ArticleJournal of chemical theory and computation2020
Bottom-Up Nonempirical Approach To Reducing Search Space in Enzyme Design Guided by Catalytic Fields.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Electrostatic Engineering of Phosphoketolase Enhances Activity on Small Nonphosphorylated Sugars and Improves Cell-Free ATP Regeneration from Inexpensive C2-Substrates.The journal of physical chemistry. B · 2026Article
- Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design.Journal of chemical information and modeling · 2025Article
- Using the Theozyme Model to Study the Dynamical Mechanism of the Post-Transition State Bifurcation Reaction by NgnD Enzyme.Molecules (Basel, Switzerland) · 2024Article
- 2D NiHeliyon · 2024Article
- Advances in optimizing enzyme electrostatic preorganization.Current opinion in structural biology · 2022Review
- Catalytic Fields as a Tool to Analyze Enzyme Reaction Mechanism Variants and Reaction Steps.The journal of physical chemistry. B · 2021Article
- Extension of an Atom-Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts.The journal of physical chemistry. A · 2021Article
- Extreme Catalytic Power of Ketosteroid Isomerase Related to the Reversal of Proton Dislocations in Hydrogen-Bond Network.The journal of physical chemistry. B · 2020Article
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Authors and funding
2 authors.
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Abstract
Currently developed protocols of theozyme design still lead to biocatalysts with much lower catalytic activity than enzymes existing in nature, and, so far, the only avenue of improvement was the in vitro laboratory-directed evolution (LDE) experiments. In this paper, we propose a different strategy based on "reversed" methodology of mutation prediction. Instead of common "top-down" approach, requiring numerous assumptions and vast computational effort, we argue for a "bottom-up" approach that is based on the catalytic fields derived directly from transition state and reactant complex wave functions. This enables direct one-step determination of the general quantitative angular characteristics of optimal catalytic site and simultaneously encompasses both the transition-state stabilization (TSS) and ground-state destabilization (GSD) effects. We further extend the static catalytic field approach by introducing a library of atomic multipoles for amino acid side-chain rotamers, which, together with the catalytic field, allow one to determine the optimal side-chain orientations of charged amino acids constituting the elusive structure of a preorganized catalytic environment. Obtained qualitative agreement with experimental LDE data for Kemp eliminase KE07 mutants validates the proposed procedure, yielding, in addition, a detailed insight into possible dynamic and epistatic effects.
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