Raji,
First, I would suggest increasing the solubilization time by attempting solubilization overnight at 4 degrees. I would also suggest a few more detergent choices. In addition to DDM, my other favories are OG and Elugent (a mixture of several detergents) for extraction from
E. coli membranes. If one of these still doesn't extract your protein of interest, you can move onto other more exotic options. I know it's a bit self-plugging, but the products division of Emerald Bio sells a 96-well detergent screen you can use to go through a wide variety of solubilization detergent options at small scale. We've used it in-house in our services division to get some nice results for several of our membrane protein projects.
However, you may be fighting a losing battle as many times protein that doesn't extract from the membranes can be misfolded or aggregated, remaining strongly associated with the membranes.
Cheers, Jim