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How is it that proteins are able to build structures, like microtubules, cell walls and bone?


Proteins are 1-dimensional chains of 'lego-like' molecules that fold into atomically-precise 3D tools. There are ~20 types of legos that have properties that differ along a number of axis like hydrophobicity, charge, reactivity, size, flexibility, etc. And those 20, in combination, seem to be enough to build all of the tools life needs to interact with its environment. Most proteins are assemblies of a few hundred such 'legos' (again, of which there are 20 types).

Those 3D structures then, because they're encoded in the 'tape-like' DNA, can actually themselves be modular, rearranged, and this chunk can be lopped off and plopped onto that chunk, or assembled with this chunk over here. When you string a 'firefly-shine' protein next to a 'in-the-nucleus' protein, the firefly-shine protein will now be physically connected to the 'in-the-nucleus' signal, so you get firefly-shine in the nucleus. Now encode all the things proteins can do: bind to things, enzymatically make things, go places, make structures, sense chemicals, light, force, electricity, other atoms, etc. - and you get little multi-part robots made of those various active 'chunks'.

If you have a protein piece that itself assembles in a hexagonal-like shape, you could imagine assembling a number of them into a soccer ball - just as a virus does to protect its DNA.

Or if there are small Brownian-aware 'ratchets' attached to stiff fiber-like proteins, you can get proteins that move or walk: https://www.youtube.com/watch?v=y-uuk4Pr2i8

The microtubule's they're walking over are themselves linear assemblies of proteins: https://www.youtube.com/watch?v=jGmz4xVP50M

Similarly, spider silk is protein: https://boltthreads.com/

And leather is protein: http://provenance.bio/

Here are some more animations. The only thing wrong is how empty the space is. In real life, there is no empty space at all - it's jammed pack with other proteins and molecules:

https://www.youtube.com/watch?v=FzcTgrxMzZk

https://www.youtube.com/watch?v=VdmbpAo9JR4

Bone is a mineral deposit, deposited by proteins within particular cells: https://en.wikipedia.org/wiki/Osteoblast#Osteogenesis

Cell walls or lipid membranes are fats that are generated in the right concentration by proteins, and then allowed to self-assemble, creating well-controlled environmental compartments for sensitive proteins to remain functional.


> The only thing wrong is how empty the space is. In real life, there is no empty space at all - it's jammed pack with other proteins and molecules

That was a huge revelation for me. I'm reading through The Machinery of Life by David S. Goodsell; his drawings drive this point home very well. It turns out the cells are so densely packed, that only small things can meaningfully move around at all (through diffusion, i.e. by bouncing around) - for larger stuff, there are dedicated mechanisms in the cell that ship big molecules around!




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