title: Evidence for proton shuffling in a thioredoxin-like protein during catalysis.
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.
authors.affiliation: Theoretical and Computational Membrane Biology, Center for Bioinformatics, Saarland University, Box 15 11 50, D-66041 Saarbrücken, Germany.
authors.forename: Daniele
authors.initials: D
authors.lastname: Narzi
authors.forename: Shirley W I
authors.initials: SW
authors.lastname: Siu
authors.forename: Christian U
authors.initials: CU
authors.lastname: Stirnimann
authors.forename: John P A
authors.initials: JP
authors.lastname: Grimshaw
authors.forename: Rudi
authors.initials: R
authors.lastname: Glockshuber
authors.forename: Guido
authors.initials: G
authors.lastname: Capitani
authors.forename: Rainer A
authors.initials: RA
authors.lastname: Böckmann
mesh_terms: D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D010084:Oxidation-Reduction; D019704:Protein Disulfide-Isomerases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D011522:Protons; D013879:Thioredoxins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; D011522:Protons; D013879:Thioredoxins; D019704:Protein Disulfide-Isomerases; C526648:dsbA protein, E coli