Molecular Machine Updates

Scientists continue to make headway understanding the detailed workings of molecular motors.  The two most famous rotary motors yielded additional secrets recently:

• ATP Synthase:  “Making ATP” was the short title of a paper in PNAS this week.¹  Xing, Liao and Oster came up with a model that linked the rotation of the gamma subunit (the camshaft) to the beta subunits in the F1 hexamer, where ATP synthesis occurs.  They identified two “bumps” in the potential curve that prevent back-slippage of the rotor.  The shaft is tightly coupled to the lobes, to produce a kind of “zipping” effect of hydrogen bonds as the beta subunits bend along a hinge during the catalytic function.
      The eta part of the stator is apparently also essential in preventing slippage, in order to couple the energy to the synthesis function.  Mutations were shown to flatten the “energy bumps” on the potential curve, making slippage more likely.
      They also noted that in ATP hydrolysis mode (the reverse cycle) ADP tends to get stuck in the mechanism; “this is hardly surprising,” they said, “because F1 evolved to synthesize, and only under laboratory conditions does the eukaryotic F1 operate in hydrolysis mode.”  The bacterial ATPase and vacuolar ion pump do operate in hydrolysis mode in vivo and presumably do not have this inhibition problem.  Their lingo on this point mixes design and evolution: “The V1 motor of the vacuolar ATPase, being designed for ion pumping, may have avoided ADP inhibition by the evolution of additional subunits” (emphasis added in both quotes).
• Bacterial Flagellum:  A Japanese and UK team publishing in Nature² found stepping behavior in the flagellar rotor by direct observation.  The torque generation by the ion flux may be responsible for the rotation taking place in measurable steps.  Their observations “indicate a small change in free energy per step, similar to that of a single ion transit.”  They mentioned that this had been seen in ATP synthase, but never before in the bacterial flagellum.  They measured about 26 discrete steps per revolution.  There was no mention of evolution in the paper.
• Type III Secretion System (TTSS):  The TTSS, a kind of molecular syringe embedded in the membrane of some bacteria that allows them to inject toxins in nearby hosts, was also described more fully in the same issue of Nature by two Yale scientists.³  They found that the protein ordnance is too large, so there are special chaperones on hand to unfold them before loading them into the barrel.

¹Xing, Liao and Oster, “Making ATP,” Proceedings of the National Academy of Sciences USA, published online before print October 10, 2005, 10.1073/pnas.0507207102.
²Sowa et al., “Direct observation of steps in rotation of the bacterial flagellar motor,” Nature 437, 916-919 (6 October 2005) | doi: 10.1038/nature04003.
³Akeda and Galan, “Chaperone release and unfolding of substrates in type III secretion,” Nature 437, 911-915 (6 October 2005) | doi: 10.1038/nature03992.  See also the News and Views section by Blaylock and Schneewind, “Microbiology: Loading the type III cannon,” Nature 437, 821 (6 October 2005) | doi: 10.1038/437821a.

Some evolutionists have identified similarities between the TTSS and the bacterial flagellum, and suggested that the flagellum evolved from the TTSS by co-option.  There are many problems with this suggestion, not the least of which is that most of the protein structural parts of the flagellum are unique.  The authors of the TTSS paper did not mention this suggestion or anything about evolution.  In fact, evolutionary theory was useless for all three papers.  Describing the machines in terms of their design was perfectly appropriate, illustrating again the utility of scientific research from a design perspective.  The two brief mentions of evolution in the ATP synthase paper were useless appendages, like vestigial organs of a less-evolved philosophy (sarcasm intended).