Coupling factor B affects the morphology of mitochondria. Grigory Belogrudov reports that if you fuse factor B with B-GFP and express it in an animal cell, the mitochondrial cristae morphology changes.
Factor B is present in mitochondria. Bovine (and human) factor B is a 175-aa protein that binds to ATP synthase and is important for good coupling between ATP synthesis and proton transport, and probably in ATP synthase dimerization. Its structure was solved at 0.96Å. Take a look in Grigory's recent review on factor B (full text) for more details, including the history of factor B research.
Essential Arg of Fo-a subunit in FoF1-ATP synthase has a role to prevent the proton shortcut without c-ring rotation in the Fo proton channel. Noriyo Mitome at al. (Masasuke Yoshida's lab) confirmed that in ATP synthase from thermophilic bacillus the conservative arginine residue in the 4th TMH of subunit a (aArg210 in E. coli) is necessary to prevent proton leaks through FO. Substitution by Glu, Ala or Val resulted in leaky FO, while substitution with Phe, Ile, Lys or Trp prevented the leak, but also blocked the coupled proton transport.
Sunil Nath attacks the common conception of chemiosmotic theory in his 2-part review in J. Bioenerg. Biomembr. Together with him, we can follow the critical analysis of classical paper by Mitchell and Moyle (1969) and conclude that their results have to be interpreted with great caution.
The reviews also contain a good compilation of studies where results inconsistent with the classical variant of chemiosmotic theory were obtained.
The alternative theory proposed by Sunil is the so-called torsional mechanism. According to his opinion,
"The torsional mechanism solves the conundrum by postulating the existence of a specific, regulated anion access channel (constructed as an anion binding pocket in the a-subunit of the FO portion of ATP synthase at the a-c lipid-water interface) in the vicinity of the proton access channel (with its binding site in the c-subunit of FO at the ac interface)."Other postulates of this hypothesis include localized electric potential difference, dynamically electrogenic but overall electroneutral mode of ion transport, and sequential translocation of membrane-permeable succinate monoanion (or Na+ or K+ counter-cation) and proton.
Unfortunately, although this brave hypothesis is over 10 years old, it still has no experimental support. And I see no reasons to go for this theory before at least some of the wonderful phenomena mentioned above are demonstrated experimentally.