Re: [ccp4bb] On pKa of Aspartic acid

[Roger Rowlett]

Residue pKa values in proteins are strongly affected by the local environment and can deviate far from the "norm". Of course, the higher the pKa of the residue, the stronger general base it will be. There is a significant thermodynamic/kinetic advantage in matching the pKa of a general base to the pKa of the proton that must be removed for catalysis. Aspartate frequently plays a role as a general base for assisting water in nucleophilic attack. I think it is unusual for water to act as a general acid (the pKa of water is 14-15, depending on how you calculate it), but if that is the case and there is compelling evidence that water is the proton donor in your reaction, it would be necessary for aspartic acid to be in its protonated form in order to assist a water-mediated protonation event. Raising the pKa of aspartic acid would allow a larger fraction of it to be in its protonated state at physiologically relevant pH values, although it would reduce the intrinsic effectiveness of Asp as a general acid. There should be a significant thermodynamic and kinetic advantage in having Asp participate directly in a general acid catalyzed reaction, rather than through a water molecule. Cheers, _______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 2/7/2012 10:00 AM, Xiaodi Yu wrote: Hi Deepak: I think it is common for the residues which participate catalysis to have a Pka deviated from the reality pKa value especially for acid/base catalysis (acid base titration assay can help you to figure out the way of catalysis). Usually the pKa values of these kind of critical residues are affected by their local environment and this character is related to the enzyme's working mechanism. I am sorry that I am not professional in enzyme, I cannot answer your questions for each questions. Yu Xiaodi Date: Tue, 7 Feb 2012 19:48:26 +0800 From: deepos...@gmail.com Subject: [ccp4bb] On pKa of Aspartic acid To: CCP4BB@JISCMAIL.AC.UK Dear colleagues, We have solved the crystal structure of a human enzyme. The pKa of a catalytically critical aspartic acid has increased to 6.44. It is hydrogen bonded (2.8 Angstroms) to a water molecule that is supposed to donate a proton during the catalysis. Can anybody help me a) interpret the significance of this increase in pKa of the aspartic acid from 3.8 to 6.44 in context with the catalysis? Is this advantageous or detrimental? b) How is pKa related to an amino acids’ ability to force a water molecule to donate a proton? c) At pH 7.4, the aspartic acid would be de-protonated irrespective of whether the pKa is 3.8 or 6.44; isn’t that true? d) Have similar increase in pKa values observed for aspartic acids before? I would be grateful if anybody could explain or comment on the above queries. Deepak Oswal