Linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry DFT exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex

Abstract

After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3-CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185-190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment.

Figure 1

Schematic (left) of cytochrome ba₃ with noted functionalities and cartoon of the same (right) showing the O₂ channel inside the lipid bilayer, the reaction chamber between Cu and Fe, and the electron- and proton-transfer “pipes”. Heme-b is not shown.

Figure 2

Catalytic “wheel” of cytochrome ba₃ focusing on the DNC. Concentration of O₂ for R → A is 90 μM for τ ≈ 9 μs, from Szundi et al.

Figure 3

Polar representation of the new 14-step catalytic mechanism. The central polar plot of the running sum, ∑ΔG°, shows the energetic course of catalysis as computed at the level of PW91.

Figure 4

Active site structure of compound 5 of ba₃. Left: smaller model used in the 2008 calculations. Right: larger model used in recent calculations, which is taken from the DNC of the high-resolution (1.8 Å) X-ray crystal structures (PDB entry: 3S8G) of ba₃ CcO from Tt. For ease of visualization, these two models are not on the same scale.

Figure 5

Plots of ∑ΔG° (kcal mol^–1) along the trajectory from 1 to 14. The top panel (A) is from the 2008 mechanism (from Table 4 for energies); the bottom panel (B) represents new work presented here. Solid black circles represent energies obtained from PW91 calculations, while reddish diamonds represent energies obtained from B3LYP* calculations. The experimental energies from 1 → 2 and 2 → 3 are obtained from refs (26) and (44)–.

Figure 6

Structure of the K path in cytochrome ba₃ as deduced from a combination of structural and mutational analyses. The top two residues are actually part of the active site structure per se. Both Glu15(II) and Y237 are protonated. This figure is taken from Figure 2 of ref (35). Reprinted with permission from ref (35). Copyright 2009 National Academy of Sciences.

Figure 7

Dipole moments of intermediates 4, 5₂, and 5. These three structures are overall neutral.

Figure 8

Plots of ∑ΔG° (kcal mol^–1) relative to state 13_H₂O along the trajectory from 11₂_2H (lower energy tautomer 1) to 1_H₂O in the cycle with the scalar water on Cu^II. The PW91 and B3LYP* energies were obtained for the smaller model (see Table S2 in the Supporting Information, SI). OLYP calculations were performed on the larger models (Tables 2 and A3).

Figure 9

Plots of ∑ΔG° (kcal mol^–1) relative to state 13 along the trajectory from 11₂_2H to 1 in the cycle without the scalar water on Cu^II. The PW91 and B3LYP* energies were obtained for the smaller model (see Tables S2 and S3 in the SI). OLYP calculations were performed on the larger models (Tables 3 and A3).