[Protein-analysis] irreversible protein aggregate

Carlo Zambonelli via proteins%40net.bio.net (by zambonel from gmail.com)
Thu Apr 17 12:35:14 EST 2008

I am trying to purify a 135 kDa protein, predicted pI=5.2. I can 
efficiently express my protein as a fusion with MBP. Affinity 
purification on amylose resin works fine at pH 6.2 while at pH 8.0 most 
of the MBP fusion does not bind to the column. This has to do with 
charge distribution/neutralization but it is (probably) irrelevant to my 
problem. After elution from amylose resin, I cleave off MBP and the 
protein I obtain is a large Mw aggregate. Purity determined after 
SDS-PAGE is no more than 60%. I tried up to 10% glycerol, 1 M NaCl, 10 
mM DTT and a number of detergents. I obtained some very slight 
improvement with the above conditions and CHAPS as the detergent, but I 
still have large aggregates as determined both by GPC and DLS. 
Desperate, I decided to try and unfold/refold my protein, which is NOT 
an enzyme and for which protein I do NOT have a functional assay! So far 
I tried denaturing with 1%SDS, 8M urea, 6M guanidine. In the presence of 
SDS I seem to obtain some reduction in the size of the aggregate (GPC, 
DLS), while with urea and guandidine I do not see any change (DLS) in 
the size of aggregate!
Any comment or suggestion? Is it possible that proteins aggregate 

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