Understanding the Catalytic Ability of Peroxiredoxins: a Combined Experimental and QM/MM Study on the Fast Thiol Oxidation Step

ARI ZEIDA; ANÍBAL M. REYES; MARIANO CAMILO GONZÁLEZ LEBRERO; RAFAEL RADI; MADIA TRUJILLO; DARIO A. ESTRIN

Congreso; 10th Congress of the World Association of Theoretical and Computational Chemists; 2014

Peroxiredoxins (Prxs) catalyze the reduction of peroxides, a process of key relevance in a variety of cellular processes, including redox signalling and antioxidant responses. The first step in the catalytic cycle of all Prxs is the oxidation of the thiolate in the peroxidatic cysteine to sulfenic acid which occurs 103-107 times faster than in the case of free cysteine [1]. In this work we present an experimental kinetic and hybrid QM/MM investigation to explore the reaction of Prxs with hydrogen peroxide. As a model for studying this reaction, we selected the one-cysteine Prx from Mycobacterium tuberculosis, alkyl hydroperoxide reductase E (MtAhpE)[2], since its oxidation can be accurately followed experimentally [3]. Experimental results suggest that the protein lowers significantly the activation enthalpy, but promotes an unfavourable entropic effect, compared to the uncatalyzed reaction. We computed the free energy profile for the reaction by means of state of the art quantum mechanics/molecular mechanics (QM/MM) umbrella sampling simulations, at the density functional theory level. We employed a DFT Gaussian basis set scheme coupled to the Amber code developed in our group, that exploits the processing power of graphical cards. [4] The QM/MM simulation yields a computed free energy profile consistent with the experimental data. The results show that the catalyzed reaction mechanism is similar to that observed in the uncatalyzed one, and that the remarkable catalytic effects are mainly due to an active-site microenvironment arrangement, which establishes a complex hydrogen bond network activating both reactive species.