jo201104v_si_001.pdf (129.89 kB)
Theoretical Comparison of p-Nitrophenyl Phosphate and Sulfate Hydrolysis in Aqueous Solution: Implications for Enzyme-Catalyzed Sulfuryl Transfer
journal contribution
posted on 2016-02-22, 14:27 authored by Shina Caroline Lynn KamerlinBoth phosphoryl and sulfuryl transfers are ubiquitous
in biology,
being involved in a wide range of processes, ranging from cell division
to apoptosis. Additionally, it is becoming increasingly clear that
enzymes that can catalyze phosphoryl transfer can often cross-catalyze
sulfuryl transfer (and vice versa). However, while there have been
extensive experimental and theoretical studies performed on phosphoryl
transfer, the body of available research on sulfuryl transfer is comparatively
much smaller. The present work presents a direct theoretical comparison
of p-nitrophenyl phosphate and sulfate monoester
hydrolysis, both of which are considered prototype systems for probing
phosphoryl and sulfuryl transfer, respectively. Specifically, free
energy surfaces have been generated using density functional theory,
by initial geometry optimization in PCM using the 6-31+G* basis set
and the B3LYP density functional, followed by single-point calculations
using the larger 6-311+G** basis set and the COSMO continuum model.
The resulting surfaces have been then used to identify the relevant
transition states, either by further unconstrained geometry optimization
or from the surface itself where possible. Additionally, configurational
entropies were evaluated using a combination of the quasiharmonic
approximation and the restraint release approach and added to the
calculated activation barriers as a correction. Finally, the overall
activation entropy was estimated by approximating the solvent contribution
to the total activation entropy using the Langevin dipoles solvation
model. We have reproduced both the experimentally observed activation
barriers and the observed trend in the activation entropies with reasonable
accuracy, as well as providing a comparison of calculated and observed 15N and 18O kinetic isotope effects. We demonstrate
that, counterintuitively, the hydrolysis of the p-nitrophenyl sulfate proceeds through a more expansive
pathway than its phosphate analogue. Additionally, we show that the
solvation effects upon moving from the ground state to the transition
state are quite different for both reactions, suggesting that the
enzymes that catalyze these reactions would need active sites with
quite different electrostatic preorganization for the efficient catalysis
of either reaction (despite which many enzymes can catalyze both phosphoryl
and sulfuryl transfer). We believe that such a comparative study is
an important foundation for understanding the molecular basis for
phosphate–sulfate cross-promiscuity within members of the alkaline
phosphatase superfamily.