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?
Some proteins have 3D structures that look like abstract art only because we don't have an intuitive understanding of what shape and amino acids are necessary to convert chemical A to chemical B, which is the main purpose of many enzymes in the body. If you look at structural proteins or motor proteins, on the other hand, their function is clear from their shape.
There are a lot of other things you can do with the shape. If it has a pore, you can estimate the size and type of small molecule that could travel through it. You can estimate whether a binding site is accessible to the environment around it. You can determine if it forms a multimer or exists as a single unit. You can see if protein A and protein B have drastically different shapes given similar sequences, which might have implications for its druggability or understanding its function.
The ribbon shape for GFP is a very cool barrel thing