261
8 Molecular Dynamics Simulations of Lipid Bilayers with Incorporated Peptides
8.5.3 Area Per Lipid
Table 8.4 shows how incorporated peptide influences the area per membrane lipid. The area occupied by the peptide is not subtracted. The peptides with small
side chains (A 24 ) induced lowest area parameter. The highest area can be found in
simulations with L 24 or I 24 . Area per lipid is increased with increasing of the size
of amino acid side chains and for more fluctuating peptide (I 24 ). Because Val has
shorter side chains than Leu or Ile, the total area for V 24 is lower than that for I 24 , L 24
or LA 12 but higher in comparison with A 24 .
8.5.4 Transitions between Trans and Gauche Conformation
The amount of transitions (Fig. 8.9) between trans and gauche conformations (per
lipid and per ns) depends on the temperature. But also peptides affect the frequency
of these changes and amount of transitions. In a gel state all peptides destabilize the
surrounding lipids and increase the amount of transitions. There are some but small
differences between peptides. A 24 , L 24 and LA 12 provide the highest amount of transitions, while I 24 the smallest one. The effect of V 24 lies between these boundaries.
In LC state the situation is exactly reversed—the Leu-based peptides modify lipid
chains into some conformation, which lies between gel and LC state. The differences in LC state are very small.
In a gel state the changes agrees with previous findings. The side chains of
I 24 and V 24 shows the highest fluctuations from all amino acids. This movement
causes steric clashes with surrounding lipids (1
st
shell) and pushes lipids away from
Table 8.4 Area per lipid (peptide is not subtracted from total area)
System
Area/lipid (nm
2
)
System
Area/lipid (nm
2
)
DMPC/gel
A 24
0.4942
DPPC/gel
A 24
0.4718
I 24
0.4956
I 24
0.4730
L 24
0.4948
L 24
0.4731
(LA) 12
0.4953
(LA) 12
0.4719
P 24
0.4958
P 24
0.4739
V 24
0.4945
V 24
0.4751
Pure
0.4640
Pure
0.4694
DMPC/LC
A 24
0.5856
DPPC/LC
A 24
0.6207
I 24
0.5881
I 24
0.6233
L 24
0.5877
L 24
0.6231
(LA) 12
0.5872
(LA) 12
0.6219
P 24
0.5862
P 24
0.6206
V 24
0.5873
V 24
0.6230
Pure
0.5860
Pure
0.6213
8 Molecular Dynamics Simulations of Lipid Bilayers with Incorporated Peptides
8.5.3 Area Per Lipid
Table 8.4 shows how incorporated peptide influences the area per membrane lipid. The area occupied by the peptide is not subtracted. The peptides with small
side chains (A 24 ) induced lowest area parameter. The highest area can be found in
simulations with L 24 or I 24 . Area per lipid is increased with increasing of the size
of amino acid side chains and for more fluctuating peptide (I 24 ). Because Val has
shorter side chains than Leu or Ile, the total area for V 24 is lower than that for I 24 , L 24
or LA 12 but higher in comparison with A 24 .
8.5.4 Transitions between Trans and Gauche Conformation
The amount of transitions (Fig. 8.9) between trans and gauche conformations (per
lipid and per ns) depends on the temperature. But also peptides affect the frequency
of these changes and amount of transitions. In a gel state all peptides destabilize the
surrounding lipids and increase the amount of transitions. There are some but small
differences between peptides. A 24 , L 24 and LA 12 provide the highest amount of transitions, while I 24 the smallest one. The effect of V 24 lies between these boundaries.
In LC state the situation is exactly reversed—the Leu-based peptides modify lipid
chains into some conformation, which lies between gel and LC state. The differences in LC state are very small.
In a gel state the changes agrees with previous findings. The side chains of
I 24 and V 24 shows the highest fluctuations from all amino acids. This movement
causes steric clashes with surrounding lipids (1
st
shell) and pushes lipids away from
Table 8.4 Area per lipid (peptide is not subtracted from total area)
System
Area/lipid (nm
2
)
System
Area/lipid (nm
2
)
DMPC/gel
A 24
0.4942
DPPC/gel
A 24
0.4718
I 24
0.4956
I 24
0.4730
L 24
0.4948
L 24
0.4731
(LA) 12
0.4953
(LA) 12
0.4719
P 24
0.4958
P 24
0.4739
V 24
0.4945
V 24
0.4751
Pure
0.4640
Pure
0.4694
DMPC/LC
A 24
0.5856
DPPC/LC
A 24
0.6207
I 24
0.5881
I 24
0.6233
L 24
0.5877
L 24
0.6231
(LA) 12
0.5872
(LA) 12
0.6219
P 24
0.5862
P 24
0.6206
V 24
0.5873
V 24
0.6230
Pure
0.5860
Pure
0.6213