title: Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase.
abstract: Cytochrome c oxidase contributes to the transmembrane proton gradient by removing two protons from the high-pH side of the membrane each time the binuclear center active site is reduced. One proton goes to the binuclear center, whereas the other is pumped to the low-pH periplasmic space. Glutamate 286 (Glu286) has been proposed to serve as a transiently deprotonated proton donor. Using unrestrained atomistic molecular dynamics simulations, we show that the size of and water distribution in the hydrophobic cavity that holds Glu286 is controlled by the protonation state of the propionic acid of heme a3, a group on the proton outlet pathway. Protonation of the propionate disrupts hydrogen bonding to two side chains, allowing a loop to swing open. Continuum electrostatics and atomistic free-energy perturbation calculations show that the resultant changes in hydration and electrostatic interactions lower the Glu proton affinity by at least 5 kcal/mol. These changes in the internal hydration level occur in the absence of major conformational transitions and serve to stabilize needed transient intermediates in proton transport. The trigger is not the protonation of the Glu of interest, but rather the protonation of a residue ∼10 Å away. Thus, unlike local water penetration to stabilize a new charge, this finding represents a specific role for water molecules in the protein interior, mediating proton transfers and facilitating ion transport.
authors.affiliation: Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Puja
authors.initials: P
authors.lastname: Goyal
authors.forename: Jianxun
authors.initials: J
authors.lastname: Lu
authors.forename: Shuo
authors.initials: S
authors.lastname: Yang
authors.forename: M R
authors.initials: MR
authors.lastname: Gunner
authors.forename: Qiang
authors.initials: Q
authors.lastname: Cui
mesh_terms: D019295:Computational Biology; D003576:Electron Transport Complex IV / Q000737:chemistry*; D018698:Glutamic Acid / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011522:Protons; D012242:Rhodobacter sphaeroides / Q000201:enzymology*; D055672:Static Electricity
chemical_list: D011522:Protons; D018698:Glutamic Acid; D003576:Electron Transport Complex IV
keywords: pKa; proton pumping