August 4, 2010 | David F. Coppedge

Fine-Tuning Found in Life’s Rotary Engine

The universal energy currency in living things is ATP.  To produce the vast quantities of this molecule required by life 24 x 7, cells employ banks of rotary engines called ATP Synthase, which we have reported on previously in these pages many times.  ATP synthase has become somewhat of a mascot of intelligent design, because there are no known precursors to this multi-faceted, exquisitely efficient motor that is so tiny, 120,000 of them could fit on the head of a pin (07/16/2002).  Scientists continue to glimpse finer details of these engines using X-ray crystallography and other techniques.  A new finding, published in PLoS Biology,1 found that water molecules play a crucial role in the rotor.  The findings were summarized on PhysOrg, “Cells use water in nano-rotors to power energy conversion.”
    The international team (primarily at Max Planck Institute for Biophysics, Frankfurt, Germany) investigated the ATP synthase motors in an unusual bacterium that lives in highly-alkaline water.  “This bacterium prefers alkaline environments where the concentration of protons (H+) is lower outside than inside the cell – the inverse of the situation usually found in organisms that prefer neutral or acidic environments,” the authors said.  These cells have a special challenge.  Many cells live in neutral or acidic waters, providing no obstacles for the free flow of protons (hydrogen ions, H+) through the membranes and into the rotors they help turn.  In alkaline conditions, the protons would tend to leak out to neutralize the environment.  These special ATP synthase motors, therefore, need to maintain a gradient that is not as alkaline as the outside.  “The extreme alkaliphile [alkali-loving] Bacillus pseudofirmus Of4 grows by oxidative phosphorylation with cytoplasmic pH values maintained 1.5-2.3 pH units below the high external pH (up to 11) of the medium,” they explained (a pH of 11 is very strongly alkalinic).  “The existence of this reversed [delta]-pH poses a major thermodynamic problem, with which these cells must cope.”
    This species has some modifications to its engine design to help it cope with its special conditions.  It has a modified a-subunit, latent activity, and, most significantly, a modified c-ring with more subunits and a different shape.  The c-ring is the primary rotor.  In most organisms, it has 10 subunits; in B. pseudofirmus, there are 13 subunits (some other organisms have 11 or 15, and some run on sodium ions, Na+, instead of protons).  Though identical in many respects to the c-rings in other species, this one has an altered shape, somewhat like a “tulip beer glass,” they said soberly.  Although the ways in which these modifications serve to function in the alkaline environment of this bacterium are not yet clear, the authors are convinced that the cooperation of the water ion in the center of each subunit is a key:

This work shows a new type of proton coordination in an F1F0 synthase rotor ring….  It is evident that the coordination network of the water itself… is a stabilizing and therefore a structural part of this c-ring.  The presence of the water has been shown to enhance the Na+-binding affinity in the Na+-binding c11 ring [in organisms with 11 c-subunits].  Given this observation we propose that the water in the c13 ring binding pocket also enhances the proton affinity.  High affinity rotor binding sites are of central importance for all ATP synthases but are especially important for ATP synthases of bacteria that grow in alkaline environments…. Perhaps the novel manner in which a water participates in proton binding is also a consequence of adaptation of the ATP synthase to alkaliphily [adaptation to alkaline environments].

