From: Mark Abraham (mark.abraham_at_anu.edu.au)
Date: Sat Jul 01 2006 - 01:25:13 CDT
> Hi, all.
> A question about the protonation states of catalytic residues.
> There are two catalytic residues in my enzyme, GLU 162 and GLU 282. The
> former acts as the protein donor while the latter works as the
> nucleophile during the catalytic process. However, the pKa prediction
> placed a (COO) proton on the 282 instead of 162. Should the protonation
> states of catalytic residues for MD simulation match with their roles
> in mechanism? Any comment please? Thanks.
They'll only match the roles in the mechanism if the assumptions required
for the pKa prediction method are compatible with the state of the enzyme
in the lead-up to the catalytic step. You need to find out what the former
and latter are and see if that compatibility might exist. This is not
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