ArticleeLife2025
Wide transition-state ensemble as key component for enzyme catalysis.
Article in eLife, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- From static structures to dynamic energy landscapes: the latest revolution in molecular biology.Current opinion in structural biology · 2026Review
- Accelerating Quantum Mechanical/Molecular Mechanical (QM/MM) Simulations with Stochastic Iso-Kinetic Nosé-Hoover Multiple Time Step Integrator in CHARMM.The journal of physical chemistry. B · 2026Article
- Biocatalytic Radical C(spResearch square · 2026Article
- Visualize Transient Water-Mediated Hydrogen Bonds Facilitating the Formation of Enzymatic Near-Attack Conformers.JACS Au · 2025Article
- A Foundational Shift in Models for Enzyme Function.Journal of the American Chemical Society · 2025Review
- Advances in uncovering the mechanisms of macromolecular conformational entropy.Nature chemical biology · 2025Review
- Targeted TPS Shooting Using Computer Vision to Generate Ensemble of Trajectories.Journal of chemical theory and computation · 2025Article
- Physics-based modeling in the new era of enzyme engineering.Nature computational science · 2025Review
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Authors and funding
6 authors.
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Abstract
Transition-state (TS) theory has provided the theoretical framework to explain the enormous rate accelerations of chemical reactions by enzymes. Given that proteins display large ensembles of conformations, unique TSs would pose a huge entropic bottleneck for enzyme catalysis. To shed light on this question, we studied the nature of the enzymatic TS for the phosphoryl-transfer step in adenylate kinase by quantum-mechanics/molecular-mechanics calculations. We find a structurally wide set of energetically equivalent configurations that lie along the reaction coordinate and hence a broad transition-state ensemble (TSE). A conformationally delocalized ensemble, including asymmetric TSs, is rooted in the macroscopic nature of the enzyme. The computational results are buttressed by enzyme kinetics experiments that confirm the decrease of the entropy of activation predicted from such wide TSE. TSEs as a key for efficient enzyme catalysis further boosts a unifying concept for protein folding and conformational transitions underlying protein function.
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