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208 Cell-Penetrating Peptides: Processes and Applications
hydrophobicity potential (MHP) (Figure 9.7.C) provides an idea about the hydrophobicity
distribution. Figure 9.7.C shows the partition of the hydrophilic (green)
and the hydrophobic (orange) areas for each of the homeodomain helices. All helices
are amphiphilic. The hydrophilic and hydrophobic partition is balanced for the first
helix; a first hydrophilic domain is made of Arg1, Tyr2, and Cys3, followed by an
important hydrophobic domain flanking a next hydrophilic domain defined by Glu6,
Glu8, Lys9, and Glu10.
For the second helix, there is an evident segregation between a bulking hydrophilic
domain (Arg1, Arg2, Arg3, and Arg4) and a C-terminal hydrophobic domain
(Ile7, Ala8, Ala10, and Leu11). Finally, the penetratin helix (pAntp) has numerous
hydrophilic domains spread all along the sequence. At the beginning of the sequence,
one is due to Arg1 and Gln3. Then, a smaller hydrophilic domain is formed by the
polar residues (Gln8, Asn9); charged residues are defining an important hydrophilic
domain at the pAntp C-terminal extremity (Lys13, Lys15, and Lys16). An important
hydrophobic domain is contributed by Trp6 and Phe7.
9.3.2.1 Uncharged Membrane Model
Figure 9.8 shows the Monte Carlo simulation results obtained for AntHD–DNA,
AntHD, and the three homeodomain helices. The graph in the middle of the figure
shows evolution of the global energetic restraint (hydrophobic and lipid perturbation
restraints are summed) for each molecule or complex as a function of their mass
center penetration Z ordinate. The two dotted lines mark the boundary of the phospholipid
polar heads of the membrane external leaflets (between 18 and 13.5 Å) and
the bilayer center corresponds to the 0 Å Z ordinate. The simulations were started
with the molecule mass center located at 35 Å. At the end of the calculation, the
lowest value of global energy restraint indicates the most probable position of the
molecules in the bilayer.
Therefore, it is revealed from simulations that the AntHD–DNA complex stabilizes
when its mass center is located at 34.5 Å from the bilayer center. When it
approaches the bilayer, the energy restraint slowly, then severely, increases as the
complex reaches 28.5 Å. Closer to the membrane, the restraint values are tremendous;
the Monte Carlo procedure predicts that the complex cannot enter the bilayer.
A similar profile is obtained for the homeodomain alone, even if the energy restraint
is higher. The AntHD stabilizes at almost the same position as it does when in the
AntHD–DNA complex (i.e., 27.5 Å).
If the energy restraint evolution curves for AntHD–DNA and AntHD penetrations
are similar, the position of each subdomain (Figure 9.8A and 9.8B) are different at
the restraint minimum value: for the AntHD–DNA complex, the third helix is in
interaction with the double-strand DNA, and the other two helices, especially the
first one (Figure 9.8C) are near the external sheet phospholipid polar heads. Conversely,
when the DNA is removed, the third helix is close to the phospholipid heads;
the other helices lie more distantly. This preferential interaction between the third
helix and the phospholipids may be attributed to its amphiphilicity.
In order to go further in our analysis and to evaluate the contribution of each
helix to interaction with the bilayer and, even more, to provide a model for penetratin