Biological complexity: the dance of enzymes (Introduction)

by David Turell , Saturday, May 05, 2018, 00:21 (2395 days ago) @ David Turell
edited by David Turell, Saturday, May 05, 2018, 00:28

They shift their shapes to do their job changing shapes by using charged ions in their structure, but are they thinking or automatically following instructions or reacting to changes they sense by electrical signals; it is not clear but fascinating to study:

https://phys.org/news/2018-05-molecular-phospholipid-synthesis.html

"The most abundant molecule in cell membranes is the lipid phosphatidylcholine (PC, commonly known as lecithin); accordingly, the enzymes responsible for synthesizing it are essential.

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"When bound to membranes, the CCT enzyme changes shape in a way that allows it to carry out the key rate-limiting step in PC synthesis. When the amount of PC making up the membrane increases, the CCT falls off the membrane, and PC production ceases.

"'The membrane is this big macromolecular array with lots of different molecules in it," Cornell said. "How does this enzyme recognize that 'Oh, I should slow down because the PC content of the membrane is getting too high?

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"'What it looks like (when you visualize the output) is your big molecule dancing in front of your eyes," Cornell said. "We set up the molecular dynamics simulation not once, not twice, but 40 different (times). It took months and months just to do the computational parts and even more months trying to analyze the data afterward. We actually spent a lot of time once we got the data just looking on the screen at these dancing molecules."

"The simulated dance of the CCT molecule showed that when the M-domain, the section of the enzyme that typically binds to the membrane, detaches from a membrane, it snags the active site of the enzyme, preventing it from carrying out its reaction. When the snagging segment was removed from the simulation, the team saw a dramatic bending motion in the docking site for the snagging element, and speculated that this bending would create a better enzyme active site for catalyzing the reaction when attached to a membrane. The team confirmed these mechanisms using biochemical laboratory experiments."

Comment: In any live process of production, that process must have limits. These processes normally are controlled by feedback loops. In this case the enzyme seems to control its own activity, but there may be unknown restrictions at work. In any case this is a giant molecule that could not have been found in any evolutionary process by chance. Only design is capable to achieving this result.