Biological complexity: enzyme acts like a clam (Introduction)

by David Turell , Tuesday, June 27, 2017, 23:07 (2488 days ago) @ David Turell

Protein molecules can make motions like tiny machines as tghey work in cell metabolism:

https://www.sciencedaily.com/releases/2017/06/170627105458.htm

The adenylate kinase enzyme is crucial to managing the energy budget of cells, accelerating the biochemical process whereby energy is stored or released. The enzyme continuously changes between open and closed states. In its closed form, adenylate kinase is particularly active biochemically and thus able to accelerate the chemical reaction of "docked" molecules that it has encased like a clam. These are called ligands.

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The adenylate kinase enzyme opens and closes like a clam: it opens to receive a ligand and closes in order to "process" it biochemically. Afterwards, it opens once again to release it and admit the next ligand. This happens 340 times per second -- much too fast to map the individual stages of the process via structural analysis. (my bold)

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Kovermann's analyses had already shown that the enzyme's affinity for reaction -- the chemical pull between the enzyme and its ligand -- increases many times over in its closed state, whereas its productive turnover decreases at the same rate. In other words: Chemical activity between ligand and enzyme is particularly high during the closed state. But turnover decreases because the ligand cannot escape the closed "clamshell," which means fewer ligands in total pass through the enzyme.

Kovermann was also able to prove that adenylate kinase's structural dynamic strongly depends upon the interaction between enzyme and ligand- i.e. upon the presence or absence of a ligand. To do so, he compared the enzyme's closed state for both variations, with and without a trapped ligand. If there is no ligand, the closed enzyme's dynamic remains unchanged as compared to its open state. However, once a ligand is present, marked changes can be observed. "This behaviour is counter-intuitive, it's not what one would expect," explains Michael Kovermann.

Comment: Once again, the activity of protein molecules is amazing as they act like moving parts. Remember that enzymes are giant molecules that control the speed of individual molecular reactions, this one at 340 time a second. Too complex for chance. Must be designed by a powerful mind.