Insertions and deletions (indels): a missing piece of the protein engineering jigsaw
CM Miton, N Tokuriki - Biochemistry, 2022 - ACS Publications
Over the years, protein engineers have studied nature and borrowed its tricks to accelerate
protein evolution in the test tube. While there have been considerable advances, our ability …
protein evolution in the test tube. While there have been considerable advances, our ability …
Dehalogenases: from improved performance to potential microbial dehalogenation applications
The variety of halogenated substances and their derivatives widely used as pesticides,
herbicides and other industrial products is of great concern due to the hazardous nature of …
herbicides and other industrial products is of great concern due to the hazardous nature of …
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate
M Pavlova, M Klvana, Z Prokop, R Chaloupkova… - Nature chemical …, 2009 - nature.com
Engineering enzymes to degrade anthropogenic compounds efficiently is challenging. We
obtained Rhodococcus rhodochrous haloalkane dehalogenase mutants with up to 32-fold …
obtained Rhodococcus rhodochrous haloalkane dehalogenase mutants with up to 32-fold …
Exploration of enzyme diversity by integrating bioinformatics with expression analysis and biochemical characterization
P Vanacek, E Sebestova, P Babkova, S Bidmanova… - Acs …, 2018 - ACS Publications
Millions of protein sequences are being discovered at an incredible pace, representing an
inexhaustible source of biocatalysts. Here, we describe an integrated system for automated …
inexhaustible source of biocatalysts. Here, we describe an integrated system for automated …
Substrate specificity of haloalkane dehalogenases
T Koudelakova, E Chovancova, J Brezovsky… - Biochemical …, 2011 - portlandpress.com
An enzyme's substrate specificity is one of its most important characteristics. The quantitative
comparison of broad-specificity enzymes requires the selection of a homogenous set of …
comparison of broad-specificity enzymes requires the selection of a homogenous set of …
Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics …
M Klvana, M Pavlova, T Koudelakova… - Journal of molecular …, 2009 - Elsevier
Eight mutants of the DhaA haloalkane dehalogenase carrying mutations at the residues
lining two tunnels, previously observed by protein X-ray crystallography, were constructed …
lining two tunnels, previously observed by protein X-ray crystallography, were constructed …
Advanced database mining of efficient haloalkane dehalogenases by sequence and structure bioinformatics and microfluidics
Next-generation sequencing doubles genomic databases every 2.5 years. The
accumulation of sequence data provides a unique opportunity to identify interesting …
accumulation of sequence data provides a unique opportunity to identify interesting …
Ancestral haloalkane dehalogenases show robustness and unique substrate specificity
P Babkova, E Sebestova, J Brezovsky… - …, 2017 - Wiley Online Library
Ancestral sequence reconstruction (ASR) represents a powerful approach for empirical
testing structure‐function relationships of diverse proteins. We employed ASR to predict …
testing structure‐function relationships of diverse proteins. We employed ASR to predict …
Light-emitting dehalogenases: reconstruction of multifunctional biocatalysts
R Chaloupkova, V Liskova, M Toul, K Markova… - ACS …, 2019 - ACS Publications
To obtain structural insights into the emergence of biological functions from catalytically
promiscuous enzymes, we reconstructed an ancestor of catalytically distinct, but …
promiscuous enzymes, we reconstructed an ancestor of catalytically distinct, but …
Properties and biotechnological applications of natural and engineered haloalkane dehalogenases
Y Nagata, Y Ohtsubo, M Tsuda - Applied microbiology and biotechnology, 2015 - Springer
Haloalkane dehalogenases (HLDs) convert halogenated compounds to corresponding
alcohols, halides, and protons. They belong to α/β-hydrolases, and their principal catalytic …
alcohols, halides, and protons. They belong to α/β-hydrolases, and their principal catalytic …