The structural properties of the light harvesting complex ( LHCII), a pigmented protein trimer inserted in lipid bilayer, are investigated to understand the trimerization process of the protein monomers. With all atom molecular dynamics simulation we study various specific interactions focusing on the role of protein and pigments on trimer formation and stability. Based on the atomistic level simulations we derive a CG model for LHCII with a particular attention to chlorophyll (CHL) b/a, a pigment in LHCII. The model is a combination of independently derived structure based bonded potentials obtained by Boltzmann inversion of respective atomistic distribution and thermodynamic based non-bonded coarse graining potentials fitting with the Martini force-field. The structural properties and partitioning behavior of CHL in the lipid bilayer are consistent with the higher resolution description. Using the CG model we aim to study the larger scale aggregation of protein trimer for the current biomolecular system.

Simulating the light harvesting complex from green plants: A multi resolution study

244th National Meeting (2012)

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