Was reading a intro Anatomy text which was going over basic transcription in the first few chapters.....anyway...

They were explaining how proteins are created in the ribosomes etc........and implied that as the string of amino acids where built the folding already starts to take place....prior to the complete chain being created.

so I was wondering what effect that would have on simulating a fold if done in a similar manner.

The proteins in Rosetta seem to be attempting to find the conformation of the complete Amino Acid sequence .......so there are hundreds to thousands of Amino Acids attempting to settle into nice comfy energy spot. With the crazy physical interactions all going on at once.

What would happen if the chain was simulated as being built stepwise one amino acid at a time, and then let the chain start folding early on before all the amino acids are even attached?

Kind of like trying to fold up a long metal link chain. Seems it would be easier to start at one end and start folding bit by bit to make it nice and compact, rather that throw the whole chain around and hope it miraculously falls into the compact orientation.

Would that give any kind of jump start to the final conformation?

You seem to essentially be asking if it might improve the prediction if the simulation were conducted from the beginning of the amino acid sequence through to the end. The beginning is called the N-termius. So this is the same question as Does the N-terminus fold first? which was recently discussed. I think you will find the discussion there interesting.

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Rosetta Moderator: Mod.Sense

Hey thanks, looks like the exact things I was looking for!