It sounds like you are purifying a recombinant protein in a cell-line that has chaperones to help with folding. If your fusion protein and chaperone are tightly associated, no purification technique will work unless you dissociate the complex (they will co-purify). Try adding ATP (5mM) to your column wash buffer to release the chaperonin:fusion protein complex before eluting your fusion protein from the amylose resin. In the past, I have encountered some recombinant proteins that are not released from chaperones even in the presence of ATP and needed to add denatured E coli lysate plus ATP to break apart the complex.

It will only work if there is a difference in induced hydrophobicity between your chaperone and your protein of interest. Run the experiment.

It sounds like you are purifying a recombinant protein in a cell-line that has chaperones to help with folding. If your fusion protein and chaperone are tightly associated, no purification technique will work unless you dissociate the complex (they will co-purify). Try adding ATP (5mM) to your column wash buffer to release the chaperonin:fusion protein complex before eluting your fusion protein from the amylose resin. In the past, I have encountered some recombinant proteins that are not released from chaperones even in the presence of ATP and needed to add denatured E coli lysate plus ATP to break apart the complex.

removal of chaperone using HIC will not be possible because chaperones would be very strongly attached to hydrophobic patches present on substrate protein molecule. There are two ways to sort out this issue.

1- adding the cofactors for chaperonin activity: chaperones require several co-factors for performing the binding and release cycle ultimately causing the folding of proteins. So in practice, if you add those cofactors such as ATP and MgCl2 in appropriate concentration it would be possible to remove the chaperone from your substrate protein. However, it would require optimizing the buffer conditions. 

2- if you are able to successfully purify the substrate chaperone complex, you may go for denaturing it in presence of high concentration of chemical denaturant following another chromatographic procedure under denaturing condition. thereafter you can refold the individual purified elution volume either by rapid dilution or through dialysis which will minimize the denaturant concentration. 

I did use the ATP and MgCl2 step, but it didnt help. Anyways I could purify it through HIC and my protein eluted with lower salt concentration. Thanks everyone for helping.