pose_from_sequence with modified residue

[Anonymous]

How can I create a pose from sequence containing acetylated lysine?
Using p = pose_from_sequence(“VSK[LYS_p:N_acetylated]GPF”,”fa_standard”) and then dumping it gives a pdb with two chains and the K residue is not modified.
thanks!

[Anonymous]

Are you getting any error messages?

One possibility if you’re using a recent release is that the syntax of patch annotation has changed. It has gone from “_p:” to just “:”. You may want to try passing the sequence “VSK[LYS:N_acetylated]GPF” instead.

Another possible complication is that the default patches being loaded has changed, and N_acetylation is no longer loaded by default. You may need to add the option “-chemical:patch_selectors PEPTIDE_CAP” to the list of commandline options when initializing PyRosetta in order for it to get loaded.

[Anonymous]

No error messages. I am using old release. So the new way ( without _p:) doesn’t work. The problem is that I am getting two chain output instead of only one. Please have a look at the attached pdb file. Is there easier ways to create peptides with any possible PTMs? Fixbb protocol? Please let me know.
thanks!

[Anonymous]

When I do it with r55950 I get an appropriately acetylated lysine – it has CP, CQ and OCP atoms, as would be expected, and pose.annotated_sequence() shows the appropriate patch level on the lysine. (‘V[VAL_p:NtermProteinFull]SK[LYS_p:N_acetylated]GPF[PHE_p:CtermProteinFull]’) Granted, it’s hard to tell from the structure because of all the overlapping atoms, though if you repack things and hide the first chain, it becomes much easier to see the acetylation on the N-terminus of the second chain.

Wait, though. Are you wanting an N-terminal acetylated lysine, or a sidechain acetylated lysine? The N_acetylated patch is for N-terminal acetylation. For sidechain acetylation, use [LYS_p:acetylated] instead.

[Anonymous]

oops…you are right. I should have used [LYS_p:acetylated]. problemo solved. Thanks!

[Author]

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