thank you, yes I am aware of propka and I know very well that the local environment of the amino acid is what contributes to its pka based on things like whether it is buried or exposed or involved in H-bonding. I am in the process of responding to a reviewer who suggests but does not give references that in vivo conditions can alter the ionisation of some amino acids differently to in vitro. I am struggling to respond to this without some sort of proof or study on the matter C
On Wednesday, August 13, 2014 2:38 PM, David Briggs <[email protected]> wrote: Dear Careina, Following on from what Herman said, if you have a structure you can use the propKa server http://propka.ki.ku.dk/ to predict pKas for amino acids in the local environment as found in your structure. Perhaps some of the propKa literature might also be helpful? HTH, Dave David Briggs about.me/david_briggs On 13 August 2014 12:40, Careina Edgooms <[email protected]> wrote: Sorry for off topic question, just wondering if anyone has come across a study that shows the residue pka of certain amino acids is different in vitro compared to in vivo? > > >Best >Careina
