Bednar D

References (30)

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 : 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 :
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
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PubMedSearch : Snajdarova_2023_Acta.Crystallogr.D.Struct.Biol__
PubMedID: 37860958

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 : 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
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PubMedSearch : Schenkmayerova_2023_Nat.Catal_6_23
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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
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PubMedSearch : Vasina_2022_Adv.Drug.Deliv.Rev_183_114143
PubMedID: 35167900

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 :
PubMedSearch : Wei_2022_ACS.Catal_12_3382
PubMedID: 35368328

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 :
PubMedSearch : Pfaff_2022_ACS.Catalysis_12_9790
PubMedID: 35966606
Gene_locus related to this paper: 9firm-PHL7

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 : 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 :
PubMedSearch : von Haugwitz_2022_ACS.Catal_12_15259
PubMedID: 36570084
Gene_locus related to this paper: thefu-1831

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 :
PubMedSearch : Planas-Iglesias_2022_Nucleic.Acids.Res__
PubMedID: 35438789

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 :
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 :
PubMedSearch : Vanacek_2021_bioRxiv__
PubMedID:

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 : Functional and Mechanistic Characterization of an Enzyme Family Combining Bioinformatics and High-Throughput Microfluidics - Vasina_2021_ResearchSquare__
Author(s) : Vasina M , Vanacek P , Hon J , Kovar D , Faldynova H , Kunka A , Badenhorst C , Buryska T , Mazurenko S , Bednar D , Stavros S , Bornscheuer U , deMello A , Damborsky J , Prokop Z
Ref : ResearchSquare , : , 2021
Abstract :
PubMedSearch : Vasina_2021_ResearchSquare__
PubMedID:
Gene_locus related to this paper: brabe-DbbA , strpu-DspB , sacko-DskA , capte-r7umg5 , shehh-b0tml1 , 9gamm-a6faz5 , 9arch-a0a1q9njs0 , 9noca-DrxA , sphsx-DspxA , 9caul-a0a1e4h0f2 , 9prot-a0a0f2rdt1 , 9noca-k0eup9 , triha-a0a0f9y4y5 , 9rhob-a0a0n7m2p6 , triha-a0a0f9x982 , rhile-DrgA , 9sphn-a0a2d6h3s9 , ensad-DeaA , 9delt-a0a0m4d813 , 9actn-a0a1g6re71 , 9actn-g7h6v4 , 9eury-j3a357 , 9alte-k7apw6 , 9sphn-a3wc35 , 9actn-a0a0c1uk61 , 9pseu-DathA , 9rhob-a0a2t6cbq8 , amys7-DaxA , lenae-DlaA , 9rhob-DpxA , 9actn-a0a1s1sm32 , 9gamm-DtacA , 9eury-a0a1i6hey7 , 9eury-m0il93 , 9actn-l7fa57 , chlad-b8g485 , 9bact-q6sht4 , 9gamm-a0z6e4 , 9rhob-a3sf89 , desps-q6ajw5 , mycmm-b2hjb4 , mycua-a0pum4 , phopr-Q93CH1 , mycav-t2gun3

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 : 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 : 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 :
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 :
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 :
PubMedSearch : Babkova_2020_Comput.Struct.Biotechnol.J_18_1497
PubMedID: 32637047
Gene_locus related to this paper: 9bact-AncHLD3 , 9bact-AncHLD2 , 9bact-AncHLD5

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 : 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 : 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 :
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 :
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 :
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 :
PubMedSearch : Liskova_2017_Angew.Chem.Int.Ed.Engl_56_4719
PubMedID: 28334478

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 : 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 :
PubMedSearch : Liskova_2015_ChemCatChem_7_648
PubMedID:
Gene_locus related to this paper: rhoso-halo1

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 :
PubMedSearch : Amaro_2015_J.Am.Chem.Soc_137_4988
PubMedID: 25815779