We describe experimental UV-visible and Fourier transform infrared (FTIR) spectroscopic methods for characterizing lipid-protein interactions for rhodopsin in a membrane bilayer environment. The combination of FTIR and UV-visible difference spectroscopy is used to monitor the structural and functional changes during rhodopsin activation. Investigations of how membrane lipids stabilize various rhodopsin photoproducts are analogous to mutating the protein in terms of gain or loss of function. Interpretation of the results entails a flexible surface model for explaining membrane lipid-protein interactions through material properties relevant to biological activity.