AIMC Topic: Enzyme Stability

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Role of electrostatics in cold adaptation: A comparative study of eury- and stenopsychrophilic triose phosphate isomerase.

Biochimica et biophysica acta. Proteins and proteomics Apr 11, 2025
Psychrophilic (cold-active) organisms have developed enzymes that facilitate sufficient metabolic activity at low temperatures to sustain life. This occurs through molecular adaptations that tend to increase protein flexibility at the expense of stab...
Triose-Phosphate Isomerase Static Electricity Adaptation, Physiological Enzyme Stability Cold Temperature Bacterial Proteins Kinetics
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Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis.

Journal of chemical theory and computation Mar 13, 2025
Protein evolution has shaped enzymes that maintain stability and function across diverse thermal environments. While sequence variation, thermal stability and conformational dynamics are known to influence an enzyme's thermal adaptation, how these fa...
Temperature Deep Learning Evolution, Molecular Protein Conformation Cytosol Malate Dehydrogenase Molecular Dynamics Simulation Enzyme Stability
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Cloning, Characterization, and Computer-Aided Evolution of a Thermostable Laccase of the DUF152 Family From Klebsiella michiganensis.

Proteins Feb 14, 2025
Bacterial laccases exhibit relatively high optimal reaction temperatures and possess a broad substrate spectrum, thereby expanding the range of potential applications for laccase enzymes. This study aims to investigate the molecular evolution of bact...
Klebsiella Animals Copper Molecular Docking Simulation Amino Acid Sequence Cloning, Molecular Binding Sites RNA, Ribosomal, 16S Mutagenesis, Site-Directed Enzyme Stability Laccase Bacterial Proteins
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Tailoring industrial enzymes for thermostability and activity evolution by the machine learning-based iCASE strategy.

Nature communications Jan 11, 2025
The pursuit of obtaining enzymes with high activity and stability remains a grail in enzyme evolution due to the stability-activity trade-off. Here, we develop an isothermal compressibility-assisted dynamic squeezing index perturbation engineering (i...
Protein Engineering Enzymes Machine Learning Enzyme Stability Directed Molecular Evolution Evolution, Molecular
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Precision Thermostability Predictions: Leveraging Machine Learning for Examining Laccases and Their Associated Genes.

International journal of molecular sciences Dec 4, 2024
Laccases, multi-copper oxidases, play pivotal roles in the oxidation of a variety of substrates, impacting numerous biological functions and industrial processes. However, their industrial adoption has been limited by challenges in thermostability. T...
Enzyme Stability Temperature Laccase Neural Networks, Computer Machine Learning
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Machine learning-guided multi-site combinatorial mutagenesis enhances the thermostability of pectin lyase.

International journal of biological macromolecules Aug 5, 2024
Enhancing the thermostability of enzymes is crucial for industrial applications. Methods such as directed evolution are often limited by the huge sequence space and combinatorial explosion, making it difficult to obtain optimal mutants. In recent yea...
Mutagenesis Mutagenesis, Site-Directed Polysaccharide-Lyases Mutation Bacillus licheniformis Molecular Dynamics Simulation Protein Engineering Enzyme Stability Machine Learning Temperature
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Enhancing Machine-Learning Prediction of Enzyme Catalytic Temperature Optima through Amino Acid Conservation Analysis.

International journal of molecular sciences Jun 6, 2024
Enzymes play a crucial role in various industrial production and pharmaceutical developments, serving as catalysts for numerous biochemical reactions. Determining the optimal catalytic temperature () of enzymes is crucial for optimizing reaction cond...
Machine Learning Conserved Sequence Algorithms Phosphoric Monoester Hydrolases Temperature Amino Acid Sequence Enzyme Stability Catalysis Amino Acids
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Improving the enzymatic activity and stability of N-carbamoyl hydrolase using deep learning approach.

Microbial cell factories Jun 4, 2024
BACKGROUND: Optically active D-amino acids are widely used as intermediates in the synthesis of antibiotics, insecticides, and peptide hormones. Currently, the two-enzyme cascade reaction is the most efficient way to produce D-amino acids using enzym...
Enzyme Stability Mutagenesis, Site-Directed Deep Learning
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MEnTaT: A machine-learning approach for the identification of mutations to increase protein stability.

Proceedings of the National Academy of Sciences of the United States of America Dec 1, 2023
Enhancing protein thermal stability is important for biomedical and industrial applications as well as in the research laboratory. Here, we describe a simple machine-learning method which identifies amino acid substitutions that contribute to thermal...
Proteins Mutation Amino Acid Sequence Machine Learning Protein Stability Enzyme Stability
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De novo design of luciferases using deep learning.

Nature Feb 22, 2023
De novo enzyme design has sought to introduce active sites and substrate-binding pockets that are predicted to catalyse a reaction of interest into geometrically compatible native scaffolds, but has been limited by a lack of suitable protein structur...
Luciferins Biocatalysis Catalytic Domain Hot Temperature Substrate Specificity Luminescence Deep Learning Enzyme Stability Luciferases Oxidation-Reduction
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