Dear all, for further discussion
I believe that using the "0-14" pH scale assumes water activity of pure water, something that is surely not matched in the surface or pocket of a protein, so keeping this in mind I always prefer to speak about apparent pKa of a group if talking about a non solvent-exposed group. Horacio 2012/2/7 Roger Rowlett <rrowl...@colgate.edu> > No. Kw = [H3O+][OH-] = 1 x 10^-14 at 25 deg C. > > So at pH 7.0, you have 10^-7 M each at equilibrium no matter how you slice > it or whatever else is in solution. If equilibrium [H3O+] goes up [OH-] > goes down commensurately. > > The "pKa" of water as an acid is based on Kw and water's effective > concentration of 55 M in pure water. This "pKa" is used to compare the > instrinsic acidity of water to other weak acids. Water is an exceptionally > weak acid or base. > > > _______________________________________ > 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 3:42 PM, Kevin Jin wrote: > > Oops, It should be: [H3O+]/[OH-]= 50/50 > > Kw = [H3O+][OH-], > > pH = pKa +log ([OH-]/[H2O]) > > H3O+ concentration of pure water is 10^-7 mol/L > > total H+ = 55.5M * 10^-7 = 5.55* 10^-6 mole. Is this right? > > Regards, > > Kevin > > > On Tue, Feb 7, 2012 at 12:13 PM, Zachary Wood <z...@bmb.uga.edu> > <z...@bmb.uga.edu> wrote: > > 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 <deepos...@gmail.com> > <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 > > -- Horacio Botti PhD MD Protein Crystallography Unit Institut Pasteur of Montevideo
