A coarse-grained (CG) model for polyethylene oxide (PEO) and polyethylene glycol (PEG) developed within the framework of the MARTINI CG force field (FF) using the distributions of bonds, angles, and dihedrals from the CHARMM all-atom FF is presented. Densities of neat low molecular weight PEO agree with experiment, and the radius of gyration R g = 19.1 ű0.7 for 76-mers of PEO (M w ≈ 3400), in excellent agreement with neutron scattering results for an equal sized PEG. Simulations of 9,18,27,36,44,67, 76, 90, 112, 135, and 158-mers of the CG PEO (442 < M w < 6998) at low concentration in water show the experimentally observed transition from ideal chain to real chain behavior at 1600 < M w < 2000, in excellent agreement with the dependence of experimentally observed hydrodynamic radii of PEG. Hydrodynamic radii of PEO calculated from diffusion coefficients of the higher M w PEO also agree well with experiment. R g calculated from both all-atom and CG simulations of PEO76 at 21 and 148 mg/cm 3 are found to be nearly equal. This lack of concentration dependence implies that apparent R g from scattering experiments at high concentration should not be taken to be the chain dimension. Simulations of PEO grafted to a nonadsorbing surface yield a mushroom to brush transition that is well described by the Alexanderde Gennes formalism.

The molecular basis of nephronophthisis, the most frequent genetic cause of renal failure in children and young adults, and its association with retinal degeneration and cerebellar vermis aplasia in Joubert syndrome are poorly understood. Using positional cloning, we here identify mutations in the gene CEP290 as causing nephronophthisis. It encodes a protein with several domains also present in CENPF, a protein involved in chromosome segregation. CEP290 (also known as NPHP6) interacts with and modulates the activity of ATF4, a transcription factor implicated in cAMP-dependent renal cyst formation. NPHP6 is found at centrosomes and in the nucleus of renal epithelial cells in a cell cycle-dependent manner and in connecting cilia of photoreceptors. Abrogation of its function in zebrafish recapitulates the renal, retinal and cerebellar phenotypes of Joubert syndrome. Our findings help establish the link between centrosome function, tissue architecture and transcriptional control in the pathogenesis of cystic kidney disease, retinal degeneration, and central nervous system development.

A revision (C35r) to the CHARMM ether force field is shown to reproduce experimentally observed conformational populations of dimethoxyethane. Molecular dynamics simulations of 9, 18, 27, and 36-mers of polyethylene oxide (PEO) and 27-mers of polyethylene glycol (PEG) in water based on C35r yield a persistence length lambda = 3.7 A, in quantitative agreement with experimentally obtained values of 3.7 A for PEO and 3.8 A for PEG; agreement with experimental values for hydrodynamic radii of comparably sized PEG is also excellent. The exponent upsilon relating the radius of gyration and molecular weight (R(g) proportional, variantM(w)(upsilon)) of PEO from the simulations equals 0.515 +/- 0.023, consistent with experimental observations that low molecular weight PEG behaves as an ideal chain. The shape anisotropy of hydrated PEO is 2.59:1.44:1.00. The dimension of the middle length for each of the polymers nearly equals the hydrodynamic radius R(h)obtained from diffusion measurements in solution. This explains the correspondence of R(h) and R(p), the pore radius of membrane channels: a polymer such as PEG diffuses with its long axis parallel to the membrane channel, and passes through the channel without substantial distortion.

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.

We have performed molecular dynamics (MD) simulations of multiple copies of un-acetylated G5 and G7, and acetylated G5 dendrimers in dimyristoylphosphatidylcholine (DMPC) bilayers with explicit water using the coarse-grained (CG) model developed by Marrink et al. (J. Phys. Chem. B. 2007, 111, 7812) with inclusion of long-range electrostatics. When initially clustered together near the bilayer, neutral acetylated dendrimers aggregate, whereas cationic un-acetylated dendrimers do not aggregate, but separate from each other, similar to observations from atomic force microscopy by Mecke et al. (Chem. Phys. Lipids. 2004, 132, 3). The bilayers interacting with un-acetylated dendrimers of higher concentration are significantly deformed and show pore formation on the positively curved portions, while acetylated dendrimers are unable to form pores. Un-acetylated G7 dendrimers bring more water molecules into the pores than do un-acetylated G5 dendrimers. These results agree qualitatively with experimental results showing that significant cytoplasmic-protein leakage is produced by un-acetylated G7 dendrimers at concentrations as low as 10 nM, but only at a much higher concentration of 400 nM for un-acetylated G5 dendrimers (Bioconj. Chem. 2004, 15, 774). This good qualitative agreement indicates that the effect on pore formation of the concentration and size of large nanoparticles can be studied through coarse-grained MD simulations, provided that long-range electrostatic interactions are included.

