The problem of low solubility and aggregation of hydrophobic protein upon gel electrophoresis can by overcome by using mild detergent such as triton X-100 with constant ionic strength using NaCl less than 0.5M in electrophoresis might help you to perform Page for hydrophobic proteins admitted no standard procedure has been used for all hydrophobic protein separation on native gel. Good luck

If the increased hydrophobic interaction of the mutant protein results in increased aggregation, the protein will probably run on native PAGE as either a larger protein (e.g. dimer v. monomer), or as an unresolved smear due to the presence of multimer higher molecular weight forms.

Thanks  Adam B Shapiro,

What, if the wt protein is a homodimer and the mutant protein hampered the dimer formation, and keep it as monomer only with more compact structure then WT monomer.

In that case, the mutant protein will most likely run faster than the wild-type protein on a native gel. You would also expect to see the difference by gel filtration chromatography, with the mutant protein eluting later than the wild-type protein.

Thank you so much 

Adam B Shapiro  and Abdelrahim Ahmad Hunaiti