Do you suspect that there are specific proteins that become misfolded, or does treatment induce a general stress?

If it is a general stress, a good starting point would be to use some expression analysis to see if chaperones become upregulated. A northern or qPCR assay for a DnaK homolog for example, or microarray, or if you have the capabilities, RiboSeq.

Proving misfolding in vivo by direct detection of unfolded species can be quite tricky, especially in bacteria. A functional experiment may be safer at first. One example would be to express some colorimetric reporter, and compare protein levels by western and quantify activity in vivo. You might be able to do something similar with antiboitic resistance. Even just GFP often is sensitive to folding stress. The key will be demonstrating that equal amounts of protein are produced under test and control conditions (not just transcribed!), but have differences in activity. But even in these cases, there can be some ambiguity if lack of function is due to some upstream effect, like perturbation in substrate availability, etc.

If you are careful, you can try something more in vitro, like lysing a culture, followed by centrifugation and western blotting to see whether reporter proteins stay soluble or enter inclusion bodies. If you have severe deficits in protein folding, this may give a satisfying result, but remember that lysis conditions can cause proteins to precipitate. This type of experiment may miss more subtle effects.

Good luck!

If you have antibodies to these proteins you can try partial digest in extract to see if there is change in their conformation. You use a general protease like trypsin or chemotyrpsin either at different concentrations or times and follow the sensitivity of the digest on a western. If the pattern is different between control and treatment the protein conformation was change which can suggest misfolding.

Good luck 

Thanks Justin and Anat. your inputs are very helpful.