Yeah.  Gel filtration should work nicely, if all you want to do is separate the monomers from the multimers.  A Sephacryl S-200 column should give you the resolution you need.  They're pricey though, if you don't have access to one already.  If you can find one and have access to an FPLC, bingo!

If gp120 is meant to be monomeric but you are getting disulfide-linked dimers, then after eluting it from the IMAC column you can add a reducing agent to get the monomeric form only. No need to separate the monomer and dimer.

Thanks Craig! We do have FPLC to begin with and using Sephacryl is a good idea. I also thought about other options like Superdex 200 Increase and Sepharose 6 Increase. What do you think about these two?

Hi Adam, Adding reducing agent is an excellant idea but at this stage am not sure at which point it becomes oligomer; need to figure that out. But thanks to both of you.

Sure thing Sugata!  Superdex 200 (10kD to 600 kD) might be even better for your purposes than Sephacyl 200 (5kD to 250kD).

I agree that gel filtration could solve the issue.I would however be careful to take the SDS-PAGE result as evidence for real dimerisation/oligomerisation, it could also be a simple gel artifact and some of the protein runs as dimer on the gel. It could also be the other way round, that you don't have a monomer in solution at all (or much less than the non-reducing gel suggests). Gel-filtration (ideally with a  MALLS system to measure the size) is definitely needed to clarify this.

I'd be careful with the suggestion of adding reducing agent to separate disulfide bridged dimers. The extracellular domain should have a number of disulfide bonds, so reducing conditions might be detrimental for the whole protein.

You don't mention under what conditions (pH, molarity, buffer salts, elution conditions) you ran the DEAE ion exchange. By raising the pH or reducing the conductivity in anion exchange you may be able to bind either monomer or dimer without binding the other. Alternatively, as the pI of the protein is fairly high (pH7.91) you might be better using cation exchange at a pH below the protein pI, perhaps pH6.5 to 7.0. Either anion or cation exchange will take some development work to determine the right conditions for separation.

I suggest you to incorporate reducing agents at regular concentrations (5-10 mM beta-mercaptoethanol or 2-5 mM dithiothreitol) in all buffers used during gp120 purification.  These concentrations should maintain the native state of the protein and should avoid the formation of artifactual oligomers. 

In case that you want to verify the formation of oligomers, another useful technique that will separate monomers from dimers, trimers, etc., is sedimentation by ultracentrifugation through sucrose gradients. A gradient of 5-20% sucrose or 5-30% sucrose in any buffer that you normally used should work.

Separation of monomers and dimers of gp120 should work with Superdex 200. I attach a separation of protein monomer from dimer (170 kDa and 340 kDa) using a Superdex 200 column with 75cm bed height. Sample volume was 3% of column bed volume.

The Sepharose path should work well, if you're patient-- we needed to remove monomer of a delicate four-subunit protein from crosslinked oligomers, and GPC was unsuitable by reason of dissassembling the subunits. You wouldn't have that problem: so GPC might be much faster, if the monomer is tolerant of pressure. But with Sepharose we needed a very long bed (100 cm), it took 20 hours, and had tremendous sample dilution. You're of course processing cold?  Sample loss is a consideration, so preventing the disulfide problem in the first place should be important, per Adam and Jose's suggestion of using a reducing agent (glutathione, DTT are traditionally used to prevent aggregates).  Do you know whether the dimers are occurring in the plant itself, before purification?

That's a lot of steps-- Jones et al. (Vaccine 1995) describe a quick method using lectin and FPLC: http://www.ncbi.nlm.nih.gov/pubmed/8525694 . Scandella et al. (1993) use processing that emphasizes preservation of glycosylation (the protein backbone is only 53 KD): http://www.ncbi.nlm.nih.gov/pubmed/8142140 .  Scandella's patent US563985 (Chiron) is now expired and describes that a quick initial precipitation in 40% ammonium sulfate is a useful purification step (the gp120 does not precipitate).

Thanks all for the comments. At this point, I am not sure at what stage the oligomers are formed and that using DTT might break the intramolecular disulphide bonds present in the monomer, thus making it non-functional. But definitely, I would like to use Superdex 200 to see if I could separate the two. For Deae resin, I have been using 20mM phosphate at pH 8. Thanks Kristin and Chris for the documents. Also, I am planning to do DLS on the FT to see what percent of oligomers I have in the mixed sample.