ArticleBiochemistry2018
Directed Evolution as a Probe of Rate Promoting Vibrations Introduced via Mutational Change.
Article in Biochemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Predicting Activation Barriers With Ring and Bond Critical Points in the Kemp Elimination Reaction.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Substrate-Specific Differences in Catalytic Strategy and Activity across Ketol-Acid Reductoisomerase Variants.The journal of physical chemistry. B · 2026Article
- Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning.Journal of chemical theory and computation · 2025Article
- The Evolution of the Acylation Mechanism inACS catalysis · 2024Article
- Protein Dynamics and Enzymatic Catalysis.The journal of physical chemistry. B · 2023Review
- Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.Journal of chemical theory and computation · 2022Review
- Engineered Tryptophan Synthase Balances Equilibrium Effects and Fast Dynamic Effects.ACS catalysis · 2022Article
- The physical origin of rate promoting vibrations in enzymes revealed by structural rigidity.Scientific reports · 2020Article
- Universality of fold-encoded localized vibrations in enzymes.Scientific reports · 2019Article
- Optimization of the Turnover in Artificial Enzymes via Directed Evolution Results in the Coupling of Protein Dynamics to Chemistry.Journal of the American Chemical Society · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
In this article, we study with transition path sampling and reaction coordinate analysis how directed evolution in the Kemp eliminase family of artificial enzymes makes differential use of rapid rate promoting vibrations as a component of their chemical mechanism. Even though this family was initially created by placing the expected active site in a fixed protein matrix, we find a shift from largely static to more dynamic active sites that make use of donor-acceptor compression as the evolutionary process proceeds. We see that this introduction of dynamics significantly shifts the order of processes in the reaction. We also suggest that the lack of "design for dynamics" may help explain the relatively low proficiency of such designed enzymes.
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Registered trials
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