Mutate residue with NCAA

[Anonymous]

Hello,

I am trying to mutate a pose with beta-amino acid residues. From what I’ve tried and read, it’s impossible with both mutate_residue and MutateResidue mover, because they only take one letter representations of the residues. My hope is that I can figure out how to do it through packing. I’m not sure how to make it work properly.

This was just my test code to see what would work:

pose = pose_from_sequence(‘A’*20)

test_pose = Pose()

test_pose.assign(pose)

mutant_position = 3

from pyrosetta.rosetta.core.pack.palette import CustomBaseTypePackerPalette

pp = CustomBaseTypePackerPalette()

pp.add_type(‘cisACHC’)

tf = pyrosetta.rosetta.core.pack.task.TaskFactory()

tf.set_packer_palette(pp)

packer = pyrosetta.rosetta.core.pack.task.PackerTask()

packer.task_factory(tf)

packer.apply(pose)

 

 I don’t know that kind of operations should be added here. How to specify which position will be changed and make sure it’s going to be changed to the residue I want? I did read the mutants script and the ALA scan script, but I still don’t understand this…

I will be grateful for any help!! Thank you

 

 

[Anonymous]

Unfortunately, neither the MutateResidueMover nor the packer can be used to convert an alpha-amino acid to a beta-amino acid.  This is because both assume that the backbone is invariant, and that only the side-chain is changing (which isn’t true if you’re inserting a methylene group in a backbone).  There is no general protocol for converting an alpha-amino acid to a beta-amino acid, since this necessarily alters the fold of the polymer.  You’re starting with a chain of alpha-alanines, so any attempt to mutate these to beta-amino acids will fail.

If the position being mutated were already a beta-amino acid,  however, either approach should work.  You can build a pose with the PeptideStubMover, using B3A instead of alanine at the positions where you want beta-amino acids, and then use either the MutateResidueMover or the packer to change the beta-amino acid identity at those positions.

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