[Protein-analysis] Re: effect of pH on oligomerization

Dr Engelbert Buxbaum via proteins%40net.bio.net (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...
> 
> hi,
> 
>  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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