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Lista de obras de Jiri Damborsky

A Pseudomonas putida strain genetically engineered for 1,2,3-trichloropropane bioremediation.

artículo científico publicado en 2014

A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB.

artículo científico publicado en 2012

AggreProt: a web server for predicting and engineering aggregation prone regions in proteins

artículo científico publicado en 2024

An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation

artículo científico publicado en 2020

Analysis of the DNA-binding activity of p53 mutants using functional protein microarrays and its relationship to transcriptional activation.

artículo científico publicado en 2010

Analysis of transactivation capability and conformation of p53 temperature-dependent mutants and their reactivation by amifostine in yeast

artículo científico publicado en 2007

Are time-dependent fluorescence shifts at the tunnel mouth of haloalkane dehalogenase enzymes dependent on the choice of the chromophore?

artículo científico publicado en 2013

Binding of fatty acids to beta-cryptogein: quantitative structure-activity relationships and design of selective protein mutants.

artículo científico publicado en 2004

Biochemical Characterization of a Novel Haloalkane Dehalogenase from a Cold-Adapted Bacterium

artículo científico publicado el 11 de mayo de 2012

Biochemical characteristics of the novel haloalkane dehalogenase DatA, isolated from the plant pathogen Agrobacterium tumefaciens C58

artículo científico publicado en 2010

Biochemical characterization of broad-specificity enzymes using multivariate experimental design and a colorimetric microplate assay: characterization of the haloalkane dehalogenase mutants.

artículo científico publicado en 2001

Biochemical characterization of haloalkane dehalogenases DrbA and DmbC, Representatives of a Novel Subfamily.

artículo científico publicado en 2009

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures

artículo científico publicado en 2012

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.

artículo científico publicado en 2014

CalFitter: a web server for analysis of protein thermal denaturation data.

artículo científico publicado en 2018

Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling

artículo científico publicado en 2017

Cation-specific effects on enzymatic catalysis driven by interactions at the tunnel mouth

artículo científico publicado en 2013

Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport

artículo científico publicado en 2019

Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8.

artículo científico publicado en 2003

Cloning, biochemical properties, and distribution of mycobacterial haloalkane dehalogenases

artículo científico publicado en 2005

Comparative binding energy analysis of haloalkane dehalogenase substrates: modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations.

artículo científico publicado en 2003

Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.

artículo científico publicado en 2001

Comparison of the QSAR models for toxicity and biodegradability of anilines and phenols

artículo científico publicado en 1997

Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway

scientific article published on 11 November 2019

Computational site-directed mutagenesis of haloalkane dehalogenase in position 172.

artículo científico publicado en 1998

Computational tools for designing and engineering biocatalysts

artículo científico publicado en 2009

Computer-Assisted Engineering of Hyperstable Fibroblast Growth Factor 2.

artículo científico publicado en 2017

Computer-assisted engineering of the synthetic pathway for biodegradation of a toxic persistent pollutant.

artículo científico publicado en 2013

Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site

artículo científico publicado en 2018

Construction and Characterization of Histidine-Tagged Haloalkane Dehalogenase (LinB) of a New Substrate Class from a γ-Hexachlorocyclohexane-Degrading Bacterium, Sphingomonas paucimobilis UT26

artículo científico publicado en 1999

Construction of cryptogein mutants, a proteinaceous elicitor from Phytophthora, with altered abilities to induce a defense reaction in tobacco cells.

artículo científico publicado en 2005

Controlled Oil/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics

artículo científico publicado en 2019

Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5

scientific article published on 24 April 2019

Crystallization and crystallographic analysis of the Rhodococcus rhodochrous NCIMB 13064 DhaA mutant DhaA31 and its complex with 1,2,3-trichloropropane

artículo científico publicado en 2011

Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands.

artículo científico publicado en 2011

Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110

artículo científico publicado en 2007

Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31

artículo científico publicado en 2014

Crystallographic analysis of new psychrophilic haloalkane dehalogenases: DpcA from Psychrobacter cryohalolentis K5 and DmxA from Marinobacter sp. ELB17.

artículo científico publicado en 2013

Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst

artículo científico publicado en 2020

Degradation of beta-Hexachlorocyclohexane by Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26

artículo científico publicado en 2005

Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from gamma-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205.

artículo científico publicado en 2007

Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips

scientific article published on 23 September 2018

Determination of haloalkane dehalogenase activity by capillary zone electrophoresis

artículo científico publicado en 2000

Development of an enzymatic fiber-optic biosensor for detection of halogenated hydrocarbons

artículo científico publicado en 2010

Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear β-Haloalkanes: Open-Solvated versus Occluded-Desolvated Active Sites.

