How Enzymes/Proteins Work at Atomic/Molecular Level

[nhmllr]

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

 

[aroc91]

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.

 

[nhmllr]

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

 

[Iainios]

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).

 

[LudusRex]

for your question. Enzymes and proteins are essential components of all living organisms and play crucial roles in various biological processes. These molecules are made up of long chains of amino acids, which are linked together by peptide bonds. The sequence and arrangement of these amino acids determine the shape and function of the enzyme/protein.

At the atomic/molecular level, enzymes and proteins work by binding to specific molecules, called substrates, and facilitating chemical reactions. This binding occurs at the active site of the enzyme, which is a specific region that is complementary in shape and chemical properties to the substrate. This specific binding is made possible by the unique arrangement of amino acids in the active site.

Once the substrate binds to the active site, the enzyme undergoes a conformational change. This means that the shape of the enzyme is altered in a way that brings the substrate closer to each other, facilitating the chemical reaction. This conformational change is often referred to as induced fit.

The enzyme then catalyzes the chemical reaction by lowering the activation energy required for the reaction to occur. This is achieved through the precise positioning of the substrate and the involvement of specific amino acids in the active site that act as catalysts.

After the reaction is complete, the products are released from the enzyme and it returns to its original shape. The enzyme can then bind to another substrate and repeat the process.

To understand this process better, I recommend watching this animation by the Howard Hughes Medical Institute: . It demonstrates the step-by-step process of enzyme action at the atomic/molecular level using the example of an enzyme called lysozyme.

In summary, enzymes and proteins are able to work at the atomic/molecular level due to their precise structure and the specific interactions between their amino acids and the substrate. This allows them to act as efficient and specific catalysts in biological reactions, despite being made up of only a few thousand atoms. I hope this helps to clarify how these tiny "machines" work in living organisms.