Dear Careina, even in vivo, the pka depends on the local environment, so the question boils down to: is the local environment in vivo different from in vitro? E.g. is your protein embedded or in contact with a membrane, is it part of a large multiprotein complex etc? Does your crystallization solution or the in vivo compartment of your protein contain molecules that could influence the pka?
Since I assume that you did not measure pka's experimentally, I assume that the remarks of the referee concern the discussion of your paper. In this case, I would use some arguments like above as response to the referee, depending on the context of course, which I do not know. Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Careina Edgooms Gesendet: Mittwoch, 13. August 2014 14:45 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] off topic 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 <drdavidcbri...@gmail.com<mailto:drdavidcbri...@gmail.com>> 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 <000002531c126adf-dmarc-requ...@jiscmail.ac.uk<mailto:000002531c126adf-dmarc-requ...@jiscmail.ac.uk>> 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