artículo científico publicado en 2017

Discovery of Novel Haloalkane Dehalogenase Inhibitors.

artículo científico publicado en 2016

DspA from Strongylocentrotus purpuratus: The first biochemically characterized haloalkane dehalogenase of non-microbial origin

artículo científico publicado el 11 de agosto de 2013

Effect of the carbon source on assessment of degrading bacteria with the spread-plating technique duringin situ bioremediation

artículo científico publicado en 2000

Effects of developmental nicotine exposure in rats on decision-making in adulthood.

artículo científico publicado en 2012

Elicitin–membrane interaction is driven by a positive charge on the protein surface: Role of Lys13 residue in lipids loading and resistance induction

artículo científico publicado en 2011

Engineering enzyme access tunnels

scientific article published on 23 April 2019

Engineering enzyme stability and resistance to an organic cosolvent by modification of residues in the access tunnel

artículo científico publicado en 2013

Engineering the protein dynamics of an ancestral luciferase

artículo científico publicado en 2021

Enzyme-Based Test Strips for Visual or Photographic Detection and Quantitation of Gaseous Sulfur Mustard

artículo científico publicado en 2016

EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities

artículo científico publicado en 2020

Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3) carrying a synthetic metabolic pathway

artículo científico publicado en 2015

Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents

artículo científico publicado en 2013

Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating.

artículo científico publicado en 2017

Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10.

artículo científico publicado en 2007

Expression of glycosylated haloalkane dehalogenase LinB in Pichia pastoris

artículo científico publicado en 2005

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants

artículo científico publicado en 2015

Fluorescence-based biosensor for monitoring of environmental pollutants: From concept to field application

artículo científico publicado en 2015

Fructose 1-phosphate is the one and only physiological effector of the Cra (FruR) regulator of Pseudomonas putida.

artículo científico publicado en 2014

Functional analysis of the aglycone-binding site of the maize beta-glucosidase Zm-p60.1.

artículo científico publicado en 2008

Gates of Enzymes

artículo científico publicado el 25 de abril de 2013

Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis

artículo científico publicado en 2002

Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates

artículo científico publicado en 2003

Haloalkane dehalogenases: biotechnological applications.

artículo científico

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information.

artículo científico publicado en 2018

Identification of Salmonella enterica serovar Typhimurium genes associated with growth suppression in stationary-phase nutrient broth cultures and in the chicken intestine

artículo científico publicado en 2002

Identification of the catalytic triad in the haloalkane dehalogenase from Sphingomonas paucimobilis UT26

artículo científico publicado en 1999

Immobilized Synthetic Pathway for Biodegradation of Toxic Recalcitrant Pollutant 1,2,3-Trichloropropane

artículo científico publicado en 2014

Impact of the access tunnel engineering on catalysis is strictly ligand-specific

artículo científico publicado en 2018

Instability restricts signaling of multiple fibroblast growth factors.

artículo científico publicado en 2015

Interaction of organic solvents with protein structures at protein-solvent interface

artículo científico publicado en 2012

Interfacing microwells with nanoliter compartments: a sampler generating high-resolution concentration gradients for quantitative biochemical analyses in droplets.

artículo científico publicado en 2014

Lincomycin biosynthesis involves a tyrosine hydroxylating heme protein of an unusual enzyme family

artículo científico publicado en 2013

LoopGrafter: a web tool for transplanting dynamical loops for protein engineering

artículo científico publicado en 2022

Maximizing the efficiency of multienzyme process by stoichiometry optimization.

artículo científico publicado en 2014

Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling.

artículo científico publicado en 2006

Mechanism-based discovery of novel substrates of haloalkane dehalogenases using in silico screening

artículo científico publicado en 2014

Metagenome-derived haloalkane dehalogenases with novel catalytic properties

artículo científico publicado en 2017

Microscopic monitoring provides information on structure and properties during biocatalyst immobilization

artículo científico publicado en 2014

Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel.

artículo científico publicado en 2003

Molecular Gating of an Engineered Enzyme Captured in Real Time

artículo científico publicado en 2018

Molecular characterization of the Thermomonospora curvata aglA gene encoding a thermotolerant alpha-1,4-glucosidase

artículo científico publicado en 2000

New Functional Handle for Use as a Self-Reporting Contrast and Delivery Agent in Nanomedicine

artículo científico publicado el 13 de junio de 2013

Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil.

