Evidence for proton shuffling in a thioredoxin-like protein during catalysis |
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Authors: | Narzi Daniele Siu Shirley W I Stirnimann Christian U Grimshaw John P A Glockshuber Rudi Capitani Guido Böckmann Rainer A |
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Affiliation: | 1 Theoretical and Computational Membrane Biology, Center for Bioinformatics, Saarland University, Box 15 11 50, D-66041 Saarbrücken, Germany 2 Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland 3 Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland |
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Abstract: | Proteins of the thioredoxin (Trx) superfamily catalyze disulfide-bond formation, reduction and isomerization in substrate proteins both in prokaryotic and in eukaryotic cells. All members of the Trx family with thiol-disulfide oxidoreductase activity contain the characteristic Cys-X-X-Cys motif in their active site. Here, using Poisson-Boltzmann-based protonation-state calculations based on 100-ns molecular dynamics simulations, we investigate the catalytic mechanism of DsbL, the most oxidizing Trx-like protein known to date. We observed several correlated transitions in the protonation states of the buried active-site cysteine and a neighboring lysine coupled to the exposure of the active-site thiolate. These results support the view of an internal proton shuffling mechanism during oxidation crucial for the uptake of two electrons from the substrate protein. Intramolecular disulfide-bond formation is probably steered by the conformational switch facilitating interaction with the active-site thiolate. A consistent catalytic mechanism for DsbL, probably conferrable to other proteins of the same class, is presented. Our results suggest a functional role of hydration entropy of active-site groups. |
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Keywords: | Trx, thioredoxin MD, molecular dynamics |
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