Is the water molecule in question coordinated to any other group(s)?
-----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kevin Jin Sent: Tuesday, February 07, 2012 10:22 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] On pKa of Aspartic acid As we know, the pKa of water is 15.7. Under pH 7.0, its protonation should be 50/50. In this case, we may need to consider water in two formats: H2O vs. H3O+ When we say water as acid, it usually stands for H3O+ in chemistry. In chemical equation, H+ represents H3O+. In enzyme catalysis, water as a general acid sounds reasonable under pH 7.0. In some famous paper, water has been concluded as the general base (pKa 15.7) to deprotonate an alpha hydrogen (pKa ~ 22) or a hydrogen from a sp3 hybridized carbon (pKa ~36). This logic may need to be reconsidered. . Recently, I have read papers for pKa perturbation. I am also interested in the general base of Asp and Glu in enzyme catalysis. I will be very happy to read your paper in the future. Regards, Kevin Jin On Tue, Feb 7, 2012 at 3:48 AM, Deepak Oswal <deepos...@gmail.com> wrote: > 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
