Photosynthetic antenna proteins can be thought of as "programmed solvents", which bind pigments at specific mutual orientations, thus tuning the overall energetic landscape and ensuring highly efficient light-harvesting. While positioning of chlorophyll cofactors is well understood and rationalized by the principle of an "energy funnel", the carotenoids still pose many open questions. Particularly, their short excited state lifetime (<25 ps) renders them potential energy sinks able to compete with the reaction centers and drastically undermine light-harvesting efficiency. Exploration of the orientational phasespace revealed that the placement of central carotenoids minimizes their interaction with the nearest chlorophylls in the plant antenna complexes LHCII, CP26, CP29 and LHCI. At the same time we show that this interaction is highly sensitive to structural perturbations, which has a profound effect on the overall lifetime of the complex. This links the protein dynamics to the light-harvesting regulation in plants by the carotenoids.Photosystem I (PSI) and Photosystem II (PSII) are large, integral membrane protein super-complexes in plants and green algae 1,2 . They are the key components of the light reactions of photosynthesis. While PSII performs water oxidation to build a transmembrane proton gradient and induce electron transfer 3 , PSI primarily produces the universal redox carrier NADPH 4 . From the functional perspective, the photosystem super-complexes are divided into the core sites of actual photochemical reactions, called reaction centers (RCs), and accessory light-harvesting complexes (LHCs). Even though the RC sub-units capture light themselves, the peripheral LHC antenna proteins of the Lhcb (in PSII) and Lhca (in PSI) families are necessary to increase the absorption cross-section and ensure optimal performance 5 . The antenna complexes transfer excitation energy with remarkable efficiency, enabling near unity quantum yield of PSI/II (one photochemical reaction per one photon captured) 6 . This is due to the fine tuning of the relative positions, orientations and excitation energies of chlorophyll (Chl) cofactors coordinated by the residues, which is the reason why LHC proteins are sometimes referred to as "programmed solvent" 2 . The current precision of pigment placement resolved from the crystal structures 7-10 allows for highly detailed models, describing both the initial steps of exciton transfer 11,12 and the subsequent charge separation in the RCs 13 . However, such models largely account only for the Chls, while the second major building block of the pigment arrays, the carotenoids (Cars), are usually disregarded.Cars are typically included in photodynamic models of bacterial systems only, where they are significant light-harvesters 14 , while their light-harvesting role in plants is minor compared to the photoprotective function 15,16 . The latter is performed primarily by quenching the Chl triplet states 17 , which would otherwise sensitize molecular oxygen to form harmful singlet oxy...

Plant light-harvesting is regulated by the Non-Photochemical Quenching (NPQ) mechanism involving the reversible formation of excitation quenching sites in the Photosystem II (PSII) antenna in response to high light. While the major antenna complex, LHCII, is known to be a site of NPQ, the precise mechanism of excitation quenching is not clearly understood. A preliminary model of the quenched crystal structure of LHCII implied that quenching arises from slow energy capture by Car pigments. It predicted a thoroughly quenched system but offered little insight into the defining aspects of this quenching. In this work, we present a thorough theoretical investigation of this quenching, addressing the factors defining the quenching pathway and possible mechanism for its (de)activation. We show that quenching in LHCII crystals is the result of slow energy transfer from chlorophyll to the centrally-bound lutein Cars, predominantly the Lut620 associated with the chlorophyll 'terminal emitter', one of the proposed in vivo pathways. We show that this quenching is rather independent of the particular species of Car and excitation 'site' energy. The defining parameter is the resonant coupling between the pigment co-factors. Lastly, we show that these interactions must be severely suppressed for a light-harvesting state to be recovered.

The bioenergetics of light-harvesting by photosynthetic antenna proteins in higher plants is well understood. However, investigation into the regulatory non-photochemical quenching (NPQ) mechanism, which dissipates excess energy in high light, has led to several conflicting models. It is generally accepted that the major photosystem II antenna protein, LHCII, is the site of NPQ, although the minor antenna complexes (CP24/26/29) are also proposed as alternative/additional NPQ sites. LHCII crystals were shown to exhibit the short excitation lifetime and several spectral signatures of the quenched state. Subsequent structure-based models showed that this quenching could be explained by slow energy trapping by the carotenoids, in line with one of the proposed models. Using Fluorescence Lifetime Imaging Microscopy (FLIM) we show that the crystal structure of CP29 corresponds to a strongly quenched conformation. Using a structure-based theoretical model we show that this quenching may be explained by the same slow, carotenoid-mediated quenching mechanism present in LHCII crystals.

It has been proposed that photoprotective non-photochemical quenching (NPQ) in higher plants arises from a conformational change in the antenna which alters pigment-pigment interactions. This brings about the formation of energy quenching "traps" that capture and dissipate excitation energy as heat. We have used the semiempirical AM1-CAS-CI method combined with the transition density cube (TDC) approach to model chlorophyll (Chl) to xanthophyll (Xanth) resonant Coulomb couplings in the crystal structure of LHCII. Due to its proposed role as the NPQ quenching site we have focused on lutein interactions and have explored how distortions to lutein conformation, as well as interpigment distances and relative orientations, affect this coupling. Our calculations indicate that distortions as well as Chl-lutein angle have a significant effect on coupling, whereas interpigment distances have a relatively minor effect. We therefore conclude that particular attention to the distortions of the Xanths should be given for calculation of energy transfer pathways and study of the NPQ mechanism.