Roger Rowlett wrote:
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
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
Hi Deepak,
Assuming that you have done the necessary things to measure the pKr of
that particular Asp, I would say that the increase is advantageous for
your enzyme. Enzyme catalysis often involves very subtle changes on the
ionization state of the active site. But you need to be very careful
: [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
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 critica
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
] On Behalf Of Xiaodi Yu
Sent: Tuesday, February 07, 2012 10:00 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] On pKa of Aspartic acid
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
:59 AM
To: 'Xiaodi Yu'; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] On pKa of Aspartic acid
Check this review, for instance:
Pace, C. et al. Protein Ionizable Groups: pK values and Their Contribution to
Protein Stability and Solubility. J. Biol Chem. 284, 13285-13289 (May 15,
2009)
Thierry
Hi,
you may also look into the papers of John A. Gerlt, who did a lot on
protonabtraction reactions and the theory behind this. Esspecially the pKa
disturbance and the match to the pkA of the substrate of the reaction.
Best Wishes
Christian
Am Dienstag 07 Februar 2012 12:48:26 schrieb
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
Maybe you would also be interested in
http://www.jinkai.org/AAD_history.html
Regards,
Kevin
On Tue, Feb 7, 2012 at 8:52 AM, Christian Roth
christian.r...@bbz.uni-leipzig.de wrote:
Hi,
you may also look into the papers of John A. Gerlt, who did a lot on
protonabtraction reactions and the
: Tuesday, February 07, 2012 3:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] On pKa of Aspartic acid
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
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+).
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,
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
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
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