Re: [ccp4bb] off topic

[Boaz Shaanan]

Hi Careina, Regardless of what I think of this reviewer's comment, the only technique of which I'm aware that can measure in vivo (and in vitro of course) the pKa's of amino-acids is NMR. Perhaps you can find some NMR literature where in-vivo and in-vitro pKa's have been compared? Just a thought.  Good luck with the reviewer.              Boaz     Boaz Shaanan, Ph.D.                                         Dept. of Life Sciences                                      Ben-Gurion University of the Negev                          Beer-Sheva 84105                                            Israel                                                                                                                  E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220  Skype: boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710                          From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Careina Edgooms [000002531c126adf-dmarc-requ...@jiscmail.ac.uk] Sent: Wednesday, August 13, 2014 3:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: 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> 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> 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