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 …

Dehalogenases: from improved performance to potential microbial dehalogenation applications

TF Ang, J Maiangwa, AB Salleh, YM Normi, TC Leow - Molecules, 2018 - mdpi.com
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 …

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 …

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 …

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 …

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 …

Advanced database mining of efficient haloalkane dehalogenases by sequence and structure bioinformatics and microfluidics

M Vasina, P Vanacek, J Hon, D Kovar, H Faldynova… - Chem Catalysis, 2022 - cell.com
Next-generation sequencing doubles genomic databases every 2.5 years. The
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 …

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 …

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 …