[Protein-analysis] Re: effect of pH on oligomerization
Dr Engelbert Buxbaum
(by engelbert_buxbaum from hotmail.com)
Fri Nov 26 13:05:19 EST 2010
In article <mailman.146.1290720060.15153.proteins from net.bio.net>,
sujeethkumar17 from gmail.com says...
> i am working on concanavalin A protein.It has the characteristics of
> forming dimer at pH<6.5 and tetramer at pH>6.5. How is this pH affecting the
> formation of oligmers.
> hope you will help me
by changing the ionization state of a amino acid side chain, which
allows/prevents association by electrostatic interactions. Presumably,
this would involve a His, whose side chain pKa is around 6.
You can try to find the X-ray structure of your protein on OCA
(http://bip.weizmann.ac.il/oca-bin/ocaids). You need to check the PDB-
files for the pH, at which the crystalls were grown. PDB-files are plain
text, you can use any text-editor (like notepad) to view them.
Structures are best viewed either with DeepView (a program you install
on your computer, from http://spdbv.vital-it.ch/index.html) or in your
browser with jmol (http://molvis.sdsc.edu/fgij/).
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