Yup. Blame on rush hour traffic addling my tired old noggin.
Simple proteins automatically fold into the appropriate structure. These can be modeled.
Yes, I was talking about the modeling...one hopes to predict the energetically favorable conformation of the known sequence of amino acids. Since a full quantum treatment is "beyond the state of the art" one uses parameterized functions for the various interactions.
If one starts the modeling with all of the amino acids already in the proper sequence, and then allows the structure to relax in search of an energetic / entropic minimum, you will end up with such-and-such a final answer for the most favorable conformations.
I was speculating / suggesting that if one starts with a single amino acid, then adds the second amino acid and allows that to relax (not much except rotational changes about a single bond, not very exciting...); then adds the third amino acid and allows that structure to relax; etc. how different would the final predicted structure be, from the one arrived at using the first method?
The second method "add one at a time and then relax" would appear to be a closer analogy to the actual physics of what is going on inside the cell...
For more complex proteins, other proteins may be involved in preventing them from taking the wrong configuration until translation is complete. Finished proteins can be a single protein, multiples of one protein or mixtures of more than two protein subunits. So he answer is not simple without a specific example.
That is exactly the info I was looking for, thanks.
Full disclosure: do you happen to know how hemoglobin in particular is built up?
Cheers!
In your example of looking at peptides built one amino acid at a time, every possible outcome is possible depending on the protein. If the peptide binds strongly in the wrong configuration it may not be possible to "straighten" it out after you've added all the amino acids. But it also may be no problem.
Wrong configurations are a problem during translation, those "helper" proteins are used to keep the protein from getting into the wrong configuration until it is complete.
The hemoglobin question is known, I just don't know it and will have to look it up, if I have it handy. If you want it it'll have to wait. Let me know.