chem.Int.Ed.Engl_56_4719 |
| ESTHER : Liskova_2017_Angew.Chem.Int.Ed.Engl_56_4719 |
| PubMedSearch : Liskova_2017_Angew.Chem.Int.Ed.Engl_56_4719 |
| PubMedID: 28334478 |
| Title : Site-specific analysis of protein hydration based on unnatural amino acid fluorescence - Amaro_2015_J.Am.Chem.Soc_137_4988 |
| Author(s) : Amaro M , Brezovsky J , Kovacova S , Sykora J , Bednar D , Nemec V , Liskova V , Kurumbang NP , Beerens K , Chaloupkova R , Paruch K , Hof M , Damborsky J |
| Ref : Journal of the American Chemical Society , 137 :4988 , 2015 |
| Abstract : Amaro_2015_J.Am.Chem.Soc_137_4988 |
| ESTHER : Amaro_2015_J.Am.Chem.Soc_137_4988 |
| PubMedSearch : Amaro_2015_J.Am.Chem.Soc_137_4988 |
| PubMedID: 25815779 |
| 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 : Bednar_2015_PLoS.Comput.Biol_11_e1004556 |
| ESTHER : Bednar_2015_PLoS.Comput.Biol_11_e1004556 |
| PubMedSearch : Bednar_2015_PLoS.Comput.Biol_11_e1004556 |
| PubMedID: 26529612 |
| Gene_locus related to this paper: rhoso-halo1 |
| Title : Balancing the stability-activity trade-off by fine-tuning dehalogenase access tunnels - Liskova_2015_ChemCatChem_7_648 |
| Author(s) : Liskova V , Bednar D , Prudnikova T , Rezacova P , Koudelakova T , Sebestova E , Kuta-Smatanova I , Brezovsky J , Chaloupkova R , Damborsky J |
| Ref : ChemCatChem , 7 :648 , 2015 |
| Abstract : Liskova_2015_ChemCatChem_7_648 |
| ESTHER : Liskova_2015_ChemCatChem_7_648 |
| PubMedSearch : Liskova_2015_ChemCatChem_7_648 |
| PubMedID: |
| Gene_locus related to this paper: rhoso-halo1 |