ArticleNature chemical biology2009
Enzymatic transition states and dynamic motion in barrier crossing.
Article in Nature chemical biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 138 papers.
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Who cites it
138 citing papers in PubMed.
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- Fast Motions in 5 Alpha Reductase and Its Impact on Enzyme Kinetics.ACS catalysis · 2026Article
- Network reorganization of a cold-adapted β-glucosidase couples conformational flexibility to catalytic efficiency under low-temperature conditions.Frontiers in microbiology · 2026Article
- Select Configurational Dynamics in Ethanolamine Ammonia-Lyase Radical Enzyme Catalysis.ACS physical chemistry Au · 2025Article
- The Shaping of Enzymatic Free Energy Barriers through the Creation of Rate-Promoting Vibrations via Inter-Residue Cross-Talk on Multiple Time Scales.The journal of physical chemistry. B · 2025Article
- Fast product release requires active-site water dynamics in carbonic anhydrase.Nature communications · 2025Article
- Transitioning enzyme catalysis towards photocatalysis.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2025Review
- Article
- Dynamic energy conversion in protein catalysis: From brownian motion to enzymatic function.Computational and structural biotechnology journal · 2025Review
- Transition Path Sampling Based Free Energy Calculations of Evolution's Effect on Rates in β-Lactamase: The Contributions of Rapid Protein Dynamics to Rate.The journal of physical chemistry. B · 2024Article
- Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib.Journal of chemical information and modeling · 2024Article
- Transition Path Sampling Study of Engineered Enzymes That Catalyze the Morita-Baylis-Hillman Reaction: Why Is Enzyme Design so Difficult?Journal of chemical information and modeling · 2024Article
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis.The journal of physical chemistry letters · 2023Article
- Targeted Mutation of a Non-catalytic Gating Residue Increases the Rate ofJournal of agricultural and food chemistry · 2023Article
- Decreased Transition-State Analogue Affinity in Isotopically Heavy MTAN with Increased Catalysis.Biochemistry · 2023Article
- Reactivity Tracking of an Enzyme Progress Coordinate.The journal of physical chemistry letters · 2023Article
- Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations.Journal of chemical information and modeling · 2023Review
- Energetics of the Glycosyl Transfer Reactions of Sucrose Phosphorylase.Biochemistry · 2023Article
78 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
What are the atomic motions at enzymatic catalytic sites on the timescale of chemical change? Combined experimental and computational chemistry approaches take advantage of transition-state analogs to reveal dynamic motions linked to transition-state formation. QM/MM transition path sampling from reactive complexes provides both temporal and dynamic information for barrier crossing. Fast (femtosecond to picosecond) dynamic motions provide essential links to enzymatic barrier crossing by local or promoting-mode dynamic searches through bond-vibrational space. Transition-state lifetimes are within the femtosecond timescales of bond vibrations and show no manifestations of stabilized, equilibrated complexes. The slow binding and protein conformational changes (microsecond to millisecond) also required for catalysis are temporally decoupled from the fast dynamic motions forming the transition state. According to this view of enzymatic catalysis, transition states are formed by fast, coincident dynamic excursions of catalytic site elements, while the binding of transition-state analogs is the conversion of the dynamic excursions to equilibrated states.
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