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wazabee t1_iw7a1gw wrote

Reply to comment by vhu9644 in Shape of a protein predicted by two different AI models (ESMFold on the left, AlphaFold on the right) by greentea387

Protein structures have both static and dynamic sections inside of them, but computer models are not not well suited to predict them. You'd need to confirm you findings with an imaging experiment, like 3d NMR, that is capable of capturing those dynamic, shifting structures.

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vhu9644 t1_iw7c7do wrote

Sure, but I’m just skeptical of the claim that these two predicted structures would give wildly different functions, or that they really are distinct on something this simple.

I cold believe it if for example the catalytic core of a barrel protein had small alterations in structure, but this is just two helices next to each other with a small disordered domain on the bottom.

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wazabee t1_iw7cgjz wrote

It can. A single point mutation of one amino acid is enough to cause a deviation in normal function, as is the case of some diseases.

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vhu9644 t1_iw7ct55 wrote

Yes I’m aware.

But these arguments by analogy don’t do it for me for something this simple, that doesn’t even look like it would have a catalytic core without some other subunit. Do you even know what protein this is?

Edit:

It’s a serotonin receptors from cricket. It’s a membrane protein so it should be stabilized by going through the membrane.

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wazabee t1_iw9uoon wrote

im a biochemist, so yes i know what a protein is. Im trying to explain the importance of maintaining the 3d structure of a protein to its function. Both proteins have the same sequence, but there is a slight difference in what the software rendered. Now, based on the sequence, a cell would reliably recreate the same protein. However, in the context of having 2 slightly different structures from the same amino acid strand, yes, you can have widely varying functions that result depending on the original purpose of the peptide strand.

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vhu9644 t1_iwau2w1 wrote

And I’m a synthetic biologist in protein engineering. What I’m skeptical about is that for this protein specifically, this change in structure plays a major role in function determination, due to its simplicity, and that we are seeing two distinct folds that are locked from each other.

The point ultimately is moot, the protein chosen is a membrane bound protein, so the lipid layer will provide stabilization.

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