• computational analysis
• LHCII
• light-harvesting
• Light-Harvesting Complex II
• non-photochemical quenching
• photoprotection
• pigments

In the photosynthetic process, light is absorbed and converted into chemical energy by photosynthetic organisms such as bacteria, algae, and plants. At the same time, photoprotective mechanisms are required to protect the photosynthetic apparatus from photooxidative damage caused by high-light intensity.
In higher plants, photosynthesis takes place in the thylakoid membrane of the chloroplast and it is carried out by multiprotein complexes called Photosystems (PSI and PSII), which comprehend “antennas” and reaction centers. (RCs). Light Harvesting Complex II (LHCII) is one of the major antenna proteins associated with PSII and contains Chlorophylls and Xanthophylls. LHCII has different functions depending on the light intensity conditions: in normal light conditions LHCII works as an antenna complex which absorbs light and transfers the related energy to the reaction center but when high-light intensity saturates it, the photoprotective activity of LHCII takes place to prevent photodamage.
In particular, in high-light conditions, the excessive light absorbed by the Chlorophylls present in the antenna can be dissipated by a process called Non-Photochemical Quenching (NPQ). In higher plants, the main NPQ component is the energy-dependent quenching (qE) that it is almost entirely related to the Xanthophylls bound to LHCII (Lutein and Zeaxanthin).
In this project, we analyzed the LHCII protein in silico, performing a conformational analysis of classical and accelerated Molecular Dynamics simulations. In the LHCII aggregational hypothesis, small alterations of each LHCII in the PSII can cause a huge variation of energy/charge transfer among the pigments involved in both the light-harvesting and photoprotection functions. For this reason, we searched for different holoprotein conformations that could have different quenching properties. In doing so, we analyzed the apoprotein secondary and tertiary structure, the pigments interactions with the apoprotein and the structural properties of pigment dimers.