As evidenced by a decreased fluorescence, OCP in its red form is capable of dissipating absorbed light energy from the phycobilisome antenna complex. According to Rakhimberdieva and coworkers, about 30-40% of the energy absorbed by phycobilisomes does not reach the reaction centers when the carotenoid-induced NPQ is active.
The exact mechanism and quenching site in both the carotenoid as well as the phycobilisome still remain uncertain.  The linker polypeptide ApcE in the allophycocyanin (APC) core of the phycobilisomes is known to be important, but is not the site of quenching.  Several lines of evidence suggest that it is the 660 nm fluorescence emission band of the APC core which is quenched by OCP.
The temperature dependence of the rate of fluorescence quenching is similar to that of soluble protein folding, supporting the hypothesis that OCP slightly unfolds when it converts to OCP.