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Structure Prediction of CPPs and Iterative Development of Novel CPPs 215
phospholipid organization. Importantly, when pAntp has reached the energy minimum,
its Trp6 residue interacts with the polar heads, whereas Trp14 is embedded
within the hydrophobic core of the bilayer model.
Simulations were then performed with a superficial charge density at the inner
leaflet of the bilayer model equal to 0.04 e – /Å 2 . As shown in Figure 9.10A, the
AntHD–DNA complex is predicted to reach the same position as with the previous
membrane model. The increase in charge density induces an increase of the charge
restraint when the complex mass center reaches positions below 28 Å, but not before.
For the AntHD without DNA (Figure 9.10B), a partial crossing of the bilayer is
observed, basically due to the charge restraint, since the hydrophobic restraint is
largely unfavorable and the lipid perturbation restraint is important too
(20kJ/mol.Å 2 ). In its final configuration, the AntHD mass center is located near the
bilayer center (–4 Å), but this implies that part of the third helix interacts with the
polar heads domain of the inner leaflet (Arg1, Arg10, Arg16 residues).
Taken separately, the first helix (Figure 9.10C) is predicted to enter the polar
heads domain of the outer leaflet, with its mass center stabilizing at 15 Å. Then, the
Monte Carlo procedure opens the way to a jump over the restraint barrier; indeed,
using this method we switch between two local energy minima. The penetration of
the first helix in the membrane is driven by the favorable charge restraint because
the hydrophobic restraint is still unfavorable during the partial crossing.
The second helix entirely crosses the bilayer hydrophobic core (Figure 9.10D
bottom) as an effect of the charge restraint, with the hydrophobic restraint, as for
the previous simulations, unfavorable during the crossing. Here again, the absence
of a continuous path to reach the most favorable position (Figure 9.10D top) is
indicative of a rapid crossing.
The third helix, pAntp, crosses the membrane, too, but the energy minimum is
less favorable than that reached in the case of helix 2 (Figure 9.10E bottom). Moreover,
pAntp orientation at its energy minimum indicates that the helix forms an angle
of –53° with the bilayer plane (Figure 9.10E top), with the pAntp N-terminal part
buried within the hydrophobic core of the membrane and the C-terminal part interacting
with the phospholipid polar heads of the inner leaflet.
9.4 CONCLUSIONS
We have developed a new computational method to simulate interactions between
chemical compounds and a modeled membrane. This method has been tested and
validated with peptides and proteins for which experimental data regarding their
interactions with membranes were available. We applied this to the Antennapedia
homeodomain and its derivatives, such as the penetratin cell-permeant peptides, in
order to account for their behavior when facing membrane models. According to
our analysis, in the case of an uncharged membrane model, neither the complete
Antennapedia homeodomain nor its constitutive helices are able to cross the bilayer.
By refining our simulation methods in order to approach more reliably true
biological membranes, we elaborated a charged bilayer model. In this context, we
observe that, with the increase of the superficial charge density of the bilayer inner