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Deconstructing the Catalytic Efficiency of Peroxiredoxin-5 Peroxidatic Cysteine

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Laboratorio de Fisicoquímica Biológica, Laboratorio de Química Teórica y Computacional and Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
§ Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
Laboratory of Cell Biology, Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
# Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
*E-mail: [email protected]. Telephone/fax: 598 2525 0749.
Cite this: Biochemistry 2014, 53, 38, 6113–6125
Publication Date (Web):September 3, 2014
https://doi.org/10.1021/bi500389m
Copyright © 2014 American Chemical Society

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    Abstract

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    Human peroxiredoxin-5 (PRDX5) is a thiol peroxidase that reduces H2O2 105 times faster than free cysteine. To assess the influence of two conserved residues on the reactivity of the critical cysteine (C47), we determined the reaction rate constants of PRDX5, wild type (WT), T44V and R127Q with one substrate electrophile (H2O2) and a nonspecific electrophile (monobromobimane). We also studied the corresponding reactions of low molecular weight (LMW) thiolates in order to construct a framework against which we could compare our proteins. To obtain a detailed analysis of the structural and energetic changes involved in the reaction between WT PRDX5 and H2O2, we performed ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations with a QM region including 60 atoms of substrate and active site described by the B3LYP density functional and the 6-31+G(d,p) basis set; the rest of the protein was included in the MM region. Brønsted correlations reveal that the absence of T44 can increase the general nucleophilicity of the C47 but decreases the specific reactivity toward H2O2 by a factor of 103. The R127Q mutation causes C47 to behave like a LMW thiolate in the two studied reactions. QM/MM results with WT PRDX5 showed that hydrogen bonds in the active site are the cornerstone of two effects that make catalysis possible: the enhancement of thiolate nucleophilicity upon substrate ingress and the stabilization of the transition state. In both effects, T44 has a central role. These effects occur in a precise temporal sequence that ensures that the selective nucleophilicity of C47 is available only for peroxide substrates.

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    Figure S1. Rationale for choosing the dielectric constant. Figure S2. UV titration curves and fits for the thiols used in the article. Table S1. Microscopic ionization constants for the aminothiols studied. Figure S3. pH profiles of the initial slope of fluorescence increase for PRDX5 T44V and R127Q reacting with mBBr at 25 °C. Table S2. Wiberg bond orders for relevant pairs of atoms at the active site of PRXD5 and EHOMO for points along the reaction coordinate. Table S3. NPA atomic charges for relevant atoms and functional groups at the active site of PRXD5 along the reaction coordinate. Table S4. Wiberg bond orders for proton acceptor/donor interactions at the active site of PRDX5. Figure S4. Evolution of the principal atomic pair distances involved in the heavy atom reorganization and proton transfer processes. Table S5. Coordinates for the optimized geometries of the IC, TS, and FC. Video SV1. An animated sequence of the structure evolution along the reaction coordinate obtained from the QM/MM calculations. This material is available free of charge via the Internet at http://pubs.acs.org.

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