Dear Peter, You could check your putative binding site to see if there are charged groups which need to be protonated for your substrate analog to bind (or whether the substrate analog needs to be protonated). In order to draw physiologically relevant conclusions, you would need a crystal structure at a pH where the protein is active. Try if you can transfer your crystals to lower pH, perhaps by significantly increasing the precipitant concentration.
Good luck! Herman -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter Hsu Sent: Tuesday, October 30, 2012 5:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] oof topic: pH effect on substrate analog Hi all, I'm working on a protein that I recently got crystals of. My functional studies show that the protein has optimal activity at lower pHs, while losing >90% activity at about pH8. I've been trying to soak/cocrystallize a substrate analog (small molecule) into my crystals (grown at ~pH8) with no real luck. I'm wondering, since I lack activity at this pH point, would it lead to no binding of a substrate analog? Thanks for any insights Peter
