December 22, 2003 | David F. Coppedge

Life Runs on Waterwheels

The cells of every living thing are filled with molecular machines, and one of the most fascinating is a rotary motor called ATP synthase (see April 2002 back issue, opening paragraph).  This is a true mechanical/electrical motor, found in every living thing from bacteria to elephants and palm trees.  It is really two motors in one; the top part, named F1, is where synthesis of ATP takes place (as described in previous entries on this subject; see Sept. 18 headline, for instance).  The bottom machine, named F0, is like a carousel of 10 to 14 proteins labeled c subunits.  This is the driving engine of this “splendid molecular machine” that spins at up to 6000 rpm.  Somehow, it converts a proton flow into rotation.
    Ever since the rotary nature of this all-important enzyme was established around 1996, scientists have been eager to explain its operation in detail.  According to four Swiss biochemists writing in a Minireview of the December issue of Structure,1 “Energy conversions are central to all life forms,” and this particular motor generates “the universal energy currency of living cells” (ATP).  For these reasons, “The central metabolic role of ATP has stimulated much interest in how it is formed using the energy of oxidations or light.  Research in this area has led to impressive progress, including some of the most spectacular discoveries in the history of biochemistry” (emphasis added in all quotes).  Scientists have made great strides in explaining the F1 part of the machine (see Sept. 18 headline, for instance), but till recently, have been baffled at how the F0 motor generates torque.  Now, these scientists present a model that suggests it spins by a water-induced electric potential – a waterwheel, on a 10-nanometer scale..
    Their model, illustrated with cartoon drawings in the article, is fascinating, but too involved to describe in detail here.  In short, they believe that water channels of different heights in the mitochondrial membrane create an electrical potential difference in the membrane that flows downhill across the stator (labeled with the letter a), a tall housing on the side of the carousel that contains tubes which open and close to prevent proton leakage.  The stator looks something like the apparatus in a gumball machine.  Think of protons as gumballs, channeled through slots that open up and allow them to roll in or out.  Now, add a carousel to your machine that the gumballs have to ride around before dropping into the outlet slot.  Then, imagine an electrical charge on the gumballs.  As the gumball (proton) drops into its seat, it rides the carousel until it approaches the stator.  There, it is repelled by a positively charged entity called Arg227 inside the stator housing, and it falls out.  The empty seat, now negatively charged, is attracted by the potential difference between the water-filled inlet and outlet channels in the membrane.  The empty seat is thus pushed through the stator, generating torque.  Here, a gumball from another channel hops into the empty seat and takes its turn around the carousel.  To summarize, water makes the wheel turn, converting electrical energy into mechanical energy, then into chemical energy in the form of ATP.
    The machinery is reversible.  When the electrical potential reverses, the motor runs the other direction, and instead of the machine generating ATP, it consumes ATP and spits out protons.  When no potential is present, the motor rocks back and forth in “idling mode” within certain angular limits, allowing protons to migrate into the gumball machine or out of it as the appropriate channels open or close.  This can equalize the proton gradient inside and outside the membrane in a controlled manner.  The machine would stay in idling mode if it weren’t for the electrical potential.  The authors believe that “the membrane potential is the crucial driving force to induce the torque required for ATP synthesis.”  Once the F0 carousel gets spinning in high gear, the attached camshaft forces precise conformational changes in the F1 subunits up above, generating three ATP per revolution.  “The capacity of this process is impressive,” the authors write; “the daily turnover of a human has been estimated to be 40 kg [about 88 lb] of ATP on average.”  Several quadrillions of these motors in your body keep your power plant running (see Feb. 5 headline), making you shine at 116 watts. 
    Other scientists had tried to envision models invoking mechanical energy, thinking that the protein gradient in a c subunit induces a conformational change that turns the wheel.  This electrical model, however, seems to not only account for the efficient generation of torque, idling, and reversibility, but also explain why some models of the motor have 14 c subunits (the seats on the carousel) and others have 10 or 11.  The number of c subunits is apparently related to the membrane potential.  A chloroplast ATP-synthase motor, with 14 subunits, runs at peak efficiency with half the potential (60 mV) required to turn a bacterial motor with 10 or 11 c subunits (120 mV).  “To investigate whether this is a general principle and to address the interesting question how the two motors, which operate with a different number of steps, are synchronized, sophisticated biochemical investigations of the enzyme’s performance are required,” they conclude.  Speaking of the performance of these machines, scientists have already determined that these motors approach 100% efficiency.  Impossible at our scale, these tiny motors “cheat” thermodynamics by using random Brownian motion like a ratchet.  Some models of the carousel run on alternate fuel: sodium ions instead of protons (hydrogen ions).
    A paper in PNAS2 last week discovered something interesting about a similar rotary machine, V0V1-ATP synthase or V-ATPase for short (see Feb. 24 headline).  Unlike the F-ATPase model, the two parts of V0V1 can detach and re-attach reversibly.  Iwata et al. studied a subunit that apparently clamps onto the two parts like a socket to hold them together, thereby keeping the central shaft locked into its correct position.  Maybe this model could be viewed as the travelling carnival carousel that can be dismantled and installed on the road.  Apparently V-ATPase motors are needed to maintain acid balance in many parts of the cell.  The scientists describe where they are found: “They reside within intracellular compartments, including endosomes, lysosomes, and secretory vesicles, and within plasma membranes of certain cells including renal intercalated cells, osteoclasts, and macrophages.  Eukaryotic V-ATPases are responsible for various cell functions including the acidification of intracellular compartments, renal acidification, born [sic; bone?] resorption, and tumor metastasis.”3  V-ATPase has a different-looking camshaft and stator; like F-ATPase, it is found in archaea, bacteria and higher organisms.  It does all the ATP synthesis for the kind of bacteria that live in hot springs.


