Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

Many biological cellular processes occur at the micro- or millisecond time scale.With traditional all-atom molecular modeling techniques it is difficult to investigate thedynamics of long time scales or large systems, such as protein aggregation or activation.Coarse graining (CG) can be used to reduce the number of degrees of freedom in sucha system, and reduce the computational complexity. In this paper the first version of acoarse grained model for transmembrane proteins is presented. This model differs fromother coarse grained protein models due to the introduction of a novel angle potential as wellas a hydrogen bonding potential. These new potentials are used to stabilize the backbone.The model has been validated by investigating the adaptation of the hydrophobic mismatchinduced by the insertion of WALP-peptides into a lipid membrane, showing that the firststep in the adaptation is an increase in the membrane thickness, followed by a tilting of thepeptide.