The change in protein conformational structure and retinal chromophore binding state have been examined by using in situ UV-vis, FTIR, and CD spectroscopies during the thermal denaturation and refolding processes in bacteriorhodopsin (bR) of purple membrane (PM), in its native trimeric and in Triton X-100 solubilized monomeric form. For the trimeric bR, it is found that heating bR through its premelting transition (T > 78 degreesC, T-m') does not cause any permanent damage in the protein secondary structure, and a reversible refolding occurs when it cools back to room temperature. For the monomeric bR, it is found that it is less thermally stable than the trimer. There is a significant change in its protein secondary structure and a complete dissociation of retinal occurs irreversibly at a temperature as low as 66 degreesC. In addition, it is found that heating the trimeric bR through its main molten state (T > 96 degreesC, T-m) changes the protein secondary structure so that bR does not refold fully into its original secondary structure. Upon cooling back to room temperature, about 90% of the bound retinal in native bR recovers after being heated through its premelting transition, whereas only about 12% of bound retinal recovers if bR is heated above its main melting temperature. It is also found that refolded bR molecules with their retinal chromophore rebound have a photocycle and are capable of pumping protons. Our results also suggest that from its molten state, protein secondary structure refolding precedes retinal rebinding to the Schiff base.