In this letter we present a variation in the optical properties of bio-organic peptide nanostructures, which are induced by molecular transformation. The self-assembled tubular structures are formed from short aromatic di-peptides. Upon thermal induction, the structure changes its molecular conformation, and the linear di-peptide closes into a cyclic peptide. This irreversible transition changes the molecular packing at the nanoscale, which results in reconstruction of the native quantum dot-like packing to quantum well-like packing and the generation of blue luminescence. We further show that the same cyclic peptide can exhibit different photoluminescence properties according to the formed structure.