Skip to main content
. Author manuscript; available in PMC: 2019 Apr 10.
Published in final edited form as: Biochemistry. 2018 Mar 29;57(14):2150–2161. doi: 10.1021/acs.biochem.7b01194

Figure 5.

Figure 5

Potential O2 pathways predicted by ILS. A) Equivalent regions to the O2 delivery pathway of cytochrome aa3. Red isosurfaces correspond to ΔG of ~-3.3 kcal/mol. Magenta isosurfaces correspond to ΔG ~-1.8 kcal/mol. Discontinuous gaps between the isosurfaces indicate unfavorable O2 insertion regions, correlated with hindrances along the pathway. Constricting residues are labeled; E286 (not shown) is located below F282 and G283. B) The entire pathway of cytochrome ba3 is highly favorable for O2. The ILS results of cytochrome ba3 were obtained by analyzing the simulation trajectories for our previous study.1 C) Other potential O2 delivery pathways in cytochrome aa3. Pink surfaces correspond to ΔG of +1 kcal/mol. The O2 pathway, highlighted in dashed red box, is the only region extending all the way from the membrane to the reduction site. The alternate pathways proposed by Oliveira et al43 start in between TM7 and TM8 and in between SII (brown), TM8 and TM9.