ReviewBiochemistry2013
Catalytic efficiency of enzymes: a theoretical analysis.
Review in Biochemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
38 citing papers in PubMed, 94 citations in OpenAlex.
- Preorganized Electric Fields in Voltage-Gated Sodium Channels.Chembiochem : a European journal of chemical biology · 2025Article
- Hydrophobicity-Based Force Field In Enzymes.ACS omega · 2024Article
- Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation.Entropy (Basel, Switzerland) · 2024Article
- Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy.The Journal of chemical physics · 2023Article
- Reactivity Tracking of an Enzyme Progress Coordinate.The journal of physical chemistry letters · 2023Article
- Proton transfer reactions: From photochemistry to biochemistry and bioenergetics.BBA advances · 2023Article
- Review
- Single-Molecule Sampling of Dihydrofolate Reductase Shows Kinetic Pauses and an Endosteric Effect Linked to Catalysis.ACS catalysis · 2022Article
- Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the CytochromeJournal of the American Chemical Society · 2021Article
- Linkage of nanosecond protein motion with enzymatic methyl transfer by nicotinamide N-methyltransferase.Turkish journal of biology = Turk biyoloji dergisi · 2021Article
- Cofactor Binding Dynamics Influence the Catalytic Activity and Selectivity of an Artificial Metalloenzyme.ACS catalysis · 2020Article
- Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase.ACS catalysis · 2020Article
- Biochemical Studies Provide Insights into the Necessity for Multiple Arabidopsis thaliana Protein-Only RNase P Isoenzymes.Journal of molecular biology · 2019Article
- Designed for life: biocompatible de novo designed proteins and components.Journal of the Royal Society, Interface · 2018Review
- Conformational Sampling of the Intrinsically Disordered C-Terminal Tail of DERA Is Important for Enzyme Catalysis.ACS catalysis · 2018Article
- Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis.Protein science : a publication of the Protein Society · 2018Article
- Quantifying the limits of transition state theory in enzymatic catalysis.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Two Dynamical Regimes of the Substrate Radical Rearrangement Reaction in BBiochemistry · 2017Article
- Catalysts by Design: The Power of Theory.Accounts of chemical research · 2017Article
- Structure-Reactivity Effects on Intrinsic Primary Kinetic Isotope Effects for Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase.Journal of the American Chemical Society · 2016Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
This brief review analyzes the underlying physical principles of enzyme catalysis, with an emphasis on the role of equilibrium enzyme motions and conformational sampling. The concepts are developed in the context of three representative systems, namely, dihydrofolate reductase, ketosteroid isomerase, and soybean lipoxygenase. All of these reactions involve hydrogen transfer, but many of the concepts discussed are more generally applicable. The factors that are analyzed in this review include hydrogen tunneling, proton donor-acceptor motion, hydrogen bonding, pKa shifting, electrostatics, preorganization, reorganization, and conformational motions. The rate constant for the chemical step is determined primarily by the free energy barrier, which is related to the probability of sampling configurations conducive to the chemical reaction. According to this perspective, stochastic thermal motions lead to equilibrium conformational changes in the enzyme and ligands that result in configurations favorable for the breaking and forming of chemical bonds. For proton, hydride, and proton-coupled electron transfer reactions, typically the donor and acceptor become closer to facilitate the transfer. The impact of mutations on the catalytic rate constants can be explained in terms of the factors enumerated above. In particular, distal mutations can alter the conformational motions of the enzyme and therefore the probability of sampling configurations conducive to the chemical reaction. Methods such as vibrational Stark spectroscopy, in which environmentally sensitive probes are introduced site-specifically into the enzyme, provide further insight into these aspects of enzyme catalysis through a combination of experiments and theoretical calculations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.