Basically, you see these 3D representations of specific proteins as a crumple of ribbons-- literally like someone ran multi-colored ribbons though scissors to make curls and dumped it on the floor (like a grade school craft project).
So... I understand that proteins are huge organic molecules composed of thousands of atoms, right? Their special capabilities arise from their structure/shape. So basically the molecule contorts itself to a low energy state which could be very complex but which enables it to "bind?" to other molecules expressly because of this special shape and do the special things that proteins do-- that form the basis of living things. Hence the efforts, like Alphafold, to compute what these shapes are for any given protein molecule.
But what does one "do" with such 3D shapes?
They seem intractably complex. Are people just browsing these shapes and seeing patterns in them? What do the "ribbons" signify? Are they just some specific arrangement of C,H,O? Why are some ribbons different colors? Why are there also thread-like things instead of all ribbons?
Also, is that what proteins would really look like if you could see at sub-optical wavelength resolutions? Are they really like that? I recall from school the equipartition theorem-- 1/2 KT of kinetic energy for each degree of freedom. These things obviously have many degrees of freedom. So wouldn't they be "thrashing around" like rag doll in a blender at room temperature? It seems strange to me that something like that could be so central to life, but it is.
Just trying to get myself a cartoonish mental model of how these shapes are used! Anyone?
That's one approach.
The thing to understand is that proteins form "binding sites": areas that are more likely to attract other particular regions of proteins or other molecules, or even atoms. Think about hemoglobin. The reason it holds onto oxygen atoms is because it has binding sites.
Binding sites are great because they represent more freedom to do things than molecules typically have. Normal chemistry consists of forming strong electronic bonds between atoms, or forming rigid lattices/crystals.
Binding sites allow molecules to do things like temporarily attach to each other and let each other go under certain circumstances, for instance when another binding site is active/inactive. This can happen through "conformation change", where a molecule bound/unbound on some binding site makes the protein change shape slightly. This is how proteins can act like machines.
> What do the "ribbons" signify
Different regions of the protein have different sequences of amino acids. Amino Acids have somewhat different shapes from each other. The ribbons are actually broader than the spindles (or threads), and less flexible. Not sure about the different colors, maybe someone else can fill in.
> Also, is that what proteins would really look like if you could see at sub-optical wavelength resolutions?
Not really, it's an abstraction. They're big molecules, so if you look closely they're made of atoms, which are (kinda, sorta not really, quantum stuff) spherical.
> So wouldn't they be "thrashing around" like rag doll in blender at room temperature?
Yes, but the attractions between the different parts of the molecule keeps it somewhat under control. So more like an undulating little creature, jellyfish perhaps.
> It seems strange to me that something like that could be so central to life
Yep, gotta remember that it's all statistical. These things are getting made, do their job, breaking, and getting degraded some insane number of times per second. Swarm behavior, sort of.