All-atom and coarse-grained (CG) molecular dynamics (MD) simulations were performed to investigate (1) peptide-peptide, peptide-monolayer, and peptide-micelle interactions; (2) effects of the dendrimer surface, size, and concentration on pore formation in lipid bilayers; and (3) hydrodynamics and shape anisotropy of polymers as they pass through the pores of membrane proteins. Circular dichroism spectroscopy and single-channel current recording experiments were also performed to complement simulation results. Future research directions are presented.
(1) Peptide interactions with lipid monolayers and micelles.
SP-B1-25 is a fragment of 79-amino acid lung surfactant protein B, an important component for preventing respiratory distress syndrome. Multiple copies of the peptide in palmitic acid monolayer were simulated with all atoms, showing that the final peptide conformation favorably compared with experiments. The peptides are anchored by hydrogen bond interactions between the cationic residues Arg-12 and Arg-17 and the hydrogen bond acceptors of the ionized monolayer headgroup, and the peptide tilt angle is modulated by the interactions of Tyr-7 and Gln-19 with the monolayer headgroup. These results can be applied to the rational design of synthetic lung surfactant peptides. [1]
Coiled-coil peptides [2,3] and the BAR peptide-SDS micelle [4] were simulated to investigate models of membrane curvature by BAR domains. Both simulation and experiment indicate that the N-terminal region (helix-0) is disordered, and that the peptide curves to adopt the micelle shape. This is consistent with notion that helix increases the peptide-membrane binding affinity.
(2) Nanoparticle induced-pore formation in the lipid bilayer: Effects of the nanoparticle size, surface charge, and concentration.
Polyamidoamine (PAMAM) dendrimers, which consist of regularly branched monomeric building blocks and surface terminal groups, are good candidate nanoparticles for use as anti-tumor therapeutics and drug delivery. To investigate the effect on pore formation of the dendrimer properties (size, surface charge, and concentration) and solution conditions (temperature and salt concentration), we simulated PAMAM dendrimers in DMPC bilayers with explicit water using the CG model. When initially clustered together near the bilayer, neutral acetylated dendrimers aggregate, whereas cationic un-acetylated dendrimers disperse, in agreement with experiments. 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. Larger un-acetylated dendrimers bring more water molecules into the pores than do smaller ones. At higher salt concentration (~500mM NaCl) or lower temperature (277 K), un-acetylated dendrimers do not insert into the bilayer. These results highlight the applicability of CG simulations, and help explain why charged dendrimers deform membranes and form pores at high concentration. [5,6,7]
(3) Hydrodynamic radius and shape anisotropy of polymers as they pass through the pores of membrane proteins
Polyethylene oxide (PEO) and polyethylene glycol (PEG) are used as probes of pore sizes of membrane channels, although many molecular details are unclear. PEO and PEG were simulated to examine anisotropy of the shape and translational diffusion tensors of these polymers as a step toward understanding their interaction with membrane pores. The calculated persistence length, the exponent u relating the radius of gyration and molecular weight (RgµMwv), and hydrodynamic radii are in quantitative agreement with experiment values. The dimension of the middle length for each of the polymers nearly equals the hydrodynamic radius obtained from diffusion measurements in solution. This implies that a polymer diffuses with its long axis parallel to the membrane channel without substantial distortion. This quantitative study also helps development of coarse-grained models of PEG and PEO for ongoing investigation of the effects of the molecular flexibility (soft linear vs. hard sphere) in membrane channels at the microsecond time scale. Single-channel current recording experiments of PEG and dendrimers are also being performed to complement simulation results. [8]
References
[1] Lee H, Kandasamy SK, and Larson RG, Molecular dynamics simulations of the anchoring and tilting of the lung-surfactant peptide SP-B1-25 in palmitic acid monolayers. Biophysical J., 2005, 89:3807-3821
[2] Sayer JA, Otto EA, O'toole JF, Nurnberg G, Kennedy MA, Becker C, Hennies HC, Helou J, Attanasio M, Fausett BV, Utsch B, Khanna H, Liu Y, Lee H, Larson RG, and Hildebrandt F et al., The centrosomal protein nephrocystin-6 is mutated in Joubert syndrome and activates transcription factor ATF4. Nature Genetics, 2006, 38:674-681
[3] Lee H, and Larson RG, Prediction of the stability of coiled coils using molecular dynamics simulations. Molecular Simulation, 2007, 33:463-473
[4] Low C, Weininger U, Lee H, Schweimer K, Pastor RW, Balbach J. Structure and dynamics of Helix-0 of the N-BAR domain in lipid micelles and bilayers. Biophysical J., submitted.
[5] Lee H, Baker JR, and Larson RG, Molecular dynamics studies of the size, shape, and internal structure of 0% and 90%-acetylated G5 PAMAM dendrimers in water and methanol. J. Physical Chemistry B., 2006, 110:4014-4019
[6] Lee H, and Larson RG, Molecular dynamics simulations of PAMAM dendrimer-induced pore formation in DPPC bilayers using a coarse grained model. J. Physical Chemistry B., 2006, 110:18204-18211
[7] Lee H, and Larson RG. Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth- and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer. J. Physical Chemistry B. 2008, In press.
[8] Lee H, Venable RM, MacKerell AD, Pastor RW. Molecular dynamics studies of polyethylene oxide and polyethylene glycol: Hydrodynamic radius and shape anisotropy. Biophysical J. 2008, In press.