Protonation states

From: Ching Wong (wongcw_at_TITAN.SFASU.EDU)
Date: Fri Jun 30 2006 - 19:04:32 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.


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