Dear Zhen,
I should also point out that the statement Matt made ("Superdex is known to
have some ion-exchange characteristics, so that it can weakly interact with
some proteins.") is not completely correct. Superdex and all chromatographic
media made from carbohydrates (dextran, agarose, etc.) are also quite
hydrophobic (which is surprising to some). The observation Zhen made is the
classic behavior of hydrophobic interaction with the gel filtration media,
which led to the development of hydrophobic interaction chromatographic (HIC).
For HIC, you load the protein in high salt, and elute with low salt or a
chaotrope (LiCl).
So when you redo you experiment, Zhen, try with AND without salt. As Matt
said, if it is an ion-exchange interaction, extra salt will make it elute more
normally. But if it gets worse, then the extra salt is increasing the
hydrophobic interactions, and you should run the column in lower salt (~50 mM
NaCl) or with a bit of detergent. Given that you are refolding your protein, a
partially folded protein may have have more hydrophobic patches. As my lab is
routinely refolding our target proteins, we are always watching for this
behavior, including on our analytical Superdex 200 10/300 columns, which is one
of our favorites. Excessive hydrophobic interactions can also lead to clogged
columns, which is not what you want for this expensive column.
Good luck,
Michael
****************************************************************
R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513
Michigan State University
East Lansing, MI 48824-1319
Office: (517) 355-9724 Lab: (517) 353-9125
FAX: (517) 353-9334 Email: rmgarav...@gmail.com
****************************************************************
On Jun 20, 2013, at 5:38 PM, Zhang, Zhen wrote:
> Hi Matthew,
>
> Thanks a lot. That is a great idea. I will try the high salt and worry about
> the crystallization later.
>
> Zhen
>
> -----Original Message-----
> From: Matthew Franklin [mailto:mfrank...@nysbc.org]
> Sent: Thursday, June 20, 2013 4:34 PM
> To: Zhang, Zhen
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Puzzling observation about size exclusion chromatography
>
> Hi Zhen -
>
> Superdex is known to have some ion-exchange characteristics, so that it
> can weakly interact with some proteins. This is why the manufacturer
> recommends including a certain amount of salt in the running buffer. I
> have had the same experience with a few proteins, including one that
> came off the column well after the salt peak! (The protein was very
> clean after this step; all other proteins had eluted earlier.)
>
> As others have said, you can't rely on molecular weight calibrations in
> this case, but this behavior alone is no reason to think that the
> protein is misfolded or otherwise badly behaved. If you don't like the
> late elution, try increasing the salt concentration of your running
> buffer to 250 or even 500 mM. You'll probably need to exchange the
> eluted protein back into a low-salt buffer for your next steps (e.g.
> crystallization) if you do this.
>
> - Matt
>
>
> On 6/20/13 3:09 PM, Zhang, Zhen wrote:
>> Dear all,
>>
>> I just observed a puzzling phenomenon when purifying a refolded protein with
>> size exclusion chromatography. The protein was solubilized by 8M Urea and
>> refolded by dialysis against 500mM Arginine in PBS. The protein is 40KDal
>> and is expected to be a trimer. The puzzling part is the protein after
>> refolding always eluted at 18ml from the superdex S200 column (10/300),
>> which is calculated to be 5KDal by standard. However, the fractions appear
>> to be at 40KDal with SDS PAGE and the protein is functional in term of in
>> vitro binding to the protein-specific monoclonal antibody. I could not
>> explain the observation and I am wondering if anyone has the similar
>> experience or has an opinion on this. Any comments are welcome.
>>
>> Thanks.
>>
>> Zhen
>>
>>
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>
>
> --
> Matthew Franklin, Ph. D.
> Senior Scientist
> New York Structural Biology Center
> 89 Convent Avenue, New York, NY 10027
> (212) 939-0660 ext. 9374
