ArticleProceedings of the National Academy of Sciences of the United States of America2013
Thermodynamic framework for identifying free energy inventories of enzyme catalytic cycles.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. 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.
- Developing crosslinkers specific for epimerization domain in NRPS initiation modules to evaluate mechanism.RSC chemical biology · 2022Article
- Testing the Limitations of MD-Based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case.The journal of physical chemistry. B · 2021Article
- Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems.The journal of physical chemistry. B · 2020Article
- Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation.The journal of physical chemistry. B · 2019Article
- Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site.Nature communications · 2019Article
- A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase.Journal of the American Chemical Society · 2016Article
- Theoretical study of enzymatically catalyzed tautomerization of carbon acids in aqueous solution: quantum calculations and steered molecular dynamics simulations.Journal of molecular modeling · 2016Article
- Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP).ACS central science · 2015Article
- Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
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Authors and funding
2 authors.
Funding
Abstract
Pauling's suggestion that enzymes are complementary in structure to the activated complexes of the reactions they catalyze has provided the conceptual basis to explain how enzymes obtain their fantastic catalytic prowess, and has served as a guiding principle in drug design for over 50 y. However, this model by itself fails to predict the magnitude of enzymes' rate accelerations. We construct a thermodynamic framework that begins with the classic concept of differential binding but invokes additional terms that are needed to account for subtle effects in the catalytic cycle's proton inventory. Although the model presented can be applied generally, this analysis focuses on ketosteroid isomerase (KSI) as an example, where recent experiments along with a large body of kinetic and thermodynamic data have provided strong support for the noncanonical thermodynamic contribution described. The resulting analysis precisely predicts the free energy barrier of KSI's reaction as determined from transition-state theory using only empirical thermodynamic data. This agreement is suggestive that a complete free energy inventory of the KSI catalytic cycle has been identified.
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