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Are there proteins whose operation we can describe from first principles using chemistry or physics?

I've had introductory college courses in biology, and some classes in neuroscience, so I know that the behavior or purpose of many proteins is well characterized. But the descriptions of how proteins work—at least in what I've read—are always sort of similar and vague, “X binds to Y and the shape of the protein changes, which does Z”. At the level of the material I'm reading, I wouldn't necessarily expect much more, but I am curious whether researchers actually have a more detailed understanding of how proteins work. Can we describe the way that (some) proteins work in the same way that an engineer can describe how an internal combustion engine works?

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closed as too broad by AliceD, MattDMo, anongoodnurse, James, kmm Nov 30 '16 at 18:17

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    $\begingroup$ That depends strongly on the resolution scale you want to look at. How ribosomes work (a classical example for a molecular machinery) is pretty well understood, though surely not the binding partners for each and every amino acid in these huge complexes is known. $\endgroup$ – Chris Nov 25 '16 at 7:21
  • $\begingroup$ Ribosomes aren't really proteins, but yes we do understand how some individual proteins work, the problem is that the interactions of charge , shape,and bonding on each amino acid interact with each other so the larger the proteins the more difficult it is to understand all of the layered interactions. that's why de novo protein design is so difficult and why even simple design needs computers. If you want to learn more "Protein structure prediction" or "Bioinformatics" are good search terms. Or you can get started here, expasy.org/proteomics $\endgroup$ – John Nov 25 '16 at 16:04
  • $\begingroup$ Yes. Hemoglobin is a very well studied example. $\endgroup$ – anongoodnurse Nov 25 '16 at 17:19
  • $\begingroup$ Yes. For a number of proteins, including certain classes of enzymes, we have a very good biochemical idea of how the reaction catalysis works - the metal catalyst ion binds to these amino acids here, the substrate binds to these other residues like so, and in doing so induces a conformational change bringing the catalytic ion and a water molecule in close proximity to the substrate, where X chemical reaction takes place, then the substrate is released and the reaction center is recharged likewise. $\endgroup$ – MattDMo Nov 25 '16 at 21:42

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