Noncanonical amino acid HIP

[Anonymous]

Hi,

I would like to run Rosetta for different pKa and for that I want to run modeling of
protein with different type of HIS, like canonical HIS and non canonical HIP, for different pKa (for example 7.4 and 6.0).

I would be very grateful if somebody can send me Rosetta parameter file for non canonical HIP residue,
or maybe there is some instructions how to build and implement new type of non canonical residue HIP from canonical
HIS.

Thank you for help.

[Anonymous]

By HIP I’m assuming you mean ND1-Phosphonohistadine ( http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=HIP&operation=ccid )

Typically the way Rosetta handles phosphorylated amino acids is via patches. Take a look at Rosetta/main/database/chemical/residue_type_sets/fa_standard/patches/ particularly the his_methylated.txt, ser_phosphorylated.txt, and tyr_phosphorylated.txt patches. You could combine the relevant portions of each, and then make a new patch file in that directory (also add the filename to the patches.txt listing file in the previous directory). Rosetta will then read phosphorylated histidines as a patched histidine.

The other alternative is to create a completely new parameter file for the HIP residue. See https://www.rosettacommons.org/node/3536. As it’s just a modification of an existing residue, you might prefer to hand-edit the params file instead of going through the whole auto-generation process.

[Anonymous]

Thank you very much.

[Author]

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