AIMC Topic: Mutagenesis, Site-Directed

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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...
Animals Molecular Docking Simulation RNA, Ribosomal, 16S Bacterial Proteins Enzyme Stability Klebsiella Binding Sites Mutagenesis, Site-Directed Copper Amino Acid Sequence Laccase Cloning, Molecular
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Computational approaches for decoding structure-saltiness enhancement and aroma perception mechanisms of odorants: From machine learning to molecular simulation.

Food research international (Ottawa, Ont.) Jan 7, 2025
The unclear relationship between structure and saltiness enhancement limits the development and application of savory odorants. The structure characteristic-saltiness enhancement perception (SEP) mechanisms of savory odorants were investigated by mac...
Hydrogen Bonding Mutagenesis, Site-Directed Receptors, Odorant Humans Odorants Machine Learning Hydrophobic and Hydrophilic Interactions Molecular Docking Simulation Sodium Chloride Smell
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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...
Machine Learning Temperature Mutagenesis Bacillus licheniformis Mutagenesis, Site-Directed Mutation Protein Engineering Molecular Dynamics Simulation Polysaccharide-Lyases Enzyme Stability
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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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Machine Learning Assisted Simultaneous Structural Profiling of Differently Charged Proteins in a Porin A (MspA) Electroosmotic Trap.

Journal of the American Chemical Society Jan 7, 2022
The nanopore is emerging as a means of single-molecule protein sensing. However, proteins demonstrate different charge properties, which complicates the design of a sensor that can achieve simultaneous sensing of differently charged proteins. In this...
Porins Mutagenesis, Site-Directed Mycobacterium smegmatis Muramidase Lactalbumin Lactoglobulins Whey Proteins Electroosmosis Nanopores Myoglobin Machine Learning Calcium
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Enhancement of protein thermostability by three consecutive mutations using loop-walking method and machine learning.

Scientific reports Jun 4, 2021
We developed a method to improve protein thermostability, "loop-walking method". Three consecutive positions in 12 loops of Burkholderia cepacia lipase were subjected to random mutagenesis to make 12 libraries. Screening allowed us to identify L7 as ...
Mutagenesis Hydrolases Mutagenesis, Site-Directed Protein Engineering Burkholderia cepacia Lipase Polymerase Chain Reaction Molecular Conformation Machine Learning Hot Temperature Computational Biology Molecular Dynamics Simulation Escherichia coli Enzyme Stability Proteins Plasmids Mutation Kinetics
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Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning.

Nature biomedical engineering Apr 15, 2021
The optimization of therapeutic antibodies is time-intensive and resource-demanding, largely because of the low-throughput screening of full-length antibodies (approximately 1 × 10 variants) expressed in mammalian cells, which typically results in fe...
Humans Animals Deep Learning Protein Binding CRISPR-Cas Systems Amino Acid Sequence Antibody Specificity Sequence Analysis, Protein Recombinational DNA Repair Hybridomas Receptor, ErbB-2 Mutagenesis, Site-Directed Trastuzumab Protein Engineering Antibody Affinity Antigens
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Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning.

Journal of the American Chemical Society Mar 8, 2021
Macrocycles, including macrocyclic peptides, have shown promise for targeting challenging protein-protein interactions (PPIs). One PPI of high interest is between Kelch-like ECH-Associated Protein-1 (KEAP1) and Nuclear Factor (Erythroid-derived 2)-li...
Recombinant Proteins Structure-Activity Relationship Crystallography, X-Ray Mutagenesis, Site-Directed Hydrogen Bonding Humans Amino Acid Motifs Fluorescence Polarization Machine Learning Cyclization Nuclear Magnetic Resonance, Biomolecular Peptides Kelch-Like ECH-Associated Protein 1 NF-E2-Related Factor 2 Protein Binding
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One-shot optimization of multiple enzyme parameters: Tailoring glucose oxidase for pH and electron mediators.

Biotechnology and bioengineering Oct 1, 2019
Enzymes are biological catalysts with many industrial applications, but natural enzymes are usually unsuitable for industrial processes because they are not optimized for the process conditions. The properties of enzymes can be improved by directed e...
Machine Learning Glucose Oxidase Nitrosamines Hydrogen-Ion Concentration Models, Statistical Directed Molecular Evolution Amino Acid Sequence Mutagenesis, Site-Directed Mutation Ferrous Compounds Kinetics Glucose
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Development and characterization of an α-l-rhamnosidase mutant with improved thermostability and a higher efficiency for debittering orange juice.

Food chemistry Nov 16, 2017
The glycoside hydrolase, α-l-rhamnosidase, could remove the bitter taste of naringin from citrus juices. However, most α-l-rhamnosidases are easily deactivated at high temperatures, limiting the practice in debittering citrus juices. The V529A mutant...
Mutagenesis, Site-Directed Temperature Aspergillus niger Protein Engineering Fruit and Vegetable Juices Glycoside Hydrolases Citrus sinensis Taste Directed Molecular Evolution
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