Self-assembly of polyethylene glycol (PEG)-grafted lipids at different sizes and concentrations was simulated using the MARTINI coarse-grained (CG) force field. The interactions between CG PEG and CG dipalmitoylglycerophosphocholine (DPPC)-lipids were parametrized by matching densities of 19-mers of PEG and polyethylene oxide (PEO) grafted to the bilayer from all-atom simulations. Mixtures of lipids and PEG(Mw = 550, 1250, 2000)-grafted lipids in water self-assembled to liposomes, bicelles, and micelles at different ratios of lipids and PEGylated lipids. Average aggregate sizes decrease with increasing PEGylated-lipid concentration, in qualitative agreement with experiment. PEGylated lipids concentrate at the rims of bicelles, rather than at the planar surfaces; this also agrees with experiment, though the degree of segregation is less than that assumed in previous modeling of the experimental data. Charged lipids without PEG evenly distribute at the rim and planar surface of the bicelle. The average end-to-end distances of the PEG on the PEGylated lipids are comparable in liposomes, bicelles (edge or planar surface), and micelles, and only slightly larger than for an isolated PEG in solution. The ability of PEGylated lipids to induce the membrane curvature by the bulky head group with larger PEG, and thereby modulate the phase behavior and size of lipid assemblies, arises from their relative concentration.

We performed molecular dynamics (MD) simulations of multiple copies of poly-L-lysine (PLL) and charged polyamidoamine (PAMAM) dendrimers in dimyristoylphosphatidylcholine (DMPC) bilayers with explicit water using the coarse-grained model developed by Marrink et al. (J. Chem. Theory and Comput. 2008, 4, 819). Membrane disruption is enhanced at higher concentrations and charge densities of both spheroidally shaped dendrimers and linear PLL polymers, in qualitatively agreement with experimental studies by Hong et al. (Bioconjugate Chem. 2006, 17, 728). However, larger molecular size enhances membrane disruption and pore formation only for dendrimers and not for the linear PLL. Despite more intimate electrostatic interactions of linear molecules than are possible for spheroidal dendrimers, only the dendrimers were found to perforate membranes, apparently because they cannot spread onto a single leaflet, and so must penetrate the bilayer to get favorable electrostatic interactions with head groups on the opposite leaflet. These results indicate that a relatively rigid spheroidal shape is more efficient than a flexible linear shape in increasing membrane permeability. These results compare favorably with experimental findings.

G4 PAMAM dendrimers grafted with poly(ethylene glycol) (PEG) of different sizes (M w = 550 and 5000) and grafting densities (12−94% of surface terminals) were simulated using the coarse-grained (CG) force fields previously developed and reparametrized in this work. Simulations are carried out for G4, G5, and G7 un-PEGylated dendrimers that are either unprotonated, terminally protonated, or protonated on both terminals and interior sites, corresponding to pH values of >10, 7, and <5, respectively. As protonation increases, simulations show only a small (∼6% for G4 and G5) change of dendrimer radius of gyration R g and show a structural transition from dense-core to dense-shell structure, both of which are in agreement with recent scattering experiments and all-atom simulations. For the PEGylated dendrimers, the R g of the fully PEG(M w = 5000)-grafted dendrimer also agrees well with experiment. Longer PEG chains with higher grafting density yield PEG−PEG crowding, which stretches dendrimer terminals toward water more strongly, leading to larger size and a dense-shell structure of the dendrimer. Long PEG chains at high grafting densities also penetrate into the dendrimer core, while short ones do not, which might help explain the reduced encapsulation of hydrophobic compounds seen experimentally in dendrimers that are 75%-grafted with long PEG’s (M w = 5000). This reduced encapsulation for dendrimers with long grafted PEG’s has previously been attributed to PEG-induced dendrimer aggregation, but this explanation is not consistent with our previous simulations which showed no aggregation even with long PEG’s but is consistent with the new simulations reported here that show PEG penetration into the core of the dendrimer to which the PEG is attached.