Dear Amber users,
I am having some difficulty with the deprotonation of cysteine residues using constant pH MD.
Has anybody routinely observed abnormally high pKa estimates for cysteine residues when using CpHMD?
I have a reasonably solvent exposed cysteine residue that interacts weakly with a number of nearby residues though electrostatic and hydrogen bonding interactions. Propka predicts a pKa value of around 9 for the residue in question. I have performed pHREMD in explicit solvent with a pH range of 5 - 12, and pHREMD in explicit solvent using the same pH range. The predicted pKa is above 13.5, but I expected a much lower value.
A colleague of mine has reproduced the titration curve for the model cys residue, and this yields the correct pKa value. The same colleague has also performed CpHREMD on a cysteine in a completely different system and did not observe any deprotonation of the cysteine residue up to pH 9.
I was wondering if anyone had also observed high pKa estimates for cys residues, and/or could offer some suggestions as to why I might be observing these unexpected values? If you need any further information, don't hesitate to ask.
Best wishes,
Angus
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Received on Mon Sep 18 2017 - 04:00:02 PDT
