Enzyme Catalysis and Immobilization

Phage-assisted continuous evolution of enzymes for noncanonical tyrosine biosynthesis

This study uses phage-assisted evolution to improve enzymes for noncanonical tyrosine biosynthesis in E. coli, increasing production of specific derivatives.

Direct measurement of PET hydrolase interfacial kinetics reveals catalysis-independent surface remodelling

This paper directly measures PET hydrolase interfacial kinetics on solid polymer surfaces, revealing catalysis-independent surface remodelling during enzyme binding.

Ancestors of Arylmalonate Decarboxylase show increased Activity, Stability and Stereoselectivity

Ancestral sequence reconstruction of a bacterial decarboxylase gave enzymes with up to 294-fold longer half-life at 45 °C, higher activity, and 99.7% ee on a vinyl malonate substrate.

Learning protein function through autonomous experimental interaction

This paper demonstrates an AI system that autonomously interacts with biological systems to discover new protein functions through continuous experimental feedback.

Deciphering the evolutionary origin of the stereoselectivity of short-chain dehydrogenases in the oxidation of the monoterpenol 1-borneol

The paper investigates how natural evolution creates enantioselectivity in plant borneol dehydrogenases through ancestral sequence reconstruction and simulations.

Data-efficient distal engineering of fluorinase using zero-shot models

This study uses zero-shot models to predict activity-enhancing mutations in fluorinase, leading to improved catalytic efficiency and stability in engineered variants.

Combining Machine Learning and Directed Evolution for Optimization of a Monooxygenase

This study combines machine learning and directed evolution to optimize the monooxygenase HpaBC for improved L-Dopa production activity.

Gram-scale one-pot enzymatic synthesis of CDP-ribitol by a designed bifunctional fusion enzyme

This paper describes a one-pot enzymatic method to produce CDP-ribitol at gram scale using a bifunctional fusion enzyme, achieving high yield and atom economy.

Conformation of the Catalytic Lysine is a Key Determinant of 2-Deoxyribose-5-phosphate Aldolase (DERA) Stereoselectivity

This study identifies the conformation of catalytic lysine as a key determinant of DERA stereoselectivity through structural and biochemical analyses.

Efficient and low-impact enzymatic glycosylation with robust sucrose synthase variants

The paper reports engineered sucrose synthase variants with enhanced activity and stability for efficient glycosylation, achieving high conversion yields and reduced environmental impact.

Machine Learning-Assisted Evolution of Broadly Functional Enzyme Libraries

This paper uses machine learning to guide the creation of enzyme libraries with broader catalytic activity, showing improved performance across multiple reactions.

Combining Stability-Centered Atomistic Design with Machine Learning for Targeted Enzyme Optimization

This paper introduces MLEE, a machine learning-assisted enzyme engineering workflow that improves hit rates for high-fitness enzyme variants compared to traditional methods.

Isosteric Engineering of Enzymes: Overcoming Activity-Stability Trade-offs by Site-Selective CH -> N Substitutions

This paper introduces azatryptophans to engineer enzymes with enhanced activity and preserved stability, demonstrating their effectiveness in PETase optimization.

Computer-guided enzyme engineering of PET hydrolase mutants towards improved PET affinity

The paper identifies a mutation that improves PET degradation efficiency in enzyme variants through computational design and experimental validation.

Function-guided design of active enzymes

The paper presents a framework for designing active enzymes from functional descriptions, achieving high catalytic activity in synthesized designs.

Acquiring Improved Protein Variants With Probabilistic Preferential Learning

This paper introduces a probabilistic preferential learning model for variant effect prediction, showing that uncertainty-aware strategies improve acquisition performance on single-mutation datasets.

Integrating Machine-learning and Ultra-high-throughput Screening for Enzyme spaces exploration

This paper introduces IMUSE, a method combining machine learning and ultra-high-throughput screening to explore enzyme spaces, identifying mutations that significantly improve enzyme activity.

Multi-lab, Multi-enzyme Study Demonstrates the Versatility of Bacterial Microcompartment Shells as a Modular Platform for Confined Biocatalysis

This paper demonstrates a modular platform for enzyme encapsulation using bacterial microcompartment shells, showing successful activity and stability for multiple enzymes.

Deep learning-guided design of hydrolases for crystalline PET depolymerization

This paper designs an engineered PET hydrolase, VenusPETase, using deep learning to enhance PET depolymerization efficiency and thermostability, achieving high TPA yields and complete degradation of commercial PET.

Data-Efficient Exploration of Enzyme Function Using Family-Specific Machine Learning

The paper combines experimental screening with sequence-based deep learning to efficiently discover high-performing enzyme variants.

Identifying a cooperative catalytic network for efficient esterase catalysis

The paper redesigns an ancestral enzyme's active site to enhance esterase activity through cooperative residue substitutions and structural changes.

Supercharged binding modules can modulate engineered poly(ethylene terephthalate) hydrolase thermostability and functional persistence

This study shows that modifying the charge of PET-binding modules can enhance the thermostability and functional persistence of PET hydrolases.

AI-assisted improvement of Aspergillus oryzae β-galactosidase using an Ensemble of Protein Language Models

This paper uses an ensemble of protein language models to identify beneficial mutations in Aspergillus oryzae β-galactosidase, improving catalytic efficiency and thermostability without supervised training.

Genuine Directed Evolution In Test Tube (GENie)

The paper introduces a test-tube directed evolution platform that enables high-throughput screening without specialized equipment, achieving significant enzyme improvement in catalytic efficiency.

Encapsulation in a bacterial microcompartment shell improves thermal stability of a glycolytic enzyme

This study shows that encapsulating the enzyme TPI in HO BMC shells improves its thermal stability up to 62°C.

Enzymatic bromination of native peptides for late-stage structural diversification via Suzuki-Miyaura coupling

This study demonstrates the use of engineered halogenase RebH variants to brominate peptides, enabling Suzuki-Miyaura coupling for functional group installation and biological activity tuning.

Hierarchically engineered multi-enzyme nanoreactors for in vitro drug biosynthesis and pathway transplantation into cells

This paper demonstrates the use of hierarchically etched MIL-101 nanoreactors to encapsulate and deliver a multi-enzyme pathway for in vitro drug biosynthesis and intracellular function.

Hydrophobic tuning with non-canonical amino acids in a copper metalloenzyme

This study introduces a method to engineer hydrophobicity in a bacterial laccase using non-canonical amino acids, resulting in improved catalytic activity.

Multi-objective Engineering of Trimethylamine Monooxygenase for Improved Thermostability and Cofactor Use

This paper improves an enzyme's thermostability and cofactor compatibility through multi-objective engineering, achieving variants with better heat resistance and higher cofactor activity retention.

Semi-rational Engineering of Terminal Deoxynucleotidyl Transferase for High-efficiency Enzymatic de Novo DNA Synthesis

This paper engineers terminal deoxynucleotidyl transferase (TdT) to improve enzymatic DNA synthesis efficiency and scalability.