title: Enzyme catalysis by entropy without Circe effect.
abstract: Entropic effects have often been invoked to explain the extraordinary catalytic power of enzymes. In particular, the hypothesis that enzymes can use part of the substrate-binding free energy to reduce the entropic penalty associated with the subsequent chemical transformation has been very influential. The enzymatic reaction of cytidine deaminase appears to be a distinct example. Here, substrate binding is associated with a significant entropy loss that closely matches the activation entropy penalty for the uncatalyzed reaction in water, whereas the activation entropy for the rate-limiting catalytic step in the enzyme is close to zero. Herein, we report extensive computer simulations of the cytidine deaminase reaction and its temperature dependence. The energetics of the catalytic reaction is first evaluated by density functional theory calculations. These results are then used to parametrize an empirical valence bond description of the reaction, which allows efficient sampling by molecular dynamics simulations and computation of Arrhenius plots. The thermodynamic activation parameters calculated by this approach are in excellent agreement with experimental data and indeed show an activation entropy close to zero for the rate-limiting transition state. However, the origin of this effect is a change of reaction mechanism compared the uncatalyzed reaction. The enzyme operates by hydroxide ion attack, which is intrinsically associated with a favorable activation entropy. Hence, this has little to do with utilization of binding free energy to pay the entropic penalty but rather reflects how a preorganized active site can stabilize a reaction path that is not operational in solution.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden;
authors.forename: Masoud
authors.initials: M
authors.lastname: Kazemi
authors.affiliation: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
authors.forename: Fahmi
authors.initials: F
authors.lastname: Himo
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden; aqvist@xray.bmc.uu.se.
authors.forename: Johan
authors.initials: J
authors.lastname: Åqvist
mesh_terms: D055162:Biocatalysis; D003564:Cytidine Deaminase / Q000378:metabolism*; D019277:Entropy; D007700:Kinetics
chemical_list: D003564:Cytidine Deaminase
keywords: computational Arrhenius plots; cytidine deaminase; density functional theory; empirical valence bond method