January 7, 2010 | David F. Coppedge

Best Look Ever at Life’s Smallest Rotary Motor

All cells trade in energy currency called ATP (adenosine triphosphate).  The molecular energy pellets are produced in profusion by molecular machines with rotary engines.  The engines contain all the standard parts: rotor, stator, energy input, and torque production.  They are embedded in the membranes of mitochondria and run on proton motive force.  We’ve reported many times on these exquisite machines (e.g., 10/20/2009 bullet 5, 05/25/2009).  They are the smallest rotary motors in the universe (so far as we know), about 10 by 20 billionths of a meter in size.  Now, scientists in Canada have imaged them in more detail than ever before – at 1.6 Angstrom resolution.  Their findings were reported in PNAS.1
    The motors come in two families: F-ATP, or ATP synthase, used to produce ATP by all living things, and V-ATP, used primarily “in reverse” to acidify vacuoles and other subcellular regions.  The engines differ only in minor details.  The rotor is on the bottom half, called F0 or V0, and ATP synthesis or degradation takes place in the top half, F1 or V1.  Lau and Rubenstein studied the V-ATPase from an archaeal microbe that inhabits hot springs, Thermus thermophilus.  They imaged 19,825 motors to increase the average resolution down to 1.6 Angstroms (16 nanometers, or billionths of a meter).  As a result, they were able to map out all the parts in better detail than ever, which are shown in photographs and diagrams in the paper.
    They were particularly interested in gaining insight on how the motor produces torque.  Putting their observations together, they deduced this is what happens: a proton flows up a channel to a negatively-charged glutamic acid (an amino acid link in one of the protein chains) in the 12-sided rotor.  This neutralizes the glutamic acid (Glu 63) and makes it turn and release the proton, which is shuttled upward out another channel to the cytoplasm.  The Glu63 is then attracted to a neighboring arginine (Arg 735) in the rotor and an arginine in the stator (Arg 563), causing a rotational step.  The next proton causes the next unit of the 12-part rotor (the L-ring) to take another clockwise step, and so on.  Just like in man-made motors, the offset force causes the rotor to spin.
    The stator contains two peripheral stalks, partially embedded in the membrane, and there is a central stalk that applies the torque produced in V0 to the ATP synthesis lobes in V1.  These come in 3 pairs that are arranged like orange slices around the stalk.  The stator and rotor do not touch, but are positioned precisely to cause an optimal torque:

The peripheral stalks are optimally arranged to counter forces attempting to push them away from or pull them towards V1.  Both peripheral stalks pushing away from or pulling toward V1 would exert a force on subunit I perpendicular to a line drawn between the stalks (Fig. 4B).  Therefore, from Fig. 4B, it is apparent that the peripheral stalks are optimally arranged to apply a force that is eccentric on the L-ring.  It is well known that application of an eccentric force on a rotor will cause it to turn, and this principle powers all man-made motors.  An attractive force between the positively charged Arg 563 residue of subunit I and a negatively charged Glu 63 residue of a L-subunit counterclockwise of the contact point (when viewed from V0 to V1), would cause the rotor to turn with a clockwise direction, as expected from the known clockwise rotation direction of the rotor during ATP synthesis.  Therefore, this eccentric force could be the basis for torque generation in V0.

The authors mentioned nothing about how this machine might have evolved.  They only mentioned the E-word in passing, making a brief offhand reference to the belief that the F-ATP and V-ATP motors are “evolutionarily related but differ in the details of subunit composition and arrangement.”

1.  Lau and Rubenstein, “Structure of intact Thermus thermophilus V-ATPase by cryo-EM reveals organization of the membrane-bound VO motor,” Proceedings of the National Academy of Sciences USA, January 6, 2010, doi: 10.1073/pnas.0911085107.

If you catch a sense of the wonder in what science has discovered about these motors since the first suggestion in 1993 that they were true rotary engines, you must be feeling goose bumps at each new revelation.  These motors power every living thing – even the simplest, most primitive microbe depends on these irreducibly-complex motors.  They are true motors.  This is not just a figure of speech: they rotate and perform work.  Their parts are arranged for this purpose.  They run on proton motive force, and they generate torque.  That torque is applied by a power-takeoff mechanism in the central stalk to manufacturing stations in the top half.  Previous reports have shown that these little machines operate at 100% efficiency.
    How on earth could any putative “prebiotic” entity get along without these machines already present?  Without a reliable source of energy, chemicals merely react and come to equilibrium.  Notice that the alignment and spacing of each part of the engine is precise, down to the charge on individual amino acid units.  This machine is composed of dozens of proteins, each one composed of hundreds of amino acids.  Getting any one of them by chance is astronomically improbable (see online book).  You are looking at exquisite manufacturing design at the fundamental units of life.  Who would have imagined such things were even possible?  Certainly not some materialist-leaning storytellers in Victorian England 150 years ago.

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