Enzyme Catalysis and Immobilization

Molecular trick to reverse SN2 mechanism in hydrolytic enzyme

This paper shows that replacing histidine with phenylalanine in haloalkane dehalogenase reverses the SN2 mechanism by remodeling the active site, enabling reversible reactions for sustainable transhalogenation.

Sequence-Based Generative AI-Guided Design of Versatile Tryptophan Synthases

This paper uses a generative AI model to design novel tryptophan synthase variants with enhanced catalytic activity and substrate promiscuity, outperforming natural and optimized versions.

Development of a highly active engineered PETase enzyme for polyester degradation

This paper develops an engineered PETase enzyme, DRK3, with improved thermal stability and PET degradation efficiency compared to existing enzymes.

A Sequence Motif Enables Widespread Use of Non-Canonical Redox Cofactors in Natural Enzymes

The paper identifies a conserved sequence motif that enables natural enzymes to use non-canonical redox cofactors, demonstrating high activity with NMN+ and other synthetic cofactors.

Mechanism-Guided Engineering of Fluorinase Unlocks EfficientNucleophilic Biofluorination

This paper enhances fluorinase catalytic efficiency by engineering mutants and optimizing reaction conditions, achieving a 60-fold increase in turnover rate.

A Mechanistic Understanding of the Activity-Stability Trade-off in PETase

This study investigates the activity-stability trade-off in PETase using simulations and experiments, revealing how reshaping loop dynamics can enhance both stability and activity.

Engineering fluoroacetate dehalogenase by growth-based selections to degrade non-natural organofluorides

This study engineers fluoroacetate dehalogenase (FAcD) variants to degrade non-natural organofluorides using growth-based selections, identifying improved activities and an inhibition pathway.

A computationally designed panel of diverse and selective peroxygenases for terpene oxyfunctionalization

The paper designs a panel of selective peroxygenases for terpene oxyfunctionalization using computational methods, resulting in improved enzymatic functions and new products.

Decoding Substrate Specificity in a Promiscuous Biocatalyst by Enzyme Proximity Sequencing

The paper uses enzyme proximity sequencing to map how mutations affect substrate specificity of DAOx, identifying key positions and combinations that enhance selectivity.

Continuous Directed Evolution of a Plant Histidinol Dehydrogenase to Extend Lifespan

This study uses directed evolution to extend the lifespan of an Arabidopsis enzyme by increasing its abundance and improving its resistance to a toxic intermediate.

A high sensitivity strategy to screen NAD(P)H-dependent oxidoreductase activity by coupled enzyme cascade

This paper introduces a fluorescence-based enzyme cascade assay to detect NAD(P)H-dependent oxidoreductase activity with significantly higher sensitivity than traditional absorbance methods.

Identification and characterization of substrate- and product-selective nylon hydrolases

The paper identifies and characterizes diverse nylon hydrolases, showing that 40% of tested enzymes have significant activity, with some showing substrate selectivity for Nylon 6,6 over Nylon 6.

KnowVolution of an efficient polyamidase through molecular dynamics simulations of incrementally docked oligomeric substrates

This paper evolves a polyamidase through molecular dynamics simulations to improve its activity and stability for polyamide hydrolysis, but depolymerization remains limited.

Mapping Selective Oxidations of Unspecific Peroxygenases

The paper maps the substrate preferences and selectivity of 15 UPOs using 16 substrates, revealing high chemo- and regioselectivity and turnover numbers.

Enzymatic Glycosylation of Anthranilates for Enhanced Functionality

This paper develops an enzymatic method to glycosylate anthranilates, producing MANT-N-glucose with improved microbial production and bird repellent efficacy.

Structural insights and rational design of Pseudomonas putida KT2440 Omega transaminases for enhanced biotransformation of (R)-Phenylacetylcarbinol to (1R, 2S)-Norephedrine

This study structures and engineers Omega transaminases from Pseudomonas putida to improve their efficiency in converting (R)-Phenylacetylcarbinol to (1R, 2S)-Norephedrine.

Ancestral reconstruction of polyethylene terephthalate degrading cutinases reveals a rugged and unexplored sequence-fitness landscape

This study uses ancestral sequence reconstruction to explore PET-degrading cutinase sequence space, revealing diverse evolutionary pathways and the effectiveness of LASE in mapping fitness landscapes.

AI.zymes - A modular platform for evolutionary enzyme design

AI.zymes improves enzyme design by integrating multiple algorithms in an evolutionary framework, enhancing catalytic activity through iterative selection and design.

Extraordinary activation of CALB by alkylammonium ions: a new paradigm for activity enhancement of enzymes

This paper identifies alkylammonium ions as a new class of enzyme activators that significantly enhance CALB activity and stability through specific binding sites.

Machine learning-assisted enzyme engineering through ultra-high throughput sorting and large-scale sequence-function data generation

This paper introduces PUSDA, a framework combining ultra-high throughput sorting and NGS to generate large-scale sequence-function data, enabling ML-driven enzyme engineering with improved efficiency and productivity.

Growth-coupled continuous directed evolution by MutaT7 enables efficient and automated enzyme engineering

This paper introduces a continuous directed evolution method called GCCDE that automates enzyme engineering by linking enzyme activity to bacterial growth, demonstrating its effectiveness in improving CelB's low-temperature activity.

Engineered Oxalate decarboxylase boosts activity and stability for biological applications

This study engineers Oxalate decarboxylase to improve its activity and stability for medical applications in hyperoxaluria treatment.

SMART platform for enzyme engineering: A novel single-molecule display approach for evolution and functional studies of D-amino acid oxidase

The paper introduces SMART, a single-molecule display platform for enzyme engineering, and demonstrates its application in evolving D-amino acid oxidase with improved substrate specificity.

Engineering of Transmembrane Alkane Monooxygenases to Improve a Key Reaction Step in the Synthesis of Polymer Precursor Tulipalin A

The paper engineers transmembrane alkane monooxygenases to improve terminal hydroxylation of isoprenyl acetate, enabling fermentative production of tulipalin A from renewable resources.

Complete enzymatic depolymerization of polyethylene terephthalate (PET) plastic using a Saccharomyces cerevisiae-based whole-cell biocatalyst

This paper develops a Saccharomyces cerevisiae-based whole-cell biocatalyst that completely depolymerizes PET plastic using a multi-enzyme cluster, achieving 4.9 mM TPA in seven days.

De Novo Negatively Charged Binders Targeting MMLVRT Nucleic Acid Binding Sites Overcome Stability-Activity Trade-offs

This paper designs negatively charged binders that enhance the stability of MMLV RT without affecting its activity, overcoming stability-activity trade-offs.

Engineering of highly active and diverse nuclease enzymes by combining machine learning and ultra-high-throughput screening

This study combines machine learning and high-throughput screening to design improved nuclease enzymes, finding a more effective variant than standard directed evolution methods.

Hyperporous encapsulation of microbes for whole cell biocatalysis and biomanufacturing

This paper develops a hyper-porous hydrogel encapsulation method for microbial cells, demonstrating improved biocatalytic efficiency in co-culture fermentation.

A Generalized Platform for Artificial Intelligence-powered Autonomous Protein Engineering

This paper introduces an AI-powered platform for autonomous protein engineering that uses machine learning and biofoundry automation to rapidly improve protein function without human intervention.

Evolving a High-Performance Terminal Deoxynucleotidyl Transferase for Enzymatic DNA Synthesis

This paper evolves a terminal deoxynucleotidyl transferase for enzymatic DNA synthesis using modified substrates, showing improved activity, template promiscuity, and thermostability.