Biological complexity: molecular machines seen clearly (Introduction)

by David Turell , Friday, October 02, 2020, 19:12 (1299 days ago) @ David Turell

The molecules act in more precise and amazing ways than previously imagined:

https://evolutionnews.org/2020/09/new-research-finds-molecular-machines-are-even-more-a...

"Images of the molecular machines that Michael Behe brought to public attention 21 years ago were dim and fuzzy at the time but were convincing enough then to make a strong case for irreducible complexity. Now, new imaging techniques such as cryo-electron microscopy allow scientists to look at individual parts of the machines at near-atomic resolution.

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"In 1997, John E. Walker shared the Nobel Prize in Chemistry with Paul Boyer and Jens Skou for discovering that ATP was synthesized in cells by a rotary engine.

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"The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. [Emphasis added.]

"A “Grotthus mechanism” is a hand-off series something like a bucket brigade. The protons that power the rotor do not just flow by themselves; they are passed along to the inlet by a bucket brigade of water molecules, which take in each proton and hand it off to the next water molecule.

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"Since 1997, researchers also found that ATP synthase machines come in pairs (dimers). The dimers, further, are mounted in rows on folds of the cristae (the membranes within mitochondria). The precise angle between the two dimerized motors and the spacing between them maximizes proton intake. The new paper says that the angle between the dimers flexes a bit, damping vibrations even more, thanks to specific molecules at the pivot of the wedge that allow some flexing, but not too much:

"Our structure of bovine dimers has a wedge made of small proteins and specific lipids in the membrane domain of each monomer that imposes a range of acute angles on the central axes of the monomers, and a pivot between the wedges accommodates rocking motions of the machine accompanying catalysis and other movements that happen independently. It also throws light on how the membrane rotor is made to turn."

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"Publishing in Nature Communications,3 Al-Otaibi and six others in the UK used cryo-electron microscopy to study the “structure of the bacterial flagellum cap complex” that “suggests a molecular mechanism for filament elongation.”

"The pentagonal cap, looking somewhat like a stool, is composed of FliD proteins. This cap is first extruded in pieces through the central channel of the hook. Its subunits self-assemble at the end, while forming “an extensive set of contacts across several subunits, that contribute to FliD oligomerization.” The cap then guides individual flagellin proteins coming up through the channel into their positions in the growing filament, as shown in the animation. This is a well-controlled process, they found, dependent on the precise arrangement of amino acids in each protein, so that contacts work as intended."

"Once outside of FliD, we propose that exposed hydrophobic residues act as a chaperone, and promote flagellin folding in its insertion site. In order to accommodate the next flagellin subunit, conformational changes need to occur to open an adjacent binding pocket. We propose that the folding of the new flagellin protomer leads to dislodging of the cap complex, that rotates by ~65°, thus positioning an adjacent cavity of the cap complex close to the next flagellin insertion site (Fig. 5). This hypothesis agrees with previously proposed mechanisms of flagellar elongation."

Comment: The best way to appreciate this degree of complexity is to view some of the videos on the internet. There are rare mistakes that are edited out. This is an older (2014) video from Facebook which takes sometime to download and does not show these newest findings. This can happen only through exact design. How much detail of these machines must be shown before a designer is accepted?