Biomedical Engineering Reference
In-Depth Information
Fig. 1.37
The simulated system (System II). (
a
) Initial framework of System II. The SWNT (
light
bluespheres
) is fully filled with water molecules (
red
-
white pillars
). Some carbon atoms of SWNT
are omitted for clarity. The other colored spheres in the middle of SWNT are the atoms of the
Aˇ
16-22
peptide. The
yellow spheres
outside the nanotube stand for the external charges (reprinted
from [
42
]. Copyright 2009 American Chemical Society) (
b
) initial structure of Aˇ
16-22
peptide
(Ace-KLVFFAE-NMe). It contains a lysine (K) residue with one positive charge (
C
1
e
) at one end
and a glutamic acid (E) residue with one negative charge (
1
e
) at the other. (
c
) Structure of the
lattice of external charges, which contains 12 charges forming a 3
4 array. The distance between
the nearest adjacent charges is 2.88 A
follows the external charges very well. In the six simulations we have performed
with different initial conditions, only in one simulation the peptide does not follow
the external charges.
We have computed the electrostatic interaction energy of the external charges
with the peptide vs. time, shown in Fig.
1.39
. The average electrostatic interaction
energy (averaged over five successful manipulation cases) is
704
˙
142 kJ/mol. In
all simulations, the distances between the COM of the peptide and the geometrical
center of the external charges range from 1.2 to 2.6 nm with an average value of
1.6 nm. We have noted that the deprotonated carboxyl group (COO) on the glutamic
acid residue of the peptide carries most (
0.9
e
) of the negative charge of the
whole residue (
1
e
). Since the external charges are positive, the interaction between
the peptide and the external charges is dominated by the interaction between the
