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 in
proposing a catalysis mechanism.
b) How is pKa related to an amino acids’ ability to force a water
molecule to donate a proton?
Are you sure that the water donates a proton? Was your resolution high
enough to observe it? How did you measure that pKr, by the way?
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?
I would say that the dominant fraction of Asp is deprotonated. But as
you can see in the papers below, the pKr of Asp can vary from 0.5 to 9.2
in folded proteins.
d) Have similar increase in pKa values observed for aspartic acids before?
there are some papers by Nick Pace's group:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708032/?tool=pubmed
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679426/?tool=pubmed
http://www.sciencedirect.com/science/article/pii/S002228360600934X
Cheers,
Clement
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On 2/7/12 8:48 PM, Deepak Oswal 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
