possibly protein is denaturated?

TCA precipitates denature protein.You can dissolve in dilNaOH ;only primary str.can be studied-like total protein content9 by colorimetric method possible) etc.

I have yet another query:

None of the protein precipitation protocols (ammonium sulfate/ethanol/acetone/tca precipitation) are selective to the proteome. What I mean to say is that if I have a solution containing proteins and polysaccharides, both of them have an equal probability of being precipitated out. Then how do we ensure that we get our biomolecule of interest?

The precipitated protein(pellets) can be separated by decanting out the liquid portin, repeated washing with distilled water, test for removal of TCA (by litmus test) centrifugation at < 5000 rpm, dissolve the pellets in dil NaOH. Polysacharides may not precipitate at the high pH of TCA;soluble sugars may come if your protein is extracted in water,and it will be only in the liquid layer when precipitated.

Thanks a lot all of you! I'll keep you guys posted about my success rate with these suggestions!