Entropy and Enzyme Catalysis

Abstract

The role played by entropy for the enormous rate enhancement achieved by enzymes has been debated for many decades. There are, for example, several confirmed cases where the activation free energy is reduced by around 10 kcal/mol due to entropic effects, corresponding to a rate enhancement of ∼10 compared to the uncatalyzed reaction. However, despite substantial efforts from both the experimental and theoretical side, no real consensus has been reached regarding the origin of such large entropic contributions to enzyme catalysis. Another remarkable instance of entropic effects is found in enzymes that are adapted by evolution to work at low temperatures, near the freezing point of water. These cold-adapted enzymes invariably show a more negative entropy and a lower enthalpy of activation than their mesophilic orthologs, which counteracts the exponential damping of reaction rates at lower temperature. The structural origin of this universal phenomenon has, however, remained elusive. The basic problem with connecting macroscopic thermodynamic quantities, such as activation entropy and enthalpy derived from Arrhenius plots, to the 3D protein structure is that the underlying detailed (microscopic) energetics is essentially inaccessible to experiment. Moreover, attempts to calculate entropy contributions by computer simulations have mostly focused only on substrate entropies, which do not provide the full picture. We have recently devised a new approach for accessing thermodynamic activation parameters of both enzyme and solution reactions from computer simulations, which turns out to be very successful. This method is analogous to the experimental Arrhenius plots and directly evaluates the temperature dependence of calculated reaction free energy profiles. Hence, by extensive molecular dynamics simulations and calculations of up to thousands of independent free energy profiles, we are able to extract activation parameters with sufficient precision for making direct comparisons to experiment. We show here that the agreement with the measured quantities, for both enzyme catalyzed and spontaneous solution reactions, is quite remarkable. Importantly, we can now address some of the most spectacular entropy effects in enzymes and clarify their detailed microscopic origin. Herein, we discuss as examples the conversion of cytidine to uridine catalyzed by cytidine deaminase and reactions taking place on the ribosome, namely, peptide bond formation and GTP hydrolysis by elongation factor Tu. It turns out that the large entropy contributions to catalysis in these cases can now be rationalized by our computational approach. Finally, we address the problem of cold adaptation of enzyme reaction rates and prove by computational experiments that the universal activation enthalpy-entropy phenomenon originates from mechanical properties of the outer protein surface.

Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A 2A adenosine receptor binding site

“…Consideration of the enthalpic and entropic components of the binding free energy has recently been suggested to be an important metric to guide fragment optimization 8 . In addition to improved predictions of relative affinities, MD/FEP calculations make it possible to characterize the driving forces behind a change in free energy, which has previously been applied successfully to study ion hydration 28 and enzyme catalysis 34 . In this work, we used the same approach to investigate the large differences in binding observed for two compound pairs from the series of adenine-based ligands.…”

Modeling the adsorption of hydrogen, sodium, chloride and phthalate on goethite using a strict charge-neutral ion-exchange theory

“…Hence, it is entropy driven, which in turn impacts the p K values (Eq (1)). Although close proximity and orientation reduces the entropy of reactions, a full understanding of the complex nature of the entropic effect will require an extensive study of the active site environment and its surroundings [55]. Similarly in this study, we propose that the enhanced adsorption strength of Cl − anions in the presence of competing phthalate anions may be due to the enhanced reactivity of the protonated surface sites by the phthalate anions.…”

Thermally‐Induced Reactions of Aromatic Crystalline Nitroso Compounds

“…Two recently published approaches intended to develop a hypothesis that the transition state in the solid-state chemical reactions is conditioned by the "softness" of the surrounding molecular arrangement. As we have mentioned in the Introduction, the first of them appears in the research of the activation enthalpy-entropy adaptations in the enzyme catalyzed reactions, [20] and the second demonstrated that a sort of the transition liquid phase appears during the solid-solid transformation. [12] By measuring and analyzing the activation parameters of the solid-state reactions of aromatic C-nitroso compounds we wish to contribute in deepening this discussion.…”

“…As it follows from the recent literature, influence of the softness of condensed phase on the organic reactivity is not limited to the reactions in the crystalline solids only. The relationship between the activation entropy term (‐ T Δ ≠ S °) in the regulation of the enzyme catalysed reaction rates that occur in various mutants, is also interpreted by the different softness of the enzyme reaction cavity . Evolutionary “cold adaptation” of organisms is based upon the enzyme mutation, which does not basically change the topotactical arrangement in the active site, but rather the outer polypeptide structure, which modifies the rigidity of the reactive cavity.…”

“…The relationship between the activation entropy term (-TΔ ¼ 6 S°) in the regulation of the enzyme catalysed reaction rates that occur in various mutants, is also interpreted by the different softness of the enzyme reaction cavity. [20] Evolutionary "cold adaptation" of organisms is based upon the enzyme mutation, which does not basically change the topotactical arrangement in the active site, but rather the outer polypeptide structure, which modifies the rigidity of the reactive cavity. By cold adaptation, the enzyme structure is changed in such a way that the catalysed reaction rate constant at lower temperature is held equal to the rate constant of the non-adapted enzyme at higher temperature.…”