They speculated that this observation applies to a wider class of specialized c-rings, too.  Further comparative studies of c-rings are needed to determine the precise role of these ion-binding pockets in the c-ring subunits.  They speculated that they may have to do with “ion affinity and selectivity during torque generation” of the rotors.
    The authors mentioned evolution four times, but two of them were mere assumptions that the motors evolved; one was a statement about the lack of evolution (“This commonality of binding pattern underlines the evolutionary and functionally conserved relationship between the pmf- and smf-driven systems”) and the fourth was only a fleeting suggestion: “The smf-driven [sodium motive force] ATP synthases have been suggested to be evolutionary pioneers in the establishment of the modern ATP synthases,” they said, referring to a 2008 paper that suggested the idea.  “If this hypothesis is correct,” they continued, indicating the tentative nature of the idea, then perhaps the unusual forms of c-rings “could be derivatives of the c11 basic structure from an evolutionary point of view.”
    Nothing else from the “evolutionary point of view” contributed to the motivation, investigation, or the findings in the paper itself.  On the contrary, the authors praised the elegance of this ubiquitous nanomotor, including the modifications of this particular alkaline-loving species: “The subtle but important differences in the H-bonding network geometry allow a fine-tuning … and serve to optimize the required solvation energy,” they said.  “;Fine tuning of these parameters is of crucial importance within the a/c-ring interface, where the rotor binding sites pass a more hydrophilic environment.”  The “fine-tuning” theme was significant enough to appear in the Abstract: “It appears in the ion binding site of an alkaliphile in which it represents a finely tuned adaptation of the proton affinity during the reaction cycle.”  And they certainly did not hesitate to describe the ATP synthase as a wondrous, functional machine: “Like the wind turbines that generate electricity, the F1F0-ATP synthases are natural ‘ion turbines’ each made up of a stator and a rotor that turns, when driven by a flow of ions, to generate the cell’s energy supply of ATP.”
    PhysOrg in its coverage of the paper heaped on additional superlatives:

ATP synthases are among the most abundant and important proteins in living cells.  These rotating nano-machines produce the central chemical form of cellular energy currency, ATP (adenosine triphosphate), which is used to meet the energy needs of cells.  For example, human adults synthesize up to 75 kg of ATP each day under resting conditions and need a lot more to keep pace with energy needs during strenuous exercise or work.  The turbine of the ATP synthase is the rotor element, called the c-ring.  This ring is 63 A [Angstroms] in diameter (6.3 nm, or 6.3 millionths of a millimeter) and completes over 500 rotations per second during ATP production.

500 rotations per second amounts to, in the terminology of more familiar motors, some 30,000 RPM.  Since three ATP molecules are synthesized for each rotation, one of these motors can generate just short of 100,000 ATP per minute – and your body has quadrillions of them working all your life, even in your sleep.
    The best way to visualize what is going on is through animation.  A simplified but effective animation can be found at University of Osnabrueck by Wolfgange Junge; see Movie #2 (QuickTime); the c-ring is at the bottom (notice this is slow-motion; imagine seeing this at 30,000 RPM).  DNA-tube has a more detailed animation (rotor at top) showing the reversibility of the engine.  Additional animations can be located with an internet search on the phrase, “ATP synthase animation”.


1.  Preiss, Yildiz, Hicks, Krulwich and Meier, “A New Type of Proton Coordination in an F1F0-ATP Synthase Rotor Ring,” Public Library of Science Biology, 8(8): e1000443.  DOI:10.1371/journal.pbio.1000443.

As usual, the references to evolution were mere incense offerings to Charlie at the start of festivities, having nothing to do with the substance of the show.  Those formalities could have been excised without any loss of information; yea, indeed, but with a net gain in clarity.  Did the authors propose any primitive ancestors of functioning machines?  Any half-way ATP synthase?  Of course not; they wouldn’t work unless completely functional from the beginning.  They admitted, “The amino acid sequence of the protein subunits in this rotor … has features common to an important group of ATP synthases in organisms from bacteria to man.”  The modifications they found for the bacterium under study were not accidents or mistakes, but purposeful modifications allowing this species to survive in its harsh environment.  To say that it evolved from a more common form begs the question of evolution.  One would have to already subscribe to evolution to believe that.
    This machine is too wonderful for laypeople to be uninformed about it.  It keeps us alive!  It’s a real, mechanical, rotary engine spinning up to 30,000 RPM by the thousands in every cell on the planet!  The thought of rotary engines keeping us alive, even in our sleep, should be shouted from the housetops!  This was only discovered in the 1990s.  Aristotle, Descartes, Voltaire, Darwin and Freud could never have dreamed life was this exquisite at its core.  Could any finding in the history of science be as awe-inspiring?  People should know this.  Amaze someone at the water cooler today.  Instead of the useless phatic utterance, “How’s it going?” try opening with, “How’s your rotary engine doing today?”  Your surprised co-worker might respond, “I don’t have a Mazda,” to which you reply: “No, I mean your rotary engines – the ones inside of you.”  Now you have the springboard for an enlivening discussion that will put the engines spinning in your brains to good use.

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