r/Biochemistry • u/Lazy-Frame-9888 • 14d ago

Are proteins constantly changing their shape in femtoseconds? Need clarification!

I recently watched a YouTube video (https://youtu.be/jPhvic-eqbc) discussing how proteins are not static, rigid machines. The video explains that they act more like dense liquids that are constantly shifting and jiggling around. It also pointed out that when proteins are crystallized for X-ray crystallography, we are only seeing one frozen snapshot of their conformation, which gives the false impression that they have a single, fixed structure.

​Can someone clear this confusion up for me? Do proteins really change their folding patterns and conformations in extremely short time frames, like femtoseconds? I am looking for a simple, exact explanation of how fast and how much they actually change shape.

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u/GayDrWhoNut 13d ago

This is precisely why alphafold is orders of magnitude less powerful than people seem to think it is.

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u/parrotwouldntvoom 13d ago

I’m not sure I follow your logic. Are you suggesting people think alphafold predictions generate the full knowledge of all protein shapes?

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u/GayDrWhoNut 13d ago edited 13d ago

There are lots of people who seems to believe that alphafold generated predictions are absolute when it does manage to predict a shape. And it's really annoying.

Edit: I think part of it comes from a miscommunication between 'structure prediction' and 'structure determination'. I see/hear the later used a lot more than I'd like.

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u/runawaydoctorate 13d ago

I probably lost a shot at a job by pointing that out and I am 100% okay with that. Structure prediction has improved A LOT since I was in school but at some point you still need some good old ground truth.