[grey_whiskers]

Hey, Cool!

Two further points:

1. Are we sure the mass of the glass bead being tugged along did not affect the mechanics?

2. I'd been playing in my mind with just such a mechanism: often people trying to get protein structure from ab initio sequences take some molecular dynamics program and let the protein "relax" to a preferred structure. But of course this isn't how proteins are constructed in vivo: if you add one peptide at a time, the lowest energy configuration of an intermediate fragment might be different than the preferred configuration of that same subsequence in the full chain. What effects would there be on predicted protein folding starting from one peptide at a time? Do we have enough CPU time to model this properly?

Extra credit: Are all proteins build "one peptide at a time" or are significant sub-assemblies built first and then put together using enzymes? I dunno? Any biochemists here have any ideas?

Cheers!

Full Disclosure: Thanks, Snarks!

[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.