There is a number of text layout errors in the published paper. I do not think It is a good idea of PLoS ONE not to show proofs of the paper to the authors.

In the XML version:
1) Fig. 3 is misplaced and appears only after Fig. 6.
2) The refs. citation format in the text is unusual throughout the paper: e.g. , [1] - [3] means [1-3]
3) Supplementary Information: Legend to Figure S1 is fused with the explanatory text, and this fused piece of text is printed twice.

In the pdf version:

1) on p.9, in the discussion section "Physiological Significance of the Ca2+-induced Inhibition" 3 major consequences of Ca binding with cytochrome oxidase are considered under 3 separate subheadings:
(i) Inhibition of the mitochondrial respiration.
(ii) Stimulation of reactive oxygen species (ROS) production.
(iii) Modulation of calcium uptake by mitochondria.
In the text as published (both, pdf and XML) the subheading hierarchy is scrambled, which may complicate somewhat reading.

2) Legend to Figure S1 is fused with the comments to the Figure.