252
M. Melicherčík et al.
In the rest of simulations, the peptide is more or less tilled. In more than half of
simulations, the peptide doesn’t stay linear, but change its main chain conformation
(more to the tilting). The peptide bends like a bow (Barlow et al. called it curved
peptide [86]), or even breaks the helical structure (kinked as mentioned by the same
authors)—see Fig. 8.4. Amount of bending is different for each simulation, but we
were not able to find correlation between composition of system and amount of
bending or place of break. But peptide A 24 keeps best the linear conformation of ideal α-helix and doesn’t bend or break (see Table 8.1—the difference between angle
of 1
st
and 2
nd
peptide half, but helicity analysis is not shown). The peptide V 24 also
keeps linear conformation—exception is DMPC/gel, where the peptides are curved.
For providing some quantification of bending we calculated the tilt of whole helix
(as axis from first to last four C
α
atoms) and tilt of separated upper and lower halves
(C
α
from 13
th
–16
th
residue)—see Table 8.1. From tilt of the helix and its length we
can calculate effective length of peptide in a membrane. The effective length is
length of projection of helix to the membrane normal (Table 8.1). In ideal case it
should be equal to thickness of membrane to minimize system internal energy.
8.4.2 Fluctuations of the Peptide
To check stability of helix itself, we have calculated RMS fluctuations of C
α
atoms
(Fig. 8.5). In general, the highest fluctuations took place at the polar part of the
membrane (both ends) and in its central, hydrophobic core. The ends are in hydrophilic regions with many small movable water molecules, while the central part is
in region of membrane of lower density. The major fluctuations occur when peptide
linear helix bends or breaks (for example I 24 /LC simulation). Beside of this, the I 24
is generally of lowest stability and the L 24 peptide is in contrast the most stable.
The V 24 and (LA) 12 fluctuate more than L 24 , but less than I 24 . The P 24 fluctuates
Fig. 8.3 Time development
of L 24 tilt. The peptide is
tilted in LC and DMPC/
gel simulations. In DPPC/
gel was peptide bended (see
Table 8.1, angle between 1st
and 2nd half of peptide)
M. Melicherčík et al.
In the rest of simulations, the peptide is more or less tilled. In more than half of
simulations, the peptide doesn’t stay linear, but change its main chain conformation
(more to the tilting). The peptide bends like a bow (Barlow et al. called it curved
peptide [86]), or even breaks the helical structure (kinked as mentioned by the same
authors)—see Fig. 8.4. Amount of bending is different for each simulation, but we
were not able to find correlation between composition of system and amount of
bending or place of break. But peptide A 24 keeps best the linear conformation of ideal α-helix and doesn’t bend or break (see Table 8.1—the difference between angle
of 1
st
and 2
nd
peptide half, but helicity analysis is not shown). The peptide V 24 also
keeps linear conformation—exception is DMPC/gel, where the peptides are curved.
For providing some quantification of bending we calculated the tilt of whole helix
(as axis from first to last four C
α
atoms) and tilt of separated upper and lower halves
(C
α
from 13
th
–16
th
residue)—see Table 8.1. From tilt of the helix and its length we
can calculate effective length of peptide in a membrane. The effective length is
length of projection of helix to the membrane normal (Table 8.1). In ideal case it
should be equal to thickness of membrane to minimize system internal energy.
8.4.2 Fluctuations of the Peptide
To check stability of helix itself, we have calculated RMS fluctuations of C
α
atoms
(Fig. 8.5). In general, the highest fluctuations took place at the polar part of the
membrane (both ends) and in its central, hydrophobic core. The ends are in hydrophilic regions with many small movable water molecules, while the central part is
in region of membrane of lower density. The major fluctuations occur when peptide
linear helix bends or breaks (for example I 24 /LC simulation). Beside of this, the I 24
is generally of lowest stability and the L 24 peptide is in contrast the most stable.
The V 24 and (LA) 12 fluctuate more than L 24 , but less than I 24 . The P 24 fluctuates
Fig. 8.3 Time development
of L 24 tilt. The peptide is
tilted in LC and DMPC/
gel simulations. In DPPC/
gel was peptide bended (see
Table 8.1, angle between 1st
and 2nd half of peptide)