ArticleBiochemistry2011
Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis.
Article in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
29 citing papers in PubMed, 78 citations in OpenAlex.
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- Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2.ACS catalysis · 2021Article
- Catalytic Principles from Natural Enzymes and Translational Design Strategies for Synthetic Catalysts.ACS central science · 2021Review
- Enhancing aChemical science · 2020Article
- Bottom-Up Nonempirical Approach To Reducing Search Space in Enzyme Design Guided by Catalytic Fields.Journal of chemical theory and computation · 2020Article
- Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- The evolution of multiple active site configurations in a designed enzyme.Nature communications · 2018Article
- Elucidating the 3D structures of Al(iii)-Aβ complexes: a template free strategy based on the pre-organization hypothesis.Chemical science · 2017Article
- Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases.ACS catalysis · 2017Article
- A redox-mediated Kemp eliminase.Nature communications · 2017Article
- Article
- Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.The Journal of chemical physics · 2016Review
- Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes.ACS catalysis · 2015Article
- Computational strategies for the design of new enzymatic functions.Archives of biochemistry and biophysics · 2015Review
- Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.Chemical Society reviews · 2015Review
- On the challenge of exploring the evolutionary trajectory from phosphotriesterase to arylesterase using computer simulations.The journal of physical chemistry. B · 2015Article
- Structure Activity Related, Mechanistic, and Modeling Studies of Gallotannins containing a Glucitol-Core andRSC advances · 2015Article
- Simulating the catalytic effect of a designed mononuclear zinc metalloenzyme that catalyzes the hydrolysis of phosphate triesters.The journal of physical chemistry. B · 2014Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
One of the fundamental challenges in biotechnology and biochemistry is the ability to design effective enzymes. Despite recent progress, most of the advances on this front have been made by placing the reacting fragments in the proper places, rather than by optimizing the preorganization of the environment, which is the key factor in enzyme catalysis. Thus, rational improvement of the preorganization would require approaches capable of evaluating reliably the actual catalytic effect. This work considers the catalytic effects in different Kemp eliminases as a benchmark for a computer-aided enzyme design. It is shown that the empirical valence bond provides a powerful screening tool, with significant advantages over current alternative strategies. The insights provided by the empirical valence bond calculations are discussed with an emphasis on the ability to analyze the difference between the linear free energy relationships obtained in solution and those found in the enzymes. We also point out the trade-off between the reliability and speed of the calculations and try to determine what it takes to realize reliable computer-aided screening.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.