[AMBER] pKa calculation

From: Tanmoy Paul <tanmoyp635.gmail.com>
Date: Wed, 17 Apr 2019 11:48:58 +0530

Dear Amber Users,
                     I am currently working on a Zn containing enzyme. The
rate determining step in the catalysis process is the deprotonation of Zn
bound water. Zn(II), being highly positively charged, has a great role in
increasing the polarizability of the O-H bond of the bound water. In the
crystal structure, Zn has a tetrahedral coordination environment around it.
But from our simulation studies, we have found that the deprotonation takes
place almost exclusively from a pseudo-penta coordinated Zn with a
distorted TBP coordination geometry. An additional water molecule comes and
sits there at one of the axial positions of the TBP coordination structure.
Now from MD we found out that this penta species is very short lived
(1-2ps). We are trying to find out whether the additional water has any
impact on the pKa of the Zn-bound water. We are following the following
paper (JACS 2004, 126, 4167-4180 <callto:2004,%20126,%204167-4180>) by
Prof. Case, for the pka calculation. But the only problem is, the penta
coordination is not long lived to have sufficiently long trajectories for
thermodynamic integration. Can you please suggest about how to proceed?

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Received on Tue Apr 16 2019 - 23:30:02 PDT
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