[furball4paws]

I will try to answer some of your questions, if you wish.

1. I have no answer for your question re:the glass bead (nice way to start, right).

2.I am confused by your use of the word "peptide". I think you mean "amino acid" instead. The paper describes the DNA dependent RNA polymerase, which reads the information on the DNA and makes a message (messenger RNA, mRNA). That message is translated on the ribosome into a protein (usually). Every 3 bases codes for an amino acid. They are added stepwise, one at a time until the message in completely translated. The protein product may be finished at that point or further modified. It could be shortened or mixed with a different protein or another of the same to make a complete protein or enzyme. Simple proteins automatically fold into the appropriate structure. These can be modeled. It used to take a Cray, but this has improved dramatically in the last 25 years. 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 the answer is not simple without a specific example. Hope this helps some.

[grey_whiskers]

2.I am confused by your use of the word "peptide". I think you mean "amino acid" instead.

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!