If you have your protein in inclusion bodies you have to take it out with guanidinium chloride or urea...But you'll denature your protein...maybe you can try to solubilize in 1% triton or sarcosyl at a non-denaturing concentration... Anyway after denaturing with guanidinium chloride some protein are refolded after removing GuCl...

so without denaturing the samples, we cant run on Native gel....is that true for inclusion bodies

So you want to run a protein in an inclusion body but without denaturing sample by heating?

You pretty much have to denature the protein to run it on native PAGE. Otherwise you would have a hard time telling which band is the monomer or protein aggregate.

For native PAGE, you should use uncharged denaturing agents such as urea.

However, urea is going to denature your protein for sure...so it would not be a native PAGE anymore...maybe you can try other detergents at low concentration (1% triton, 1% NP-40, etc)...good luck

Proteins in inclusion bodies are probably denatured aggregates to begin with. So you likely won't get much information running it on native PAGE.

If you want to estimate size of the protein, gel filtration chromatography should work -even for insoluble proteins. You do not have to denature it before running the column.

its impossible to take the proteins out of the inclusion bodies without denaturing it, you have to treat the inclusion bodies with urea, gua-HCl or other chemicals to denature it and get the protein in soluble form