September 22, 2010 | David F. Coppedge

Piston Engine Joins Rotary Engine in Cells

The rotary engine ATP synthase has been discussed frequently in these pages (e.g., 12/22/2003, 08/10/2004, 08/04/2010) as an exquisite “molecular machine” that produces the cell’s energy pellets (ATP) with a rotary, turbine-like mechanism.  Now, a piston-driven engine has been found at work in every cell’s energy factory.
    ATP synthase operates at the end of a sequence of machines in the respiratory chain that generates chemical energy (in the form of ATP) from the food we eat (or from sunlight, in the case of plants).  The enzyme runs on proton motive force – a flow of protons that drive its carousel-like rotor.  But how does the proton gradient get established?  That’s the job of Respiratory Complex I, the first machine (enzyme) in the chain.  Complex I takes electrons from food, stored in NADH molecules, and transfers them down a chain of electron receptors to parts of the machine that pump protons across the mitochondrial membrane into the periplasm, setting up a proton gradient.  It now becomes evident that Complex I includes parts that move like pistons.
    Complex I was reported in a July Science Express paper as having a railroad-like coupling rod (see 07/06/2010).  This week, The Scientist described it as “A piston proton pump,” referencing a paper from Nature last May:1  Richard P. Grant reported,

The mechanism proposed by Leonid Sazanov’s group at the Medical Research Council in Cambridge is “almost completely unexpected,” says Faculty Member Thomas Meier.  Unlike the ATP synthase, which “drives protons across the membrane in a rotary turbine-like motion,” writes Faculty member Nathan Nelson in his review, the transfer of electrons from NADH cause a slight widening of one part of the complex, forcing the long helix to move like the a [sic] row of pistons that shove protons across the membrane.

Some scientists feel this important finding will rival the excitement about the discovery that a rotary engine produces ATP.  One faculty member “predicts that it will become one of the most cited papers in respiratory chain research, as important to our complete understanding of energy generation as is the mechanism of ATP synthase.
    The original paper in Nature1 used the same piston metaphor and contained the same enthusiasm:

The overall architecture of this large molecular machine is now clear.  F-ATPase [ATP Synthase] has been compared to a turbine.  In a similar vein, complex I seems to resemble a steam engine, where the energy of the electron transfer is used to move a piston, which then drives, instead of wheels, a set of discontinuous helices.

Tomoko Ohnishi, commenting on this paper in the same issue of Nature, continued the piston metaphor in his title, “Structural biology: Piston drives a proton pump.2  He described how the food we eat goes through a “highly efficient process” called oxidative phosphorylation in the mitochondria, ending in the synthesis of ATP.  Complex I was known to have some distance between its electron acceptors and the transmembrane antiporters.  It was unknown how the parts were coupled.  Now, the mechanism of the first enzyme, Complex I, is becoming clear:

The membrane-spanning enzyme known as complex I couples the movement of electrons to that of protons as a way of converting energy.  Crystal structures suggest how electron transfer drives proton pumping from afar.
    Complex I is one of the energy-converting enzyme complexes found in the membranes of the cell’s fuel factories, the mitochondria, and was the last such complex without a structural portrait.  But in an epoch-making paper in this issue, Sazanov and colleagues1 describe X-ray structures of bacterial complex I, and report that it has an unusual ‘piston’ mechanism for controlling proton movement across mitochondrial membranes (see page 441).

Both the original paper and Ohnishi’s summary contain diagrams showing how the piston mechanism works in conjunction with the connecting rod described in the 07/06/2010 entry.
    ATP Synthase was mentioned in a PNAS commentary this week.3  Stuart L. Ferguson [Oxford U] recounted the decades of effort to determine how ATP was generated.  He indicated that much remains to be learned, including why different life forms have different numbers of c-subunits in the F0 rotor (for background, see 12/22/2003, 08/10/2004, 08/04/2010), but mentioned “the apparently universal nature of the ATP synthase” in passing, indicating that even lowly bacteria have these elegant machines.  Eukaryotes (including all plants and animals) and eubacteria, but not archaea, “are from sequence analyses very similar,” he mentioned.  Archaea also use forms of ATP synthase that differ from those of eukaryotes in some respects.

