crc press - E-Lib FK UWKS

Structure Prediction of CPPs and Iterative Development of Novel CPPs 211
TABLE 9.2
Internalization of Simulated Peptides as a Function
of the Inner Sheet Superficial Charge Density
Inner sheet charge
(e – /Å 2 ) AntHD + DNA AntHD 1st helix 2nd helix pAntp
No charge – – – – –
0.005 – – – – –
0.01 – – – – +
0.02 – – – – +
0.04 – ± ± + ++
The AntHD–DNA complex stabilizes when its mass center is located at a distance
of 28 Å, where the minimum value of the total restraint is reached. This is
closer to the bilayer than when this one is uncharged, due to the charge restraint,
which tends to bring the complex close to the membrane. Nevertheless, there is no
membrane insertion because the hydrophobic restraint increases, thus impairing any
insertion. From 28 to 25 Å, the total restraint increases, suggesting that a localization
of the complex close to the membrane is unlikely.
The lipid perturbation restraint is low (maximum value: 8 kJ/mol.Å 2 ) compared
with the other restraints. This is consistent since the complex only partially penetrates
within the polar head domain; therefore, it does not disturb the acyl chains of the
phospholipids. When the homeodomain is not associated with the DNA
(Figure 9.9B), its mass center comes near the external bilayer leaflet because of the
charge distribution in the internal leaflet. Here again, the hydrophilic and hydrophobic
balance of the homeodomain prevents the crossing: the hydrophobic restraint is
unfavorable from 28 Å and increases when the homeodomain mass center
approaches the bilayer.
The same graphics have been made for simulations of the isolated helices
(Figure 9.9C, D, E, bottom). Moreover, in every helix we chose two reference atoms
to draw a segment parallel to the helix axis. This allowed us to follow the evolution
of the total restraint as a function of the positions of the mass center and of the
angles of the helix axis vs. the bilayer plane center (Figure 9.9C, D, E, top).
Now, considering each helix separately, it appears that, for the first helix, which
is the less charged, the most probable position is reached when its mass center is
located at 20 Å. When the mass center gets closer to the membrane both hydrophobic
and charge restraints increase. At the energy minimum, the helix makes an angle of
–5° (from the N-term to the C-term) with respect to the bilayer plane; several residues
(Gln3, Leu7, Phe11) therefore enter within the polar heads domain (results not
shown).
For the second helix observations are similar, but the charge restraint is more
favorable (this helix has a charge of +4.00). The mass center is then located at the
external limit of the polar heads of the external leaflet (18 Å). Here again, hydrophobic
restraint prevents the penetration of the second helix into the hydrophobic