Re: [ccp4bb] On pKa of Aspartic acid

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: On pKa of Aspartic acid
From: Kevin Jin kevinjin {- at -} GMAIL {- dot -} COM
Date: 2012-02-07

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Subject: Re: On pKa of Aspartic acid
From: "Fischmann, Thierry" thierry {- dot -} fischmann {- at -} MERCK {- dot -} COM
Date: 2012-02-07

Subject: Re: On pKa of Aspartic acid
From: "Fischmann, Thierry" thierry {- dot -} fischmann {- at -} MERCK {- dot -} COM
Date: 2012-02-07

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

________________________________
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] 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 catalysis (acid base titration assay can help you to figure out the way of catalysis). Usually the pKa values of these kind of critical residues are affected by their local environment and this character is related to the enzyme's working mechanism.

I am sorry that I am not professional in enzyme, I cannot answer your questions for each questions.

Yu Xiaodi

________________________________
Date: Tue, 7 Feb 2012 19:48:26 +0800
From: deeposwal@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 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
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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: On pKa of Aspartic acid
From: Kevin Jin kevinjin {- at -} GMAIL {- dot -} COM
Date: 2012-02-07

Next message:
Subject: Re: On pKa of Aspartic acid
From: "Fischmann, Thierry" thierry {- dot -} fischmann {- at -} MERCK {- dot -} COM
Date: 2012-02-07