ArticleProceedings of the National Academy of Sciences of the United States of America2018
Influence of water and enzyme SpnF on the dynamics and energetics of the ambimodal [6+4]/[4+2] cycloaddition.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Physics-based modeling in the new era of enzyme engineering.Nature computational science · 2025Review
- Using the Theozyme Model to Study the Dynamical Mechanism of the Post-Transition State Bifurcation Reaction by NgnD Enzyme.Molecules (Basel, Switzerland) · 2024Article
- Article
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- Enzymatic Control over Reactive Intermediates Enables Direct Oxidation of Alkenes to Carbonyls by a P450 Iron-Oxo Species.Journal of the American Chemical Society · 2022Article
- Mechanism of the Stereoselective Catalysis of Diels-Alderase PyrE3 Involved in Pyrroindomycin Biosynthesis.Journal of the American Chemical Society · 2022Article
- Byproduct formation during the biosynthesis of spinosyn A and evidence for an enzymatic interplay to prevent its formation.Tetrahedron · 2022Article
- Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons*.Angewandte Chemie (International ed. in English) · 2021Article
- Mechanisms and Dynamics of Synthetic and Biosynthetic Formation of Delitschiapyrones: Solvent Control of Ambimodal Periselectivity.Journal of the American Chemical Society · 2021Article
- Discovery and investigation of natural Diels-Alderases.Journal of natural medicines · 2021Review
- Enzymatic reactions in teleocidin B biosynthesis.Journal of natural medicines · 2021Review
- Diversity of the reaction mechanisms of SAM-dependent enzymes.Acta pharmaceutica Sinica. B · 2021Review
- Aggregation and Solvation of Sodium Hexamethyldisilazide: Across the Solvent Spectrum.The Journal of organic chemistry · 2021Article
- Ab Initio Molecular Dynamics Simulations of the SJournal of the American Chemical Society · 2021Article
- Mechanism of 3-Methylglutaconyl CoA Decarboxylase AibA/AibB: Pericyclic Reaction versus Direct Decarboxylation.Angewandte Chemie (International ed. in English) · 2020Article
- Computational Investigation of the Mechanism of Diels-Alderase PyrI4.Journal of the American Chemical Society · 2020Article
- Unusual KIE and dynamics effects in the Fe-catalyzed hetero-Diels-Alder reaction of unactivated aldehydes and dienes.Nature communications · 2020Article
- The expanding world of biosynthetic pericyclases: cooperation of experiment and theory for discovery.Natural product reports · 2019Review
- Selective hydrogenation of 1,3-butadiene catalyzed by a single Pd atom anchored on graphene: the importance of dynamics.Chemical science · 2018Article
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12 authors.
Funding
Abstract
SpnF is the first monofunctional Diels-Alder/[6+4]-ase that catalyzes a reaction leading to both Diels-Alder and [6+4] adducts through a single transition state. The environment-perturbed transition-state sampling method has been developed to calculate free energies, kinetic isotope effects, and quasi-classical reaction trajectories of enzyme-catalyzed reactions and the uncatalyzed reaction in water. Energetics calculated in this way reproduce the experiment and show that the normal Diels-Alder transition state is stabilized by H bonds with water molecules, while the ambimodal transition state is favored in the enzyme SpnF by both intramolecular hydrogen bonding and hydrophobic binding. Molecular dynamics simulations show that trajectories passing through the ambimodal transition state bifurcate to the [6+4] adduct and the Diels-Alder adduct with a ratio of 1:1 in the gas phase, 1:1.6 in water, and 1:11 in the enzyme. This example shows how an enzyme acts on a vibrational time scale to steer post-transition state trajectories toward the Diels-Alder adduct.
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