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Insight into the phosphodiesterase mechanism from combined QM/MM free energy simulations
Author(s) -
Wong KinYiu,
Gao Jiali
Publication year - 2011
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/j.1742-4658.2011.08187.x
Subject(s) - chemistry , nucleophile , leaving group , molecular dynamics , catalysis , activation energy , reaction mechanism , stereochemistry , computational chemistry , organic chemistry
Molecular dynamics simulations employing a combined quantum mechanical and molecular mechanical potential have been carried out to elucidate the reaction mechanism of the hydrolysis of a cyclic nucleotide cAMP substrate by phosphodiesterase 4B (PDE4B). PDE4B is a member of the PDE superfamily of enzymes that play crucial roles in cellular signal transduction. We have determined a two‐dimensional potential of mean force (PMF) for the coupled phosphoryl bond cleavage and proton transfer through a general acid catalysis mechanism in PDE4B. The results indicate that the ring‐opening process takes place through an S N 2 reaction mechanism, followed by a proton transfer to stabilize the leaving group. The computed free energy of activation for the PDE4B‐catalyzed cAMP hydrolysis is about 13 kcal·mol −1 and an overall reaction free energy is about −17 kcal·mol −1 , both in accord with experimental results. In comparison with the uncatalyzed reaction in water, the enzyme PDE4B provides a strong stabilization of the transition state, lowering the free energy barrier by 14 kcal·mol −1 . We found that the proton transfer from the general acid residue His234 to the O3′ oxyanion of the ribosyl leaving group lags behind the nucleophilic attack, resulting in a shallow minimum on the free energy surface. A key contributing factor to transition state stabilization is the elongation of the distance between the divalent metal ions Zn 2+ and Mg 2+ in the active site as the reaction proceeds from the Michaelis complex to the transition state.