1.  Efremov, Baradaran, and Sazamov, “The architecture of respiratory complex I,” Nature 465 (27 May 2010), pages: 441?445, doi:10.1038/nature09066.
2.  Tomoko Ohnishi, “Structural biology: Piston drives a proton pump,” Nature 465 (27 May 2010), pages 428?429, doi:10.1038/465428a.
3.  Stuart L. Ferguson, “ATP synthase: From sequence to ring size to the P/O ratio,”>Proceedings of the National Academy of Sciences, published online before print September 21, 2010, doi: 10.1073/pnas.1012260107.

So what can evolutionists do with the discovery of rotary engines and piston engines in the simplest forms of life, all the way up to humans?  They just attribute it all to the remarkable creative power of the goddess Evolution.
    A Nature Education article by Nick Lane (cf. 08/11/2010) referred to the piston paper by Efremov et al, saying “Again, the structure betrays the mechanism – in this case not a rotary motor but, even more surprisingly, a lever mechanism not unlike the piston of a steam engine (Figure 2),”  But then, Lane invoked Michael Russell’s lame hydrothermal waste dump myth (02/15/2008) – you remember, the one that falsified the primordial soup myth (02/05/2010) – to draw a parallel from simple proton gradients in deep sea vents to the proton gradients that drive pistons and rotors in the cell.
    That’s like comparing rolling stones to automobiles, or clouds to aircraft.  Look at his convoluted reasoning to get from rolling stones to automobiles without intelligent design:

There are, of course, big open questions – not least, how the gradients might have been tapped by the earliest cells, which certainly lacked such sophisticated protein machinery as the ATP synthase,” Lane admitted.  “There are a few possible abiotic mechanisms, presently under scrutiny in Russell’s lab and elsewhere.  But thermodynamic arguments, remarkably, suggest that the only way life could have started at all is if it found a way to tap the proton gradients.

  So tell us, Nick, did Life try to tap into these gradients on purpose?  After all, if it “found a way,” it must have been looking for it.  In Lane’s vision quest, Life, in some nebulous form lacking ATP and a proton gradient, studies those deep-sea vents with furrowed brow, asking “How can we tap into that?”  But wait – without a way to tap into it already, it would have no energy to look for, discover, and harness the proton gradient.  Well, that must imply, then, that all the machinery just “arose” all together, fully formed, by chance.  Maybe it was a miracle: “the acquisition of mitochondria and the origin of complexity could be one and the same event,” he said.
    Only an evolutionist gets away with this kind of nonsense in scientific lit.  But that’s not all.  Lane proceeded to extend his mythology to all complex life, with all its organs and functions, speculating how it all originated with proton gradients.  In the end, though, he had to admit the whole idea was a myth:

The question is, what kind of a cell acquired mitochondria in the first place?  Most large-scale genomic studies suggest that the answer is an archaeon – that is, a prokaryotic cell that is in most respects like a bacterium.  That begs the question, how did mitochondria get inside an archaeon?  The answer is a mystery but might go some way toward explaining why complex life derives from a single common ancestor, which arose just once in the 4 billion years of life on Earth.

Well, at least he recognized he left some “big open questions” begging.  Nothing more needs to be said.  He just shot any claim to science out from under his own feet and showed himself belonging to a “mystery” cult, along with the editors of Nature, who, by printing his speculations, became willing accomplices in promoting the mystery cult.
    Take Nick Lane’s freak show (08/11/2010) to Mad Magazine where it belongs.  The rest of us are enjoying this confirmation of intelligent design at the smallest scale of life.  You’re running on pistons and rotary engines.  Cool!  Lane gets a teeny bit of credit for sharing one amazing factoid in his article about the electrical potential in your body set up by these proton gradients: “A membrane potential of 150 mV across the 5-nanometer membrane gives a field strength of 30 million volts per meterequivalent to a bolt of lightning.”  You’ve got lightning in your tank.  Hot!

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