A multiscale modeling approach is used to develop an implicit-solvent intermediate resolution model, LIME (Lipid Intermediate Resolution Model), to simulate the behavior of phospholipids in solution. The LIME geometric and energetic parameters are obtained by collecting data from atomistic simulations of a system composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecules and explicit water and then grouping the atoms on DPPC into 14 coarse-grained sites with unique properties. The interactions between coarse-grained sites are represented by hard sphere and square well potentials, as opposed to Lennard Jones potentials, thereby allowing us to use discontinuous molecular dynamics (DMD) , a fast alternative to traditional molecular dynamics. DMD simulations on systems containing 256 DPPC molecules show spontaneous formation of a bilayer from a random solution in less than 4 hours. The structural properties of the DPPC bilayer are accurately reproduced including the area per lipid, bilayer thickness, bond order and mass density profiles.  DMD/LIME simulations are also applied to aqueous bilayers composed of two types of phospholipids: those containing phosph-L-serine (PS) head groups and those containing phosphatidylcholine (PC) head groups. Our simulations predict that this system changes from an initially-homogeneous state (at neutral pH) to a phase-separated state at low pH phase in agreement with the results of our collaborator Stavorula Sofou ( Rutgers University) on a similar system,  DPPC and 1,2-distearoyl-sn-glycero-3-phospho-L-serine (DSPS).

Multiscale modeling of phospholipid bilayers: LIME/ DMD simulations

246th National Meeting (2013)

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