Dear Amber users,
I am looking for a methodology to capture the deprotonation/protonation
mechanism of a specific residues and their effect on protein conformational
dynamics.
The protein, I am working with, have a deprotonated threonine residues
coordinated with an ion and it is postulated that threonine get protonated
and break the interaction with ion during the activation process. I wonder
which simulation methodology can be mot suitable to provide a direct
picture of the activation mechanism where the ion-coordinated deprotonated
Thr breaks its coordination with ion and get protonated and how this
deprotonation-protonation switch the overall protein conformational
dynamics (active state)?
Any suggestions would be highly appreciated.
Best regards
Anu
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Received on Fri Apr 27 2018 - 03:00:02 PDT