1Peter Dimroth, Christoph von Ballmoos, Thomas Meier, and Georg Kaim, “Minireview: Electrical Power Fuels Rotary ATP Synthase,” Structure Vol 11, 1469-1473, December 2003.
2Iwata et al., “Crystal structure of a central stalk subunit C and reversible association/dissociation of vacuole-type ATPase,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0305165101, published online Dec. 18, 2003.
3Presumably, due to a failure in the system; the authors do not elaborate.  See this article that suggests increased V-ATPase activity in a tumor is a response aimed at provoking cell death, or apoptosis.

A popular book for young people and adults is called The Way Things Work by David Macaulay.  He describes the inner workings of car engines, computers, the space shuttle, and many kinds of artificial machines.  We need a book like this about cells.  Now that we know a cell is composed of thousands of machines, wouldn’t it be cool to see them visualized in a popular way?  The definitive textbook The Molecular Biology of the Cell is heavy, expensive ($120) and difficult to read, but creationist reviewers who understand it have remarked that it is filled with powerful evidence for design.  We need to get this information before the eyes of the public.  ATP synthase just screams for some high-tech, 3D fly-through computer animation.  This one molecular machine, so small you would have to shrink yourself down a billionfold to even see it, could demolish Darwinism* all by itself.  But then to think that the cell is filled with ten thousands of similar wonders (see yesterday’s headline, for instance, and another article in the same issue of Structure that argues a certain “chaperone machine should be regarded as a molecular motor,” actively employing force to fold a protein), and – well!  Does the word overkill mean anything when raised to the fourth power?

*Consider that this machine is made up of multiple, discrete units, each one a protein, and each protein is made up of hundreds of amino acids in a precise sequence.  The Arg227 described above is an arginine amino acid residue in the 227th position of the stator protein.  It is so critical to the operation of the motor, that if that one amino acid is changed to something else, the motor won’t work at all.  (Scientists find these things out by artificially mutating individual amino acids and watching what happens.)
    The motor itself is irreducibly complex, but even more complex is the DNA code that contains all the genetic blueprints for all the parts, and the molecular machinery that builds the parts and then assembles them together in the right order, in the right place, in the right time.  Think about how each protein must be folded properly by another host of machines that operate under strict quality control (see Dec. 21 headline).  As the coup-de-grace, now realize that every living thing, down to the most primitive bacteria, already have working ATP synthase motors.  Can anyone really believe this all evolved by chance?  The gulf between the simplest living cell and any precursor is not just a canyon; it’s a light-year.  Read our online book, Evolution: Possible or Impossible? if you need a little more convincing.

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