4 ms·

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 inter

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?

radus 6y ago
No, not by a long shot unfortunately.
hobofan 6y ago
Especially for proteins there is not a single "precise shape" for the whole protein. It might take on slightly different shapes dependent on a number of factors (e.g. pH of the environment). Interactions between a protein and some other molecule might also alter the shape of the protein. So overall, a slight change in any of those values can have cascading effects in how it interacts with any other molecule (which themselves share the same problem).
- DoofusOfDeath 6y ago
  So you're saying that given a particular instance of a protein molecule, the surrounding environment can cause its shape to change, but the set of bonds stays constant? 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?
  - hobofan 6y ago
    The covalent bonds stay the same (which is why it's still the same molecule), apart for sometimes localized modification (e.g. protonation). 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.
  - DoofusOfDeath 6y ago
    > The 3D structure (= shape) however, is mostly dependent on the hydrogen bonds (among other things) between the amino acids that make up a protein. 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?
- COGlory 6y ago
  No, because presumably they're solvated and that will change things dramatically. We have no idea, for instant, what the dielectric constant of water is in the middle of a protein, and therefore, no way to do these calculations.

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?

radus 6y ago

No, not by a long shot unfortunately.

hobofan 6y ago

Especially for proteins there is not a single "precise shape" for the whole protein. It might take on slightly different shapes dependent on a number of factors (e.g. pH of the environment). Interactions between a protein and some other molecule might also alter the shape of the protein. So overall, a slight change in any of those values can have cascading effects in how it interacts with any other molecule (which themselves share the same problem).

DoofusOfDeath 6y ago
So you're saying that given a particular instance of a protein molecule, the surrounding environment can cause its shape to change, but the set of bonds stays constant? 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?
- hobofan 6y ago
  The covalent bonds stay the same (which is why it's still the same molecule), apart for sometimes localized modification (e.g. protonation). 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.
- DoofusOfDeath 6y ago
  > The 3D structure (= shape) however, is mostly dependent on the hydrogen bonds (among other things) between the amino acids that make up a protein. 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?
COGlory 6y ago
No, because presumably they're solvated and that will change things dramatically. We have no idea, for instant, what the dielectric constant of water is in the middle of a protein, and therefore, no way to do these calculations.