Fishing for Catalysis: Experimental Approaches to Narrowing Search Space in Directed Evolution of Enzymes

JACS Au, Journal Year: 2023, Volume and Issue: 3(9), P. 2402 - 2412

Published: Aug. 18, 2023

Directed evolution has transformed protein engineering offering a path to rapid improvement of properties. Yet, in practice it is limited by the hyper-astronomic sequence search space, and approaches identify mutagenic hot spots, i.e., locations where mutations are most likely have productive impact, needed. In this perspective, we categorize discuss recent progress experimental (broadly defined as structural, bioinformatic, dynamic) spot identification. Recent successes harnessing dynamics machine learning provide new opportunities for field will undoubtedly help directed reach its full potential.

Language: Английский

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Machine learning for <i>in silico</i> protein research

Acta Physica Sinica, Journal Year: 2024, Volume and Issue: 73(6), P. 069301 - 069301

Published: Jan. 1, 2024

<i>In silico</i> protein calculation has been an important research subject for a long time, while its recent combination with machine learning promotes the development greatly in related areas. This review focuses on four major fields of <i>in that combines learning, which are molecular dynamics, structure prediction, property prediction and molecule design. Molecular dynamics depend parameters force field, is necessary obtaining accurate results. Machine can help researchers to obtain more field parameters. In simulation, also perform free energy relatively low cost. Structure generally used predict given sequence. high complexity data volume, exactly what good at. By scientists have gained great achievements three-dimensional proteins. On other hand, predicting properties based known information study protein. More challenging, however, Though marching made breakthroughs drug-like small design years, there still plenty room exploration. summarizing above andlooks forward application research.

Language: Английский

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Metalloenzyme-inspired approach to the design and applications of phosphatase-mimetic nanozymes. Bridging the inorganic and organic worlds

Environmental Science Nano, Journal Year: 2024, Volume and Issue: 11(8), P. 3268 - 3285

Published: Jan. 1, 2024

Both nanozymes (cerium oxide) and natural enzymes can destroy toxic organophosphates (pesticide paraoxon ethyl) using analogous reaction mechanisms.

Language: Английский

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Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 6, 2024

Abstract Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation a variety of cancers by replacing its conventional activity with neomorphic that generates an oncometabolite. Little is understood the mechanistic differences among tumor-driving IDH1 mutants. We previously reported R132Q mutant unusually preserves while catalyzing robust oncometabolite production, allowing opportunity to compare these reaction mechanisms within single active site. Here, we employ static and dynamic structural methods observe that, compared R132H, site adopts conformation primed for catalysis optimized substrate binding hydride transfer improved over R132H. This remodeling reveals possible mechanism resistance selective therapeutic inhibitors. work enhances our understanding fundamental pinpointing regions improving inhibitor selectivity.

Language: Английский

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Designing Efficient Enzymes: Eight Predicted Mutations Convert a Hydroxynitrile Lyase into an Efficient Esterase

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 24, 2023

Hydroxynitrile lyase from rubber tree (HbHNL) shares 45% identical amino acid residues with the homologous esterase tobacco, SABP2, but two enzymes catalyze different reactions. The x-ray structures reveal a serine-histidine-aspartate catalytic triad in both along several differing within active site. Previous exchange of three site HbHNL corresponding residue SABP2 (T11G-E79H-K236M) created variant HNL3, which showed low activity toward p-nitrophenyl acetate. Further structure comparison reveals additional differences surrounding contains an improperly positioned oxyanion hole and solvation aspartate. We hypothesized that correcting these structural would impart good on variant. To predict substitutions needed to correct structure, we calculated shortest path maps for correlated movements acids enzymes. Replacing four (C81L-N104T-V106F-G176S) whose are connected yielded HNL7TV (stabilizing substitution H103V was also added), efficiency comparable SABP2. intermediate variant, HNL6V, altered aspartate partially corrected hole. This dramatic increase demonstrates ability outside contribute activity.

Language: Английский

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