Histidine phosphorylation by a patch

[Anonymous]

Dear all

I am trying to do some minimizations of a phosphorylated protein in a histidine (modification at the NE2) through a patch. To model phospho-histidine at the NE2, I need to delete the HE2 proton and protonate the ND1.

I’ve modified the his_methylated.txt patch (which I’m attaching) but it seems that whenever I try to delete the NE2 proton the minimization crashes:

caught exception 

[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/Patch.cc line: 333

ERROR: Failed to apply a PatchOperation to HIS_D

The system works fine if I keep the HE2 proton, but it is clearly not correct! I suspect that rosetta cannot handle the HIS_E tautomer by default…is that right? how can I fix this. The residue in the protein is named as HIS, should I change it?

thanks in advance!

felipet

[Anonymous]

Rosetta handles histidine tautomers with two ResidueTypes / params files for histidine: HIS and HIS_D.  By elimination, HIS must be HIS_E.

Probably your patch is being applied to both HIS and HIS_D when you want it only applied to one of those.  I don’t know how to tell it to patch only one and not the other.

 

First I think try deleting your whole “general case”, since you know what you want.  Second, look at some of the HIS-related patches already in the database – see how VirtualProteinResidue.txt handles HIS and HIS_D separately, see if you can copy that selection nomenclature?

[Anonymous]

Thanks smlewis

I am still blocked!. Following your recommendation I add the selectors used in VirtualProteinResidue.txt (NOT PROPERTY TAUTOMER for the HIS). Using the following patch the relax also crashes, it is like trying to use the HIS_D tautomer and not the HIS:

ERROR: Failed to apply a PatchOperation to HIS_D

ERROR:: Exit from: src/core/chemical/Patch.cc line: 333

 

his_phosphorylated:

NAME phosphorylated

TYPES PHOSPHORYLATION

 

## general requirements for this patch

 

BEGIN_SELECTOR

PROPERTY PROTEIN

NAME3 HIS

AA HIS

NOT VARIANT_TYPE PHOSPHORYLATION

NOT VARIANT_TYPE PROTONATED

NOT VARIANT_TYPE DEPROTONATED

END_SELECTOR

 

## now we search for a case that matches the residue, take the first one

## so put generic case last

 

BEGIN_CASE #### HIS ##########################################

 

BEGIN_SELECTOR

NOT PROPERTY TAUTOMER

AA HIS

END_SELECTOR

 

SET_IO_STRING NEP X

SET_INTERCHANGEABILITY_GROUP NEP

## these are the operations involved

DELETE_ATOM  HE2

ADD_ATOM  P   Phos X    1.50  ## Best guess from the small molecule ligand params file generator molfile_to_params.py

ADD_ATOM  O1P OOC  OC   -0.78 ## The charge is taken from the free oxygen atoms of the phosphate backbone in DNA residues

ADD_ATOM  O2P OOC  OC   -0.78

ADD_ATOM  O3P OOC  OC   -0.78

ADD_BOND  NE2  P

ADD_BOND  P   O1P

ADD_BOND  P   O2P

ADD_BOND  P   O3P

…

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