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.cytidine deaminase | density functional theory | empirical valence bond method | computational Arrhenius plots M any hypotheses have been put forward to explain the rate acceleration of chemical reactions by enzymes. One of the most influential of these is Jencks' so-called "Circe effect" (1), which posits that the key catalytic effect is associated with substrate binding and that part of the favorable (negative) binding free energy is spent on destabilization of the bound substrate in its ground state. Such ground-state destabilization could, in principle, have different possible physical origins, such as reduction of translational, rotational, and conformational substrate entropies; steric and conformational strain; or electrostatic destabilization and desolvation effects (1). In particular, the entropic explanation enjoys widespread popularity and is often invoked to rationalize the catalytic power of enzymes in terms of proximity and alignment of the reacting groups (2). It is then assumed that part of the substrate-binding free energy is spent on restricting the substrate motions and correctly aligning the substrate for reaction, which implies a negative contribution to the binding entropy. This scenario, in turn, would enable the substrate to climb the activation barrier with a smaller entropy loss than in solution, because the entr...

Enzyme surface rigidity tunes the temperature dependence of catalytic rates

“…The empirical valence bond (EVB) model (11,12) provides a very efficient method for this purpose, because it allows extensive all-atom molecular dynamics (MD) sampling of the reaction system and can be used to directly construct computational Arrhenius plots (8,9). This strategy has also recently been validated both for solution (13) and enzyme (14) reactions and was found to yield activation enthalpies and entropies in excellent agreement with experiment.…”

QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes

“…For full enzyme models, minimization based calculations are generally less useful due to the enormously large number of stationary points and therefore minimum energy pathways (MEPs) on the high-dimensional PES, and it is challenging (if not impossible) to estimate the proper statistical weights from these MEPs[109, 138]. Another important limitation of minimization type of calculations is the lack of thermal uctuations and therefore entropic contribution to the reaction energetics; along this line, it is important to recall that protein and solvent uctuations (not just the reactive motifs) can’t be ignored when considering the entropic contribution[74, 140]. Therefore, it is generally difficult to compare the results from a limited number of MEP calculations to experimental free energy data, although qualitative insights may still be obtained from the analysis of MEP calculations.…”

Dispelling the effects of a sorceress in enzyme catalysis

“…Harnessing these abilities in designed catalysts would transform our ability to design protein and biomimetic catalysts for practical applications. Using computer simulation, Kazemi et al (1) have now analyzed a classic example in enzymology, and show that a long-cherished and influential theory of enzyme catalysis is wrong.…”

“…E. coli cytidine deaminase contains a zinc ion that is bound tightly at the active site. Kazemi et al (1) first identified the likely mechanism of reaction in the enzyme, using DFT calculations on a small model containing the zinc ion, a few important amino acid sidechains, and the cytidine substrate. The DFT calculations show that a water molecule is deprotonated by Glu104 in cytidine deaminase and the resulting hydroxide ion (bound to zinc) is the nucleophile that attacks the Using computer simulation, Kazemi et al have now analyzed a classic example in enzymology, and show that a long-cherished and influential theory of enzyme catalysis is wrong.…”

“…Simulations have an essential role in determining enzyme mechanisms, analyzing contributions to catalysis, and in interpreting experiments [e.g., to reveal and quantify dynamical effects (13)]. As the work of Kazemi et al (1) shows, simulations are revealing the pragmatic molecular sorcery of biological catalysis (14).…”