Sirtuins, a family of NAD+-dependent protein deacetylases, has led to extensive investigation into its unique chemical mechanism. Employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized its complete catalytic reaction mechanism for Sir2Tm-catalyzed deacetylation and determined its multistep free-energy reaction profiles for the first time. The overall reaction has been suggested to proceed in four consecutive stages: (i) the formation of the a-1'-O-alkylamidate intermediate, (ii) the formation of the bicyclic intermediate, (iii) the collapse of this bicyclic intermediate by water attack, and (iv) the protonation and collapse of the tetrahedral intermediate. Our results indicated that the third stage, which is shown to be the rate-controlling step, employs a novel stepwise mechanism. This proposed mechanism is consistent with all available experimental data and provides deeper insight into the nature of the chemical transitions that occur on these sirtuins enzymes.

Catalytic reaction mechanism of Sir2Tm-catalyzed deacetylation determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations

243rd National Meeting (2012)

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