Thursday, July 29, 2010

16th EBEC: short notes

One of the most exciting ATP synthase news on the EBEC conference(Warsaw, July 17-22) was a new structure of bovine F1+c-oligomer structure that had eight c-subunits in the c-ring (John Walker's talk). John also pointed out that since the sequence of mammalian (and avian, as far as I can remember) c-subunit is identical for all organism sequenced so far, it is highly probable that c8 is the stoichiometry for all mammals (and birds?). This also suggests that their H+/ATP ratio is 2.67.

Other things:

A crystal structure of bovine F1 grown in the presence of phosphonate had ADP bound in all 3 catalytic sites, but the low affinity site lacks Mg2+ (John Walker's group). Does Mg2+ dissociate before nucleotide?

Another new structure - thermoalkaliphilic Caldalkalibacillus thermarum F1 at 3 Å resolution (Greg Cook in collaboration with John Walker) crystallized in the presence of ADP. Unlike the previous structure where all three catalytic sites were empty and that had a curved subunit gamma, the new structure is pretty similar to bovine ones, suggesting that deformation of gamma in the first structure was due to crystallization conditions. In the new structure one can also see an ATP molecule bound to the epsilon subunit. Since no ATP was added to the crystallization mix, it seems that the nucleotide binding site on C. thermarum epsilon is highly selective at room temperature: usually the ATP contamination in commercial ADP does not exceed 0.5%.

Toshiharu Suziki from Masasuke Yoshida's lab succeeded in expressing human F1 in E. coli and characterized its rotation at single-molecule level. This opens a way to study the effects of mutations on mitochondrial F1 activity.

Ryota Iino from Hiroyuki Noji's lab reported clearly distinguishable 36o rotation steps in E. coli ATP synthase with mutation aE219H introduced to slow the rotation in FO.

For the rest of ATP synthase EBEC reports take a look in the special BBA Bioenergetics issue with 16th EBEC Proceedings for full-text papers and in the volume supplement with poster abstracts.

Sunday, June 27, 2010

Recent FoF1 papers: June

A few personal comments on some of the recent papers related to ATP synthase:

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.

Monday, June 21, 2010

Who is interested in ATP synthase?

Or - to be precise - where are they located?

About two years ago I made a world map overlay for visits of (04.2006-04.2008). In the last two years (06.2008-06.2010) the picture remained essentially the same:


United States

United Kingdom









Thursday, June 10, 2010

ATP synthase blog launched

The idea is to occasionally share my thoughts on topics related to ATP synthase.

This includes ideas and observations that are usually omitted from peer-reviewed publications, comments on scientific papers, etc.

Comments, critics, suggestions are most welcome.