Hi Kevin, Hate to point this out, but under pH 7.0, the protonation state of water is not 50:50, and it is not a good acid. The H30+ concentration of pure water is 10^-7 Molar. In pure water (assuming 55.5 M) only 1:555,000,000 water molecules is in the protonated, charged state (H3O+). This is why when an enzyme uses water in its mechanism as a nucleophile, base, or acid, there is usually an acid/base catalyst or metal that protonates or deprotonates the water to 'activate it'.
Best regards, Z *********************************************** Zachary A. Wood, Ph.D. Assistant Professor Department of Biochemistry & Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: 706-583-0303 FAX: 706-542-1738 *********************************************** On Feb 7, 2012, at 11:22 AM, Kevin Jin wrote: > 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 <[email protected]> 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 >
