259
8 Molecular Dynamics Simulations of Lipid Bilayers with Incorporated Peptides
ature also affected the order parameters. With increasing of the temperature the
disorder increases and consequently the order parameters decrease. The decrease
of order parameters for membranes in gel state has been confirmed experimentally
[16, 21, 89]. This effect is probably correlated with decreasing of membrane thickness (see below).
In simulations with DPPC in LC state, the order parameters increase. The only
exception is longer P 24 . In the DMPC membrane the 1
st
lipid shell is less ordered
than in 2
nd
shell (with exception of P 24 ). The same holds also for the membrane in
a gel state. In experiments with WALP peptides De Planque et al. found that the
ordering of membrane can increase and decrease depending mainly on the peptide
length [89] (using the same type of the membrane). The order parameters for L 24
or P 24 peptides are comparable with that reported by Tieleman et al. [90] and those
obtained in experiments [83, 85, 91]. Unfortunately there is no sufficient information for comparison of the behavior of other peptides.
There is also observable effect of different side chains of peptides. I 24 shows biggest stabilizing effect (higher order parameters) and V 24 also orders surroundings
lipids, but less than I 24 . The Leu based peptides (L 24 together with LA 12 and P 24 )
cause high disordering. But A 24 induced very small disordering effect. It is probably
due to small volume of A 24 side chains, which are less hydrophobic in comparison
with other simulated peptides.
8.5.2 Fraction of Dihedral Angles in Trans Conformation
Another parameter, which can be used for characterizing the phase state of the lipids, is amount of dihedral angles in trans conformation (Table 8.3). There is correlation between this parameter and the temperature—the higher temperature, the
more energy have atoms and are able to change conformation from nearly all-trans
state. But there is also influence of peptide on this transition. In a pure gel state the
membrane has around 90 % of dihedral angles in the trans conformation, but in a
LC state it is 70–75 % [80]. We detected this fraction in 2
nd
lipid shell to be approx.
85 % for gel state and between 72 and 78 % for LC membrane state. In 1
st
shell in
a gel phase this fraction decrease is even lower by 2–4°. The lowest decrease of dihedral angles has been caused by I 24 and V 24 peptides, while A 24 and all Leu-based
(L 24 , LA 12 and P 24 ) produced drop up to 6°. As for LC state, the highest increase
in dihedral angles in both shells has been observed for I 24 . The angle increase has
been produced also by V 24 , LA 12 , L 24 . Slight angle decrease is possible for A 24 or
P 24 peptides. But these changes were lower than 3° for all analyzed peptides. All
changes noticed above suggest, that the peptides modify surrounding lipids to produce some type environment. The properties of this environment (order parameters,
trans fraction, etc.) correspond to the structural state between gel and LC phase, but
are shifted nearer to LC.
8 Molecular Dynamics Simulations of Lipid Bilayers with Incorporated Peptides
ature also affected the order parameters. With increasing of the temperature the
disorder increases and consequently the order parameters decrease. The decrease
of order parameters for membranes in gel state has been confirmed experimentally
[16, 21, 89]. This effect is probably correlated with decreasing of membrane thickness (see below).
In simulations with DPPC in LC state, the order parameters increase. The only
exception is longer P 24 . In the DMPC membrane the 1
st
lipid shell is less ordered
than in 2
nd
shell (with exception of P 24 ). The same holds also for the membrane in
a gel state. In experiments with WALP peptides De Planque et al. found that the
ordering of membrane can increase and decrease depending mainly on the peptide
length [89] (using the same type of the membrane). The order parameters for L 24
or P 24 peptides are comparable with that reported by Tieleman et al. [90] and those
obtained in experiments [83, 85, 91]. Unfortunately there is no sufficient information for comparison of the behavior of other peptides.
There is also observable effect of different side chains of peptides. I 24 shows biggest stabilizing effect (higher order parameters) and V 24 also orders surroundings
lipids, but less than I 24 . The Leu based peptides (L 24 together with LA 12 and P 24 )
cause high disordering. But A 24 induced very small disordering effect. It is probably
due to small volume of A 24 side chains, which are less hydrophobic in comparison
with other simulated peptides.
8.5.2 Fraction of Dihedral Angles in Trans Conformation
Another parameter, which can be used for characterizing the phase state of the lipids, is amount of dihedral angles in trans conformation (Table 8.3). There is correlation between this parameter and the temperature—the higher temperature, the
more energy have atoms and are able to change conformation from nearly all-trans
state. But there is also influence of peptide on this transition. In a pure gel state the
membrane has around 90 % of dihedral angles in the trans conformation, but in a
LC state it is 70–75 % [80]. We detected this fraction in 2
nd
lipid shell to be approx.
85 % for gel state and between 72 and 78 % for LC membrane state. In 1
st
shell in
a gel phase this fraction decrease is even lower by 2–4°. The lowest decrease of dihedral angles has been caused by I 24 and V 24 peptides, while A 24 and all Leu-based
(L 24 , LA 12 and P 24 ) produced drop up to 6°. As for LC state, the highest increase
in dihedral angles in both shells has been observed for I 24 . The angle increase has
been produced also by V 24 , LA 12 , L 24 . Slight angle decrease is possible for A 24 or
P 24 peptides. But these changes were lower than 3° for all analyzed peptides. All
changes noticed above suggest, that the peptides modify surrounding lipids to produce some type environment. The properties of this environment (order parameters,
trans fraction, etc.) correspond to the structural state between gel and LC phase, but
are shifted nearer to LC.