Back to Search
Start Over
Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations
- Source :
- Biochimica et biophysica acta. 1857(9)
- Publication Year :
- 2016
-
Abstract
- Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. While proton uptake channels as well as water exit channels have been identified for A-type CcOs, the means by which water and protons exit B-type CcOs remain unclear. In this work, we investigate potential mechanisms for proton transport above the dinuclear center (DNC) in ba3-type CcO of Thermus thermophilus. Using long-time scale, all-atom molecular dynamics (MD) simulations for several relevant protonation states, we identify a potential mechanism for proton transport that involves propionate A of the active site heme a3 and residues Asp372, His376 and Glu126(II), with residue His376 acting as the proton-loading site. The proposed proton transport process involves a rotation of residue His376 and is in line with experimental findings. We also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. We identify two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane, which can potentially also act as proton exit transport pathways. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151(II) and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected by protonation of residue His376.
- Subjects :
- Proton
Cytochrome
Biophysics
Analytical chemistry
Protonation
Molecular Dynamics Simulation
010402 general chemistry
01 natural sciences
Biochemistry
Article
Electron Transport Complex IV
Proton transport
0103 physical sciences
010304 chemical physics
biology
Chemistry
Active site
Water
Cell Biology
Thermus thermophilus
Proton Pumps
biology.organism_classification
0104 chemical sciences
Proton pump
biology.protein
Protons
Subjects
Details
- ISSN :
- 00063002
- Volume :
- 1857
- Issue :
- 9
- Database :
- OpenAIRE
- Journal :
- Biochimica et biophysica acta
- Accession number :
- edsair.doi.dedup.....2319aa52a8d94b7a0ac8b44845389d27