title: Redox-linked protonation state changes in cytochrome bc1 identified by Poisson-Boltzmann electrostatics calculations.
abstract: Cytochrome bc(1) is a major component of biological energy conversion that exploits an energetically favourable redox reaction to generate a transmembrane proton gradient. Since the mechanistic details of the coupling of redox and protonation reactions in the active sites are largely unresolved, we have identified residues that undergo redox-linked protonation state changes. Structure-based Poisson-Boltzmann/Monte Carlo titration calculations have been performed for completely reduced and completely oxidised cytochrome bc(1). Different crystallographically observed conformations of Glu272 and surrounding residues of the cytochrome b subunit in cytochrome bc(1) from Saccharomyces cerevisiae have been considered in the calculations. Coenzyme Q (CoQ) has been modelled into the CoQ oxidation site (Q(o)-site). Our results indicate that both conformational and protonation state changes of Glu272 of cytochrome b may contribute to the postulated gating of CoQ oxidation. The Rieske iron-sulphur cluster could be shown to undergo redox-linked protonation state changes of its histidine ligands in the structural context of the CoQ-bound Q(o)-site. The proton acceptor role of the CoQ ligands in the CoQ reduction site (Q(i)-site) is supported by our results. A modified path for proton uptake towards the Q(i)-site features a cluster of conserved lysine residues in the cytochrome b (Lys228) and cytochrome c(1) subunits (Lys288, Lys289, Lys296). The cardiolipin molecule bound close to the Q(i)-site stabilises protons in this cluster of lysine residues.
authors.affiliation: Structural Biology/Bioinformatics Group, University of Bayreuth, Germany.
authors.forename: Astrid R
authors.initials: AR
authors.lastname: Klingen
authors.forename: Hildur
authors.initials: H
authors.lastname: Palsdottir
authors.forename: Carola
authors.initials: C
authors.lastname: Hunte
authors.forename: G Matthias
authors.initials: GM
authors.lastname: Ullmann
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D045303:Cytochromes b / Q000737:chemistry* / Q000378:metabolism*; D014450:Electron Transport Complex III / Q000737:chemistry* / Q000378:metabolism*; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D018698:Glutamic Acid / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006639:Histidine / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D007506:Iron-Sulfur Proteins / Q000378:metabolism; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D009010:Monte Carlo Method; D010084:Oxidation-Reduction; D011485:Protein Binding; D011487:Protein Conformation; D021122:Protein Subunits / Q000737:chemistry; D011522:Protons; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D017550:Spectroscopy, Fourier Transform Infrared; D055672:Static Electricity; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D014451:Ubiquinone / Q000737:chemistry / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D007506:Iron-Sulfur Proteins; D008024:Ligands; D021122:Protein Subunits; D011522:Protons; D014451:Ubiquinone; D018698:Glutamic Acid; D006639:Histidine; D045303:Cytochromes b; D014450:Electron Transport Complex III