artículo científico publicado en 2012

Organic co-solvents affect activity, stability and enantioselectivity of haloalkane dehalogenases

artículo científico publicado en 2013

PKD2 mutations in a Czech population with autosomal dominant polycystic kidney disease

artículo científico publicado en 2004

Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations.

artículo científico publicado en 2009

Phylogenetic analysis of haloalkane dehalogenases

artículo científico publicado en 2007

Physiological and proteomic approaches to evaluate the role of sterol binding in elicitin-induced resistance.

artículo científico publicado en 2012

Plectin repeats and modules: strategic cysteines and their presumed impact on cytolinker functions

artículo científico publicado en 2001

PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations

artículo científico publicado en 2014

Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.

artículo científico publicado en 2005

Quantitative structure-function and structure-stability relationships of purposely modified proteins

artículo científico publicado en 1998

Quantitative structure–activity relationships for toxicity and genotoxicity of halogenated aliphatic compounds: Wing spot test of Drosophila melanogaster

artículo científico publicado en 2007

Rad52 SUMOylation affects the efficiency of the DNA repair

artículo científico publicado en 2010

Reaction mechanism and stereochemistry of gamma-hexachlorocyclohexane dehydrochlorinase LinA.

artículo científico publicado en 2000

Reconstruction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB

scientific journal article

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

artículo científico publicado en 2009

Release of halide ions from the buried active site of the haloalkane dehalogenase LinB revealed by stopped-flow fluorescence analysis and free energy calculations

artículo científico publicado en 2013

Repositioning the catalytic triad aspartic acid of haloalkane dehalogenase: effects on stability, kinetics, and structure.

artículo científico publicado en 1997

Retron reverse transcriptase rrtT is ubiquitous in strains of Salmonella enterica serovar Typhimurium

artículo científico publicado en 2003

Role of SdiA in Salmonella enterica serovar Typhimurium physiology and virulence

artículo científico publicado en 2002

Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods

artículo científico publicado en 2008

Site-Specific Analysis of Protein Hydration Based on Unnatural Amino Acid Fluorescence

artículo científico publicado en 2015

Software tools for identification, visualization and analysis of protein tunnels and channels.

artículo científico

Sphingobium baderi sp. nov., isolated from a hexachlorocyclohexane dump site.

artículo científico publicado en 2012

Sphingobium czechense sp. nov., isolated from a hexachlorocyclohexane dump site.

artículo científico publicado en 2012

Stability of Complexes of Aromatic Amides with Bromide Anion:  Quantitative Structure−Property Relationships

article

Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics

artículo científico publicado en 2007

Stepwise enhancement of catalytic performance of haloalkane dehalogenase LinB towards β-hexachlorocyclohexane.

artículo científico publicado en 2014

Stereoselectivity and conformational stability of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110: the effect of pH and temperature

artículo científico publicado el 27 de junio de 2011

Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites

artículo científico publicado en 2014

Structure–specificity relationships for haloalkane dehalogenases

artículo científico publicado el 1 de diciembre de 2001

Substrate Anchoring and Flexibility Reduction in CYP153A M.aq Leads to Highly Improved Efficiency toward Octanoic Acid

Substrate inhibition by the blockage of product release and its control by tunnel engineering

artículo científico publicado en 2021

Substrate specificity of haloalkane dehalogenases.

artículo científico publicado en 2011

Systems biology at work

artículo científico publicado en 2010

TRITON: in silico construction of protein mutants and prediction of their activities

artículo científico publicado en 2000

The PCNA interaction protein box sequence in Rad54 is an integral part of its ATPase domain and is required for efficient DNA repair and recombination

artículo científico publicado en 2013

The effect of a unique halide-stabilizing residue on the catalytic properties of haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58.

artículo científico publicado en 2013

The identification of catalytic pentad in the haloalkane dehalogenase DhmA from Mycobacterium avium N85: reaction mechanism and molecular evolution

artículo científico publicado en 2006

The new platinum-based anticancer agent LA-12 induces retinol binding protein 4 in vivo

artículo científico publicado en 2011

Three-block bi-focal PLS (3BIF-PLS) and its application in QSAR

artículo científico publicado en 2004

Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, encode haloalkane dehalogenases with novel structures and substrate specificities

artículo científico publicado en 2005

Varenicline and nicotine enhance GABAergic synaptic transmission in rat CA1 hippocampal and medial septum/diagonal band neurons.

artículo científico publicado en 2013

Weak Activity of Haloalkane Dehalogenase LinB with 1,2,3-Trichloropropane Revealed by X-Ray Crystallography and Microcalorimetry

artículo científico publicado en 2007