(5bo) Simulation and Experimental Studies of the Interactions of Membranes with Peptides, Synthetic Polymers and Nanoparticles

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-B_1-25 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 (R_gµM_w^v), 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-B_1-25 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.