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Molecular Dynamics of Light Harvesting Complexes

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The Peridinin­ - Chlorophyll a - Protein (PCP) is a light-harvesting complex that works as antenna in the photosynthetic process of dinoflagellates. Its function is to collect incoming light also in the range where chlorophyll does not absorb, thanks to the peridinin molecules. In the protein each non­-equivalent peridinin molecule has absorption peaks at different wavelengths and can transfer the absorbed energy to chlorophyll. This spectra modulation, which has the fundamental functional role to extend the absorption spectra of the light harvesting complex, is originated by a combined effect of the distorted conformation and of the protein field. Recent high resolution X­-ray diffraction data on a reconstructed PCP, the refolded peridinin­ - chlorophyll a - protein (RFPCP) [1], opened the way to the mechanistic understanding of peridinin spectral tuning, peridinin­-chlorophyll energy transfer and photoprotective mechanisms [2]. RFPCP consist of two symmetric domains, each one binding a cluster of different cofactors: one chlorophyll a molecule, four peridinin molecules and one digalactosyldiacylglycerol (DGD) molecule. The high carotenoid:chlorophyll ratio (4:1) makes PCP unique among the light­-harvesting systems and assigns to peridinin an important role in the energy transfer mechanism. We perform classical molecular dynamics simulations of the RFPCP in explicit water solution: we analyse the structure and dynamics of the full protein and of its pigments to investigate the role of the four non­-equivalent peridinins in the protein function. We perform also electronic structure calculations (QM/MM) to study the Triplet Excitation Energy Transfer (TEET) mechanism [3] between the chlorophyll and one of the peridinin molecules.  

1 T. Schulte, D. M. Niedzwiedzki, R. R. Birge, R. G. Hiller, T. Polivka, E. Hofmann, and H. A. Frank, PNAS 106, 20764­20769 (2009).
2 A. Damjanovic, T. Ritz and K. Schulten, Biophysical Journal, 79, 1695­1705 (2000).
3 M.T.A. Alexandre, D.C. Lührs, I.H.M. von Stokkum, R. Hiller, M.L. Groot, J.T.M. Kennis, R. van Grondelle, Biophysical Journal, 93, 2118-2128 (2007).


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A) Arrangement of the QM/MM system: the MM part (thin line) includes the backbone (blue) and the cofactors (red); the QM box (bold line) contains one chlorophyll (green) and one peridinin (orange)

B) Localization of the spin density (difference between the density of the spin_up and spin_down orbitals) for the triplet state of chlorophyll (green) and peridinin (orange)


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