Fundamental Reaction Pathways and Free-Energy Barriers for Ester Hydrolysis of Intracellular Second-Messenger 3‘,5‘-Cyclic Nucleotide

Abstract

We have performed a series of first-principles electronic structure calculations to study competing reaction pathways and the corresponding free-energy barriers for the ester hydrolysis of intracellular second-messenger adenosine 3′,5′-cyclic monophosphate (cAMP) and related phosphodiesters including trimethylene phosphate (TMP). Reaction coordinate calculations show three fundamental reaction pathways for the ester hydrolysis, including (A) attack of a hydroxide ion at the P atom of the phosphate anion (an S N 2 process without a pentacoordinated phosphorus intermediate), (B) direct attack of a water molecule at the P atom of the anion (a three-step process), and (C) direct attack of a water molecule at the P atom of the neutral ester molecule (a two-step process). The calculated energy results show that for the reactions in the gas phase the freeenergy barrier for pathway A is the highest and the barrier for the rate-controlling step of pathway C is the lowest. However, for the reactions in aqueous solution, the free-energy barrier calculated for pathway A becomes the lowest, and the two main hydrolysis pathways are A and B. We also have demonstrated how the pK a of the ester and the pH of the reaction solution affect the relative contributions of different hydrolysis pathways to the total hydrolysis rate. Reaction pathway A should be dominant for the cAMP hydrolysis in neutral aqueous solution. However, the relative contribution of pathway A to the total hydrolysis rate should decrease with decreasing pH of the solution. For pH < ∼3.7, the contribution of pathway B is larger. For pH > ∼3.7, the contribution of pathway A is larger. The reliability of our theoretical predictions is supported by the excellent agreement of the calculated free-energy barrier with available experimental data for the hydrolysis of TMP in solution.

Reaction pathway and free energy barrier for urea elimination in aqueous solution

“…Our previous calculations on a variety of chemical reactions showed that the energy barriers determined by the SVPE calculations using both the default 0.001 au and 0.002 au contours were all qualitatively consistent with the corresponding experimental activation energies [25,26,28]. As the SVPE procedure using 0.001 au contour was shown to be reliable for evaluating the bulk solvent effects [17–21,23,26,27, 29, 35, 36], the 0.001 au [16] contour was also used in this study for all of the SVPE calculations. The dielectric constant (ε) used in the SVPE calculations for solvent water is dependent on the temperature ( T ) [37], with ε = 78.5 at T = 298.15 K. The free energies in solution were obtained by adding the gas phase free energies to solvent shifts obtained from the SVPE calculations.…”

“…The converged SVPE results merely rely on the contour value at a given dielectric constant and a certain QM calculation level [16]. Our previous calculations on a variety of chemical reactions showed that the energy barriers determined by the SVPE calculations using both the default 0.001 au and 0.002 au contours were all qualitatively consistent with the corresponding experimental activation energies [25,26,28]. As the SVPE procedure using 0.001 au contour was shown to be reliable for evaluating the bulk solvent effects [17–21,23,26,27, 29, 35, 36], the 0.001 au [16] contour was also used in this study for all of the SVPE calculations.…”

“…Our previous computational studies on hydrolysis reactions of a variety of compounds, including carboxylic acid esters, amides, and phosphate esters, showed that the energy barriers determined by the SVPE-based quantum mechanical (QM) calculations were all reasonably consistent with available experimental activation energies [25,26,28]. The SVPE-based QM approach was also used to examine reaction pathways and free energy profiles for hydrolysis of urea and 1,1,3,3-tetramethylurea (Me 4 U) [13].…”

Reaction pathways and free energy profiles for spontaneous hydrolysis of urea and tetramethylurea: unexpected substituent effects

“…27 Our previous calculations on hydroxide ion-catalyzed hydrolysis of a series of carboxylic acid esters and phosphate esters showed that the energy barriers determined by the SVPE calculations using both the default 0.001 au and 0.002 au contours were all qualitatively consistent with the corresponding experimental activation energies. 23, 38–39 As the SVPE procedure using 0.001 au contour was shown to be reliable for evaluating the bulk solvent effects, 29–31, 33–35, 39–43 the 0.001 au 27 contour was also used in this study for all of the SVPE calculations. The dielectric constant ( ε ) used in the SVPE calculations for solvent water is dependent on the temperature ( T ), 44 with ε = 78.5 at T = 298.15 K. The free energies in solution were obtained by adding the gas phase free energies to solvent shifts obtained from the SVPE calculations.…”

Analysis of proton wires in the enzyme active site suggests a mechanism of c‐di‐GMP hydrolysis by the EAL domain phosphodiesterases

“…On the theoretical side, no simulations on enzyme hydrolysis of the cyclic dimeric GMP have been reported in the literature, although several computational works describe the hydrolysis mechanism for the monomeric species c‐AMP and c‐GMP in aqueous solution and in the enzymes. An important difference should be pointed out when comparing c‐AMP or c‐GMP hydrolysis catalyzed by phosphodiesterases 4 and 5 and c‐di‐GMP hydrolysis by the EAL domain PDEs.…”