Derivation of coarse-grained simulation models of chlorophyll molecules in lipid bilayers for applications in light harvesting systems

摘要: The correct interplay of interactions between protein, pigment and lipid molecules is highly relevant for our understanding the association behavior light harvesting complex (LHCII) green plants. To cover time length scales in this multicomponent system, a multi-scale simulation ansatz employed that subsequently uses classical all atomistic (AA) model to derive suitable coarse grained (CG) which can be backmapped into AA resolution, aiming seamless conversion two scales. Such an approach requires faithful description not only protein components, but also interaction functions indispensable molecules, chlorophyll b (referred as chl b/chl a). In paper we develop CG dipalmitoylphosphatidyl choline (DPPC) bilayer system. structural properties distribution within simulations are consistent with those reference simulations. non-bonded potentials parameterized such they fit thermodynamics based MARTINI force-field protein. shows aggregation supported by fluorescence quenching experiments. It shown derived well suited stable, structurally consistent, trimeric LHCII future used study their large scale behavior.