Kiera H. Sumida
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View article: Computational design of serine hydrolases
Computational design of serine hydrolases Open
The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of RFdiffusion with an ensemble generation…
View article: Computational Stabilization of a Non‐Heme Iron Enzyme Enables Efficient Evolution of New Function
Computational Stabilization of a Non‐Heme Iron Enzyme Enables Efficient Evolution of New Function Open
Deep learning tools for enzyme design are rapidly emerging, and there is a critical need to evaluate their effectiveness in engineering workflows. Here we show that the deep learning‐based tool ProteinMPNN can be used to redesign Fe(II)/αK…
View article: Computational Stabilization of a Non‐Heme Iron Enzyme Enables Efficient Evolution of New Function
Computational Stabilization of a Non‐Heme Iron Enzyme Enables Efficient Evolution of New Function Open
Deep learning tools for enzyme design are rapidly emerging, and there is a critical need to evaluate their effectiveness in engineering workflows. Here we show that the deep learning‐based tool ProteinMPNN can be used to redesign Fe(II)/αK…
View article: Computational design of serine hydrolases
Computational design of serine hydrolases Open
Enzymes that proceed through multistep reaction mechanisms often utilize complex, polar active sites positioned with sub-angstrom precision to mediate distinct chemical steps, which makes their de novo construction extremely challenging. W…
View article: Computational stabilization of a non-heme iron enzyme enables efficient evolution of new function
Computational stabilization of a non-heme iron enzyme enables efficient evolution of new function Open
Directed evolution has emerged as a powerful tool for engineering new biocatalysts. However, introducing new catalytic residues can be destabilizing, and it is generally beneficial to start with a stable enzyme parent. Here we show that th…
View article: Improving Protein Expression, Stability, and Function with ProteinMPNN
Improving Protein Expression, Stability, and Function with ProteinMPNN Open
Natural proteins are highly optimized for function but are often difficult to produce at a scale suitable for biotechnological applications due to poor expression in heterologous systems, limited solubility, and sensitivity to temperature.…
View article: Improving protein expression, stability, and function with ProteinMPNN
Improving protein expression, stability, and function with ProteinMPNN Open
Natural proteins are highly optimized for function, but are often difficult to produce at a scale suitable for biotechnological applications due to poor expression in heterologous systems, limited solubility, and sensitivity to temperature…
View article: Biocatalytic control of site-selectivity and chain length-selectivity in radical amino acid halogenases
Biocatalytic control of site-selectivity and chain length-selectivity in radical amino acid halogenases Open
Biocatalytic C–H activation has the potential to merge enzymatic and synthetic strategies for bond formation. Fe II /αKG-dependent halogenases are particularly distinguished for their ability both to control selective C–H activation as wel…
View article: Regioselective control of biocatalytic C–H activation and halogenation
Regioselective control of biocatalytic C–H activation and halogenation Open
Biocatalytic C–H activation has the potential to merge enzymatic and synthetic strategies for bond formation. Fe II /αKG-dependent halogenases are particularly distinguished for their ability both to control selective C-H activation as wel…