You can run a "native gel" in which no denaturation is performed (no detergent or boiling).  This resolves proteins based on molecular weight, though conformation and charge can have an effect.  There is also a version called isoelectric focusing (IEF) which resolves proteins based on pI.  You can buy gels and buffers for these, which I would recommend if you don't have a lab around that does them.  If you are thinking about some hybrid between SDS and native PAGE with a mild detergent, I haven't heard of it, but you might work out a new method.

Thanks. Yes, I'm thinking about using a different detergent with less or more denaturing capacity than SDS to use in probing and quantifying the kinetic stability of proteins.

Manning, M and Colón, W. (2004) Structural basis of protein kinetic stability: Resistance to sodium dodecyl sulfate suggests a central role for rigidity and a bias towards beta-sheet structure. Biochemistry, 43, 11248-11254.

Xia, K, Zhang, S., Bathrick, B., Liu, S., Garcia, Y., and Colon, W. (2012) Quantifying the kinetic stability of hyperstable proteins via time-dependent SDS-trapping. Biochemistry, 51, 100-107.

Interesting approach, Wilfredo. Do you know a detergent that has a higher denaturation efficiency than SDS?

Cheers, Christian 

Hi Christian. Sodium tetradecyl sulfate appears to be more effective in our hands, but is not practical for SDS-PAGE due to its low solubility. I do not know of anything else that is better than SDS.

Hi Wilfredo. In case your question is still relevant:

For an increased denaturing conditions you can incorporate some urea in your gel and samples. You should be able to find an appropriate protocol online.

On the milder side you can try a native blue PAGE that uses non-denaturing negatively charged Coomassie blue as SDS alternative.

Thank you Ram!