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How to design a stand-alone loop from a binding interface?

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How to design a stand-alone loop from a binding interface?

Hi, Dear colleagues!

I am new to Rosetta and am now finding whether there is a solution to my problem using powerful Resetta.

I want to cut a loop which is responsible for the binding of A to B from protein A. I need to constrain this loop so it will maintain its bound conformation though it is now in the apo form.

The problems are:
1) I need to find a way to automatically constrain it either by using disulfide bond and cyclization;
2) The loop is disulfide-bonded to the rest of the protein and this disulfide bond may be responsible for maining a turn in its bound conformation;

Is there anyone that know how can achieve this using Rosetta?
Thanks in advance!

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Fri, 2011-02-11 21:11

I'm not sure I understand the question.

You have the conformation of a loop. You want to create a short peptide that maintains the same conformation in solution.

Your question is, what can Rosetta do to help ensure the loop will maintain its conformation?

I guess the counter question is, what are you willing to do to the peptide? You mention cyclization. Did you want to test locations to anchor that disulfide and then test that it will maintain conformation?

I'm not aware of anyone working with cyclic peptides currently (and I'm not an expert on disulfides). There's no hits for cyclic peptides in the codebase.

I think Rosetta is up to the task of modeling this peptide, but I don't think we have any protocols already written to do it. In other words, I think you'd need to write a fair amount of code yourself. (You may want to try it in PyRosetta, on the theory that python is easier to write in than C++.)

Sun, 2011-02-13 12:21