| Abstract [eng] |
Light harvesting is carried out by photosystems I and II (PSI and PSII) that are located in the thylakoid membrane of chloroplasts. Excessive light can cause photo-oxidative damage to the plant, so for this reason they have developed protective mechanisms such as nonphotochemical quenching (NPQ). Quenching sites have been identified in LHCII and CP29 complexes of PSII. NPQ in LHCII is thought to be correlated with Chl–Chl charge-transfer (CT) states so this could also be the case for CP29. CT states can be analyzed using quantum mechanics, however, it is known that the energies of CT states are sensitive to small conformational changes of the target system, so molecular dynamics (MD) simulations could be employed to analyze this dependence; using quantum mechanical methods for different conformational states of a system that is composed of several thousand atoms would be computationally expensive. The aim of this work was to perform a molecular dynamics simulation of light-harvesting complex CP29 and to analyze the geometries and CT states of Chl–Chl dimers at different moments of simulation. The high resolution crystal structure of spinach photosynthetic complex CP29 (PDB ID: 3PL9) was inserted into DOPC lipid bilayer membrane and solvated in water using CHARMM-GUI tool. Pigments were described using force field (FF) parameters from literature, and Amber FFs ff14SB, Lipid21 and TIP3P were used to describe the protein chain, membrane and water respectively. Hydrogen atoms and ions were added using LEaP tool. A three-step energy minimization, a \si 1{ns} heating simulation, a \si 5{ns} relaxation simulation and a \si{20}{ns} production simulation were performed using Amber. A root-mean-square deviation (RMSD) analysis of resulting trajectory was performed using Cpptraj tool, and excited states of dimers were calculated using time-dependent density functional theory (TD-DFT) at 8 different time steps. It was found that during the energy minimization, relaxation and MD simulation chlorophylls b614 and a615 had the biggest structural and positional changes; the difference between the initial and final position of Chl b614 porphyrin ring was \si{3.24}{\textrm{Å}}. Ten CT states were identified in five Chl dimers, with the lowest energy CT states forming in dimers b606–a604 and b614–a613; the CT states in these two dimers are most likely to take part in PSII processes such as NPQ. The time dependences of the distance and the angle between chlorophyll porphyrin rings in a dimer were calculated and compared with the changes in energies of the identified CT states. In four of the five analyzed dimers a correlation between the energies of the CT states and the distances and the angles between chlorophyll porphyrin rings was observed – smaller distances and bigger angles corresponded to lower energies. This correlation was not observed in dimer a611–a615; this could be explained by the fact that the chlorophyll porphyrin rings in this dimer are facing each other asymmetrically. |
