ArticleProtein science : a publication of the Protein Society2010
Evaluation and ranking of enzyme designs.
Article in Protein science : a publication of the Protein Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
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- Quantum Methods in Drug Discovery: An Introduction to the Theoceptor (Theoretical Receptor) Approach.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Computational design of serine hydrolases.Science (New York, N.Y.) · 2025Article
- Computational design of serine hydrolases.bioRxiv : the preprint server for biology · 2024Article
- Advances in Drug Discovery and Design using Computer-aided Molecular Modeling.Current computer-aided drug design · 2024Review
- Article
- EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation.Journal of chemical information and modeling · 2023Article
- De Novo Computational Design of a Lipase with Hydrolysis Activity towards Middle-Chained Fatty Acid Esters.International journal of molecular sciences · 2023Article
- Computation-Aided Engineering of Cytochrome P450 for the Production of Pravastatin.ACS catalysis · 2022Article
- Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.Journal of chemical theory and computation · 2022Review
- The road to fully programmable protein catalysis.Nature · 2022Review
- Evolution of Enzyme Function and the Development of Catalytic Efficiency: Triosephosphate Isomerase, Jeremy R. Knowles, and W. John Albery.Biochemistry · 2021Article
- Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations.Journal of chemical information and modeling · 2021Article
- Protein-Protein Interactions: Insight from Molecular Dynamics Simulations and Nanoparticle Tracking Analysis.Molecules (Basel, Switzerland) · 2021Article
- Harnessing Conformational Plasticity to Generate Designer Enzymes.Journal of the American Chemical Society · 2020Review
- Computational Design of Enantiocomplementary Epoxide Hydrolases for Asymmetric Synthesis of Aliphatic and Aromatic Diols.Chembiochem : a European journal of chemical biology · 2020Article
- Enhancing aChemical science · 2020Article
- Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations.Journal of chemical theory and computation · 2019Article
- Article
- Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation.ACS central science · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
In 2008, a successful computational design procedure was reported that yielded active enzyme catalysts for the Kemp elimination. Here, we studied these proteins together with a set of previously unpublished inactive designs to determine the sources of activity or lack thereof, and to predict which of the designed structures are most likely to be catalytic. Methods that range from quantum mechanics (QM) on truncated model systems to the treatment of the full protein with ONIOM QM/MM and AMBER molecular dynamics (MD) were explored. The most effective procedure involved molecular dynamics, and a general MD protocol was established. Substantial deviations from the ideal catalytic geometries were observed for a number of designs. Penetration of water into the catalytic site and insufficient residue-packing around the active site are the main factors that can cause enzyme designs to be inactive. Where in the past, computational evaluations of designed enzymes were too time-extensive for practical considerations, it has now become feasible to rank and refine candidates computationally prior to and in conjunction with experimentation, thus markedly increasing the efficiency of the enzyme design process.
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