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#34761 02/01/15 09:07 PM
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talbers Offline OP
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Hi All!

I'm looking at a zinc peptidase, which amongst other things has a tyrosine coordinated to the Zn(2+) ion. It wouldn't be unlikely if that tyrosine were deprotonated, but I can't find a patch for deprotonated tyrosine in CHARMM36. Would anyone have a patch for deprotonated tyrosine, or have other suggestions how to treat that residue properly?

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The patch SERD in toppar/top_all36_prot.rtf gives a deprotonated serine, but more importantly, it explains how it got those parameters. It points to RESI ETO in toppar/stream/prot/toppar_all36_prot_model.str , which I believe are the fragments used to derive the protein force field. Looking in that file also reveals RESI PHEN (phenol) and RESI PHEO (phenoxide). Inspection of those residues allows one to determine the appropriate atom types and charges for deprotonated tyrosine. Thanks kevo for the helpful comment in the .rtf.

PRES TYRD -1.00 ! patch to deprotonate tyrosine by rlh
DELETE ATOM HH ! modeled off SERD patch by kevo
ATOM CE1 CA -0.60 ! from RESI PHEO in toppar_*_prot_model.str
ATOM HE1 HP 0.28
ATOM CE2 CA -0.60
ATOM HE2 HP 0.28
ATOM CZ CA 0.40
ATOM OH OC -0.76

Alex MacKerell, should this patch be put into toppar/top_all36_prot.rtf ?

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To answer talbers' question more directly, as one who is not a forcefield expert, there is likely some bonded character between the zinc and the tyrosine which complicates matters in your case, though deprotonating the tyrosine is probably better than not deprotonating it. I stumbled across this question while looking for deprotonated tyrosine parameters for use in constant pH simulations, so I figured I would post the answer I found.


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