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Self assembly of peptides near or within membranes using coarse grained MD simulations

A. Khalfa W. Treptow Bernard Maigret 1 M. Tarek 
1 ORPAILLEUR - Knowledge representation, reasonning
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
Abstract : Coarse grain modeling has recently emerged as an alternative to classical atomistic simulations in the study of spontaneous self assembly and structural organization of complex molecular systems. For surfactant and lipid systems, it was shown to allow, under appropriate conditions, in-silico self assembly of a variety of architectures. Recently, this approach has been extended to peptides for which force fields allowing self assembly of mixed peptides–lipid systems were proposed. Here we introduce elements of a coarse grained force field that accurately describe self assembly of hydrophobic cyclic peptides [Trp–Leu]4 and their reorganization within lipid membranes to form transmembrane channels in agreement with experiments. Extension to hydrophobic helical transmembrane, and amphipatic helical antimicrobial peptides show that the model is robust enough to constitute a building block for more complete and appropriate force field describing peptide interactions with membranes.
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Submitted on : Monday, November 23, 2009 - 4:45:54 PM
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A. Khalfa, W. Treptow, Bernard Maigret, M. Tarek. Self assembly of peptides near or within membranes using coarse grained MD simulations. Chemical Physics, Elsevier, 2009, 358 (1-2), pp.161-170. ⟨10.1016/j.chemphys.2009.01.012⟩. ⟨inria-00435164⟩



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