Re: [ccp4bb] On pKa of Aspartic acid

[Roger Rowlett]

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> 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> 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