Molecular Dynamics Simulations of PAMAM Dendrimer-Induced Pore Formation in DPPC Bilayers with a Coarse-Grained Model

Abstract

We have performed 0.5-micros-long molecular dynamics (MD) simulations of 0%, 50%, and 100% acetylated third- (G3) and fifth-generation (G5) polyamidoamine (PAMAM) dendrimers in dipalmitoylphosphatidylcholine (DPPC) bilayers with explicit water using the coarse-grained (CG) model developed by Marrink et al. (J.Phys. Chem. B 2004, 108, 750-760), but with long-range electrostatic interactions included. Radii of gyration of the CG G5 dendrimers are 1.99-2.32 nm, close to those measured in the experiments by Prosa et al. (J. Polym. Sci. 1997, 35, 2913-2924) and atomistic simulations by Lee et al. (J. Phys. Chem. B 2006, 110, 4014-4019). Starting with the dendrimer initially positioned near the bilayer, we find that positively charged un-acetylated G3 and 50%-acetylated and un-acetylated G5 dendrimers insert themselves into the bilayer, and only un-acetylated G5 dendrimer induces hole formation at 310 K, but not at 277 K, which agrees qualitatively with experimental observations of Hong et al. (Bioconj. Chem. 2004, 15, 774-782) and Mecke et al. (Langmuir 2005, 21, 10348-10354). At higher salt concentration (approximately 500 mM NaCl), un-acetylated G5 dendrimer does not insert into the bilayer. The results suggest that with inclusion of long-range electrostatic interactions into coarse-grained models, realistic MD simulation of membrane-disrupting effects of nanoparticles at the microsecond time scale is now possible.

Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

“…The mapping of coarse-grained sites to atoms is similar to the model developed by Lee and Larson [90] (Figure 5). Coarse-grained parameters for non-bonded and bonded potentials were derived using an all-atom molecular dynamics simulation of a G6 PAMAM dendrimer in the gas phase.…”

Molecular analysis of interactions between dendrimers and asymmetric membranes at different transport stages

“…We mapped the atomic structures of the G4 and G5 PAMAM dendrimers generated using the Material Studio package to the CG structures 18 (Fig. 2) 16 The CG structures of the G4 and G5 PAMAM dendrimers contain 250 and 506 CG particles, respectively, and 64 and 128 positive charges, respectively.…”

A mechanistic view of lipid membrane disrupting effect of PAMAM dendrimers

“…The interaction between cell membranes and nanocarriers, such as dendrimers, is very important, because in the most cases carriers have to get across the lipid bilayer without disrupting it. Previous studies based on atomic force microscopy (AFM) [12][13][14][15][16][17] isothermal titration calorimetry (ITC), fluorescence correlated spectroscopy (FCS) [17][18], in vitro experiments [13,[19][20] and molecular dynamics simulations (MD) [14,17,[21][22][23][24] showed that cationic dendrimers disrupt lipid bilayers by forming holes on the bilayer surface and may remove lipids from it. The degree of the disruption depends on the size and charge of the dendrimer.…”