Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015 - pubs.rsc.org
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

Haloalkane dehalogenases: biotechnological applications

T Koudelakova, S Bidmanova, P Dvorak… - Biotechnology …, 2013 - Wiley Online Library
Abstract Haloalkane dehalogenases (EC 3.8. 1.5, HLDs) are α/β‐hydrolases which act to
cleave carbon‐halogen bonds. Due to their unique catalytic mechanism, broad substrate …

Modeling enzymatic enantioselectivity using quantum chemical methodology

X Sheng, M Kazemi, F Planas, F Himo - ACS Catalysis, 2020 - ACS Publications
The computational study of enantioselective reactions is a challenging task that requires
high accuracy, as very small energy differences have to be reproduced. Quantum chemical …

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 …

Computer-aided understanding and engineering of enzymatic selectivity

L Wu, L Qin, Y Nie, Y Xu, YL Zhao - Biotechnology Advances, 2022 - Elsevier
Abstract Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric
synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally …

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 …

Enzyme tunnels and gates as relevant targets in drug design

SM Marques, L Daniel, T Buryska… - Medicinal Research …, 2017 - Wiley Online Library
Many enzymes contain tunnels and gates that are essential to their function. Gates
reversibly switch between open and closed conformations and thereby control the traffic of …

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 …

Phylogenetic analysis of haloalkane dehalogenases

E Chovancová, J Kosinski, JM Bujnicki… - PROTEINS …, 2007 - Wiley Online Library
Haloalkane dehalogenases (HLDs) are enzymes that catalyze the cleavage of carbon–
halogen bonds by a hydrolytic mechanism. Although comparative biochemical analyses …

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 …