Layman's question: if we know the precise shapes of two molecules, is that enough information for us to compute every interesting detail about how they'll interact?
Or are you saying that the shape change involves a change to the set of bonds, but for some reason we continue to call it the same "kind" of protein?
The 3D structure (= shape) however, is mostly dependent on the hydrogen bonds (among other things like bisulfide bonds) between the amino acids that make up a protein. So the deprotonated variant of a amino acid side chain might not be able to interact in the same way as its protonated form, which will cause a different 3D structure for the whole protein, which in turn influences how it interacts with other molecules.
That's really interesting. So now that this new microscopy technique is available, is it practical for chemists to determine every useful detail about the covalent bonds and hydrogen bonds in the imaged molecule?