In photosynthesis, specialized light harvesting pigment- protein complexes (PPCs) are used to capture incident sunlight and funnel its energy to the reaction center. In Cryptophyte algae these complexes are suspended in the lumen, where the pH ranges between ~5-7, depending on the prolongation of the incident sunlight. However, the pKa of the several kinds of bilin chromophores encountered in these complexes and the effect of its protonation state on the energy transfer process is still unknown. Here, we combine quantum chemical and continuum solvent calculations to estimate the intrinsic aqueous pKas of different bilin pigments. We then use Propka and APBS classical electrostatic calculations to estimate the change in protonation free energies when the bilins are embedded inside five different phycobiliproteins (PE545, PC577, PC612, PC630 and PC645), and critically asses our results by analysis of the changes in the absorption spectral line shapes measured within a pH range from
4.0 to 9.4. Our results suggest that each individual protein environment strongly impacts the intrinsic pKa of the different chomophores, being the final responsible of their protonation state
