September 28, 2007 | David F. Coppedge

Molecular Machines Under the Nanoscope

Seeing machines just billionths of a meter long seems impossible, but cell biologists are now routinely looking into the cellular black box.  Using indirect but powerful methods, they can actually begin to visualize the gears and wheels and cogs of the protein machines that make life possible.  Some of our favorite cell gadgets were examined in recent papers.

  1. Bacterial flagellum:  A paper in Nature: Molecular Systems Biology1 juxtaposed design language with evolutionary speculation.  Rajagopala et al began with high praise for the Ferrari of the cellular world:

    Motility in most bacterial species depends on a sophisticated molecular machine called the flagellum.  The flagellar apparatus is made of dozens of different proteins and thousands of individual subunits.  The bacterial flagellum is actually a mechanical nanomachine with a rotation frequency of 300 Hz, an energy conversion rate of nearly 100%, and the ability to self assemble.

    So far this sounds like Michael Behe’s writing.  Indeed, these authors representing three countries found even more essential protein parts for the flagellum – take one away, in other words, and motion stops.  But the gist of their paper was that the variety of flagella in different species shows evolution: “Many features of the bacterial flagellum have changed over the course of evolution,” they said.  “This is reflected in the surprisingly different composition and protein interaction patterns in the flagella of different species, which may reflect adaptations to species-specific motility needs.”
        Yet their argument was based entirely on homology.  They did not explain how needs produced functional, adapting flagella.  They merely built an evolutionary tree based on similarities:

    The bacterial flagellum represents an interesting entity to study the evolution of complex biological machines.  For an evolutionary view of the flagellum on the protein level, we constructed a phylogenetic supertree solely based on flagellar protein sequences.  As anticipated, this tree closely recapitulates phylogenetic relationships identified, employing traditional phylogenetic marker molecules such as rRNAs.
        Whereas it is generally believed that the motility machinery evolved from an ancient type III secretion system, the detailed steps leading to current structures have yet to be defined….
        Similar to protein sequences and structures, interactions among proteins are often conserved in the course of evolution.  In fact, the phylogenetic relationships of different species are partially reflected by the phylogenetic interaction profile of the integrated network.

    Conservation is not evolution.  Phylogenetic tree construction, furthermore, presumes the very question under investigation: that flagella evolved in the first place.  And as any creationist would say, adaptation is not proof of evolution; it is proof of design.
        In summary, these authors could not help but marvel at the flagellum.  They found an even more amazing network of interactions among the conserved protein parts.  Their conclusions about evolution, however, were based only on arguably circular arguments from homology.  Indeed, “the detailed steps leading to current structures have yet to be defined” in their own article.

  2. ATP Synthase:  A team of UK scientists publishing in PNAS investigated one detail of the other sophisticated rotary motor in all of life: ATP synthase.2 (See 09/18/2003, 07/16/2002.)  They wanted to know how a regulatory protein named IF1 inhibits the motor, like a Denver boot.  (After all, a high-performance motor usually comes with brakes.)  Stopping a spinning motor is not a simple matter.  They found it takes a complex set of protein interactions that forms an “inhibitory complex” with the machine like – well, let them explain:

    To form these complex interactions and penetrate into the core of the enzyme, it is likely that the initial interaction of the inhibitor with F1 forms via the open conformation of the {beta}E subunit.  Then, as two ATP molecules are hydrolyzed, the {beta}E-{alpha}E interface converts to the {beta}DP-{alpha}DP interface via the {beta}TP-{alpha}TP interface, trapping the inhibitor progressively in its binding site and a nucleotide in the catalytic site of subunit {beta}DP.  The inhibition probably arises by IF1 imposing the structure and properties of the {beta}TP-{alpha}TP interface on the {beta}DP-{alpha}DP interface, thereby preventing it from hydrolyzing the bound ATP.

  3. Transfer RNA:  One of the most amazing sets of machines, on which all forms of life depend, is the crew of translators that know which amino acid goes with which codon from the DNA code.  A family of 20 of these molecules, known as aminoacyl-tRNA synthetases, or aaRS for short, exists – one for each amino acid.  Each one knows its own amino acid and tRNA so well the accuracy of their operation is stunning.  Even when there are cognate codons (three-letter codes that differ yet code for the same amino acid), the machines rarely make a mistake.  For instance, metRS, the synthetase for methionine, can match two cognate codons with the right amino acid every time and eject very similar ones.
        Herein lies a mystery: if you look at a tRNA molecule (which looks something like a letter t), and the synthetase that works on it, the two active sites are separated by some distance.  The anticodon on the tRNA is on the bottom of the “t”, but the amino acid binding site is at the other end – a whopping seven nanometers away.  Seven nanometers may not sound like a lot, but at the molecular scale, that’s a lot.  How does one end of a blind machine communicate with the other end?
        To find out, two Indian researchers investigated metRS in detail and published their results in PNAS.3  They found that vibrations ripple through the amino acids of the enzyme along four pathways.  The strongest one overrules the others when the twist is just right.  Furthermore, they found that these communications caused conformational changes – swings like a lever arm, flips and turns – that had to match the substrate in order to work.  The amino acid would only attach if all the contact points were just right:

    Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site.  This study has provided the detailed paths of communication, which are consistent with experimental results…. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine.

The second two articles did not discuss how these mechanisms could have evolved.  Indeed, it would be a challenge to think of a scenario how they could evolve, since life at the most basic, primitive level depends on the activity of these specialized enzymes.

1Rajagopala et al, “The protein network of bacterial motility,” Nature: Molecular Systems Biology 3 Article number: 128 doi:10.1038/msb4100166.
2Gledhill, Montgomery, Leslie and Walker, “How the regulatory protein, IF1, inhibits F1-ATPase from bovine mitochondria,” Proceedings of the National Academy of Sciences USA, published online before print September 25, 2007, Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0707326104.
3Ghosh and Vishveshwara, “A study of communication pathways in methionyl-tRNA synthetase by molecular dynamics simulations and structure network analysis,” Proceedings of the National Academy of Sciences USA, published online before print September 26, 2007, Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0704459104.

Let the evolutionists speculate and spin their webs of belief; we have the observational evidence in front of our noses that shout design.  The precision of fit of these parts, and the accuracy of their performance, is beyond any theory of chance and blind stumbling in the dark.  We do not accept the circular reasoning of the Darwinists who keep saying they evolved because they have a phylogenetic tree, and they have a phylogenetic tree because they evolved.  Those dependent clauses collapse in on themselves.  Neither do we accept the merry-go-round reasoning that says they are wonderfully adapted because they evolved, and they must have evolved because they are wonderfully adapted.  No more Darwinian rhetorical tricks.  Look, behold, wonder, and use your God-given common sense.

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