Histidine protonation

Histidines in Rosetta are assumed to be in the neutrally charged state. (No net electric charge.) This matches the case for the vast majority of histidines in normal protein structures.

The complication is that histinine can have two tautomers in the neutral state: having the proton on the epsilon nitrogen of the ring, or the proton on the delta nitrogen. Certain programs make a distinction between the two states, calling one HIE and the other HID (or HSE/HSD). Rosetta will actually automatically consider both states, and calls both states “HIS”. (In three letter codes: in the full specification it calls the epsilon version HIS, and the delta protonated version HIS_D, but there’s still interchangable.)

Biologically, both of these states are accessible, and will readily interconvert with each other, depending on the structure of the surrounding residues, and where the hydrogen bonding donors and acceptors are. This is why Rosetta will freely interconvert between the two – it matches what happens biologically. 

The HIS_P.params in the database is for the *doubly* protonated variant of histidine – that is, the version which carries a net postive (+1) charge. By default, Rosetta will not consider this charged state. It’s only for the pKa/pH-mode code that the protonated variant will be considered. You can force regular (non pH-mode) Rosetta to read in residues as charged histidine, but its not commonly done, and needs special contorsions. 

I’m not sure what the question is.  Do you mean “I want the deprotonated histidine” or “I want the doubly-protonated histidine”?  Rosetta handles the normal singly protonated tautomers automatically.  Try overwriting that residue in your input structure with the three-letter code that matches the histidine protonation you wanted, for the unusual-charge states.

Rosetta doesn’t force the distinction between the protonation variants. While other programs might force you to choose a protonation state and stick with it, Rosetta automatically chooses which (neutral) protonation variant it will use in each situation, and it’s difficult or impossible to force a particular protonation state: whatever the best (lowest energy) variant is for that position, in that particular context, will be the one used. That’s why HIE/HID/HSD/HSE don’t work with Rosetta: specifying a particular protonation state is somewhat nonsensical in the approach Rosetta uses.

Regarding forcing in a double-protonated (positively charged) histidine, an “easy” way to do it is to make a copy of HIS_P.params, change the IO_STRING name to something like ‘HIP’, and then make the corresponding change (to HIP) in the input PDB. 

I can’t add more to this other than to say I’ve struggled with this same issue (see thread: https://www.rosettacommons.org/node/9726), so I’d definitely be interested in hear how to get this to work.  In my case I really need the doubly protonated form for my work (a protonated his is required for binding).

When you say “can’t recognize it”, what error message is it giving you? Is it something with the reading of the params file, or are you talking about loading of the protein?

One issue I immediately see is that you don’t have a single letter code in the IO_STRING line. You’ll want something like 

IO_STRING HIP H

Also, depending on the protocol you’re using, you may need to also provide a centroid-mode version of the params file passed to `-extra_res_cen` – To a first approximation, this is just the HIS centroid params file (Rosetta/database/chemical/residue_type_sets/centroid/residue_types/l-caa/HIS.params) with the NAME and IO_STRING lines changed appropriately. 

That was interesting to track down.

Apparently, in addition to changing the name, you’ll need to comment out/delete the VARIANT PROTONATED and the AA HIS lines, and then copy the PROPERTIES line and the METAL_BINDING_ATOMS line from the standard HIS parameters to your HIP parameters. (Add the CHARGED entry from the PROPERTIES line in HIS_P.params to the copied line.)

That was interesting to track down.

Apparently, in addition to changing the name, you’ll need to comment out/delete the VARIANT PROTONATED and the AA HIS lines, and then copy the PROPERTIES line and the METAL_BINDING_ATOMS line from the standard HIS parameters to your HIP parameters. (Add the CHARGED entry from the PROPERTIES line in HIS_P.params to the copied line.)

That was interesting to track down.

Apparently, in addition to changing the name, you’ll need to comment out/delete the VARIANT PROTONATED and the AA HIS lines, and then copy the PROPERTIES line and the METAL_BINDING_ATOMS line from the standard HIS parameters to your HIP parameters. (Add the CHARGED entry from the PROPERTIES line in HIS_P.params to the copied line.)

Hi,

I find different HIS.params from different file folder，and have different  PROPERTIES line and the METAL_BINDING_ATOMS lines

For example

At rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types/l-caa, it is

PROPERTIES PROTEIN CANONICAL_AA ALPHA_AA L_AA POLAR SC_ORBITALS METALBINDING

METAL_BINDING_ATOMS O ND1 NE2

while 

rosetta/main/database/chemical/residue_type_sets/fa_standard_pre_talaris2013/residue_types/l-caa is

PROPERTIES PROTEIN ALPHA_AA POLAR SC_ORBITALS L_AA

(and not METAL_BINDING_ATOMS line )

Is it accroding to the score? Which version should I add?

The `fa_standard` one is the most recent one, and the one to model off of, unless you have compelling reasons not to.

The `fa_standard_pre_talaris2013` is from an older, “pre-talaris2013” version, and is not used by default.  It’s only kept around for compatibility with certain commandlines and protocols which need access to the older version of the residue types.