The challenge of predicting distal active site mutations in computational enzyme design

S Osuna - Wiley Interdisciplinary Reviews: Computational …, 2021‏ - Wiley Online Library
Many computational enzyme design approaches have been developed in recent years that
focus on a reduced set of key enzymatic features. Initial protocols mostly focused on the …

Applications and advances of metabolite biosensors for metabolic engineering

D Liu, T Evans, F Zhang - Metabolic engineering, 2015‏ - Elsevier
Quantification and regulation of pathway metabolites is crucial for optimization of microbial
production bioprocesses. Genetically encoded biosensors provide the means to couple …

From directed evolution to computational enzyme engineering—a review

R Chowdhury, CD Maranas - AIChE Journal, 2020‏ - Wiley Online Library
Nature relies on a wide range of enzymes with specific biocatalytic roles to carry out much of
the chemistry needed to sustain life. Enzymes catalyze the interconversion of a vast array of …

Enantioselective enzymes by computational design and in silico screening

HJ Wijma, RJ Floor, S Bjelic, SJ Marrink… - Angewandte Chemie …, 2015‏ - Wiley Online Library
Computational enzyme design holds great promise for providing new biocatalysts for
synthetic chemistry. A strategy to design small mutant libraries of complementary …

Computational tools for the evaluation of laboratory-engineered biocatalysts

A Romero-Rivera, M Garcia-Borràs… - Chemical …, 2017‏ - pubs.rsc.org
Biocatalysis is based on the application of natural catalysts for new purposes, for which
enzymes were not designed. Although the first examples of biocatalysis were reported more …

Computational redesign of acyl-ACP thioesterase with improved selectivity toward medium-chain-length fatty acids

MJ Grisewood, NJ Hernández-Lozada, JB Thoden… - ACS …, 2017‏ - ACS Publications
Enzyme and metabolic engineering offer the potential to develop biocatalysts for converting
natural resources to a wide range of chemicals. To broaden the scope of potential products …

Going beyond the local catalytic activity space of chitinase using a simulation-based iterative saturation mutagenesis strategy

J Li, S Wang, C Liu, Y Li, Y Wei, G Fu, P Liu, H Ma… - ACS …, 2022‏ - ACS Publications
Many advances in modifying enzyme properties have been made based on the computation
of stable transition states and experimental directed evolution. However, there are still great …

Rational enzyme engineering through biophysical and biochemical modeling

S Acebes, E Fernandez-Fueyo, E Monza… - ACS …, 2016‏ - ACS Publications
Due to its importance in the pharmaceutical industry, ligand dynamic simulations have
experienced a great expansion. Using all-atom models and cutting-edge hardware, one can …

The iterative protein redesign and optimization (IPRO) suite of programs

RJ Pantazes, MJ Grisewood, T Li… - Journal of …, 2015‏ - Wiley Online Library
Proteins are an important class of biomolecules with applications spanning across
biotechnology and medicine. In many cases, native proteins must be redesigned to improve …

Inverting the enantiopreference of nitrilase‐catalyzed desymmetric hydrolysis of prochiral dinitriles by resha** the binding pocket with a mirror‐image strategy

S Yu, J Li, P Yao, J Feng, Y Cui, J Li… - Angewandte Chemie …, 2021‏ - Wiley Online Library
A mirror‐image strategy, that is, symmetry analysis of the substrate‐binding pocket, was
applied to identify two key amino acid residues W170 and V198 that possibly modulate the …