Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase

Abstract

Cytochrome C oxidase plays a crucial role in cellular respiration and energy generation. It reduces O to water and uses the released free energy to move protons across mitochondrial and bacterial cell membranes adding to the essential electrochemical gradient. Energy storage requires that protons are taken up from the high pH, N-side and released to the low pH, P-side of the membrane. We identify a potential proton exit from a buried cluster of polar residues (the proton loading site) to the P-side of CcO via paths made up of waters and conserved residues. Two water cavities connect the proton exit pathway to the surface only when hydrated. Changing the degree of hydration may control otherwise energetically favorable proton backflow from the P-side.

Tracing the Pathways of Waters and Protons in Photosystem II and Cytochrome c Oxidase

“…Hydrogen bond connections made in many snapshots in an MD trajectory or the many accepted microstates of an GCMC analysis can be subjected to a network analysis [119]. Programs such as Cytoscape [120] and Gephi [121], permit visualization of the network (see Figures 3b and 4).…”

“…MCCE [70] carries out GCMC analysis of the water orientation and occupancy and the protonation state and proton positions of residues in the whole protein. Network analysis [119] then generates a hydrogen bond matrix for the resultant Boltzmann distribution. Long-range connections between residues bridged by water chains are found.…”

“…Recent simulations with MCCE hydrogen bond network analysis in Rb. sphaeroides CcO [119] proposed a different proton exit pathway via N96, T100, S168 (Rb. sphaeroides numbering) with the exit close to H93/E182.…”

“…MD snapshots of Rb. sphaeroides CcO were subjected to MCCE network analysis [119]. Well hydrated MD snapshots show connections from a polar residue cluster on the N-side of the protein through the D-channel to the PLS and on to the P-side of the protein (Figure 4).…”

“…However, the K-channel remains disconnected [155]. The exit of the hydrogen bond network [119] is near several identified water exit pathways [118]. The network analysis was also carried out on snapshots from MD trajectories run changing the protonation states of key residues that lead to changes in hydration.…”