Energy-dependent quenching of excitons in photosystem II of plants, or qE, has been positively correlated with the transient production of carotenoid radical cation species. Zeaxanthin was shown to be the donor species in the CP29 antenna complex. We report transient absorbance analyses of CP24 and CP26 complexes that bind lutein and zeaxanthin in the L1 and L2 domains, respectively. For CP24 complexes, the transient absorbance difference profiles give a reconstructed transient absorbance spectrum with a single peak centered at ϳ980 nm, consistent with zeaxanthin radical cation formation. In contrast, CP26 gives constants for the decay components probed at 940 and 980 nm of 144 and 194 ps, a transient absorbance spectrum that has a main peak at 980 nm, and a substantial shoulder at 940 nm. This suggests the presence of two charge transfer quenching sites in CP26 involving zeaxanthin radical cation and lutein radical cation species. We also show that lutein radical cation formation in CP26 is dependent on binding of zeaxanthin to the L2 domain, implying that zeaxanthin acts as an allosteric effector of charge transfer quenching involving lutein in the L1 domain.Regulation of light capture during photosynthesis occurs primarily within the antenna of photosystem II, the peripheral portion of which is comprised of trimeric light-harvesting complex (LHC) II 4 (1) and the monomeric minor LHCs CP24, CP26, and CP29 (2). Regulation of light capture is critical for plant fitness (3) and is achieved predominantly by a process termed energy-dependent quenching, or qE (4), one of a composite of processes involved in the non-photochemical quenching (NPQ) of excess absorbed light energy (5-7). Several characteristics distinguish qE from the other components of NPQ. First, qE is reversible on the seconds-to-minutes time scale, a feat that is thought to reflect rapid changes in the thylakoid lumen pH, which transmit information to the antenna where the molecular mechanism of qE is modulated. Secondly, the npq1 and npq4 mutant strains of Arabidopsis thaliana, which lack the capacity for generating zeaxanthin (Z) (8) and the PsbS protein (9), respectively, exhibit very little qE, consistent with Z and PsbS being necessary for qE.The peripheral antenna is generally thought to be the location of the molecular mechanism of qE, although within precisely which of the LHCs, as well as by what molecular mechanism(s), are issues currently under intense investigation (10 -13). Assigning where and by what mechanism(s) qE occurs is hindered by the fact that qE is, by definition, a phenomenon requiring an intact system, complicating purely deconstructive approaches for studying this mechanism. Nonetheless, several recent studies have combined various approaches to correlate the phenomenology of qE with various components and molecular mechanisms. For example, it was recently shown that excitation energy transfer from singlet-excited chlorophyll (Chl) to the S 1 state of lutein (Lut) occurs both within isolated LHCII trimeric complexes (13), p...