# Mathematical Enzyme

## Main Question or Discussion Point

So I've learned in biology about the amino acids forming chains/trees, and having different interacting "R groups"
Can somebody link to me an animation or careful description of how a specific enzyme/protein moves its parts step by step on an atomic/molecular level? I cannot find one.
I want to have an idea about how such tiny "machines" can work with only a few thousand atoms, and if I see one specific example I think I will understand how this works better.
Thank you

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This is ATP synthase. The top portion acts like a waterwheel of sorts that sits in the inner mitochondrial membrane. Via the electron transport chain, protons are built up on the outside and the only way to get to the inside is through the "waterwheel". That force (because they're trying to reach equilibrium) spins the top part around and the shaft that it's connected to. The rotation of the shaft shifts the bottom domains back and forth so when ADP and a phosphate ion bind when the active site is open, it pinches them together when it closes, binding them and making ATP.

I hope that helped.

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This is ATP synthase. The top portion acts like a waterwheel of sorts that sits in the inner mitochondrial membrane. Via the electron transport chain, protons are built up on the outside and the only way to get to the inside is through the "waterwheel". That force (because they're trying to reach equilibrium) spins the top part around and the shaft that it's connected to. The rotation of the shaft shifts the bottom domains back and forth so when ADP and a phosphate ion bind when the active site is open, it pinches them together when it closes, binding them and making ATP.

I hope that helped.
Yes, this is the sort of thing I was talking about!
Very interesting video... I didn't understand how mechanical enzymes could be

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Not all enzymes have such dramatic mechanical motions. Kinases are good examples. They takes a phosphate group from ATP and attaches it to one of the side chains (aka 'R groups') on another protein, the substrate:

Here, the enzyme activity isn't as mechanical, its chemical. The substrate and the enzyme have complimentary charges and geometry, so that only specific substrates can get close enough, and hang around long enough, for the phophate to be transferred.

This is also a great example of cellular control. It effectively allows computations to be done by taking in inputs (the regulatory proteins, such as cyclin or inhibitors) and gives an output (either the substrate is phosphorylated or it isn't).

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