256
M. Melicherčík et al.
Their results agree with our findings that stability decreases in following order:
Ile > Val > Leu > Ala.
8.4.3 Other Helix Parameters
We also calculated (using program g_helix from Gromacs package) other helix parameters—rise per residue, twist per residue, helix radius, Φ and Ψ angles, etc. The
values computed from simulations are presented in Table 8.2. But the algorithms
used by g_helix are influenced by changes of dihedral angles and by linearity of analyzed helix. For example on Fig. 8.7 there are two nearly identical structures from
I 24 /DMPC/LC simulation (from 2 ps distant snapshots). Each structure has only 1
amino acid (different in each) outside the favored region for α-helix (Fig. 8.8), but
for frame 1 the twist per residue is 100.95° and for frame 2 it is 83.23°. The values
of radius of helix are 0.2436 nm (frame 1) and 0.2635 nm (frame 2)—graph not
shown. Also the rise per residue and consequently also the helix length are affected
(which is computed by multiplying the previous one by number of amino acids).
Moreover, it seems that there is correlation between decreasing of the twist and in
increasing of the rise per residue.
Problem with calculating of radius of helix is in using single helix axis. Axis is
fitted to z-axis and using Pythagorean theorem the radius is calculated from x and y
positions of C
α
atoms. As the helix is bended or kinked, some atoms are moved to
one side and other to opposite one. In both cases it causes increasing of helix radius.
But in part, which is near to axis, the radius is (relatively) lowered.
There are virtually no changes in Φ and Ψ angles and during the simulation most
of the time all angles are in most favorable region for α-helices. Also the averages
angle values do not deviate from ideal values for the helix (Table 8.2).
8.5 Changes in the Membrane
The membrane affects the conformation of the peptide due to the difference in the
length of their hydrophobic cores and vice versa the peptide affect the membrane
structural state. In the case of positive difference, lipids could extend around helix
to compensate (at least) part of the difference [8]. We can analyze deuterium order
parameters, fraction of dihedral angles in trans conformation, frequency of changes
between trans and gauche dihedral angles conformation and thickness of membrane
surrounding peptide. All of these parameters are calculated for two cylindrical
shells of lipids. First one is up to 0.8 nm and second one lies between 0.8 till 1.6 nm
from peptide surface, respectively. Tieleman reported that the effect of peptide on
the lipids is negligible at distances surpassing 1.6 nm from the peptide surface [88].
Due to this property we divided lipids into following three groups—1
st
shell, 2
nd
shell and the rest of the lipids. We calculated parameters only for first two groups.
M. Melicherčík et al.
Their results agree with our findings that stability decreases in following order:
Ile > Val > Leu > Ala.
8.4.3 Other Helix Parameters
We also calculated (using program g_helix from Gromacs package) other helix parameters—rise per residue, twist per residue, helix radius, Φ and Ψ angles, etc. The
values computed from simulations are presented in Table 8.2. But the algorithms
used by g_helix are influenced by changes of dihedral angles and by linearity of analyzed helix. For example on Fig. 8.7 there are two nearly identical structures from
I 24 /DMPC/LC simulation (from 2 ps distant snapshots). Each structure has only 1
amino acid (different in each) outside the favored region for α-helix (Fig. 8.8), but
for frame 1 the twist per residue is 100.95° and for frame 2 it is 83.23°. The values
of radius of helix are 0.2436 nm (frame 1) and 0.2635 nm (frame 2)—graph not
shown. Also the rise per residue and consequently also the helix length are affected
(which is computed by multiplying the previous one by number of amino acids).
Moreover, it seems that there is correlation between decreasing of the twist and in
increasing of the rise per residue.
Problem with calculating of radius of helix is in using single helix axis. Axis is
fitted to z-axis and using Pythagorean theorem the radius is calculated from x and y
positions of C
α
atoms. As the helix is bended or kinked, some atoms are moved to
one side and other to opposite one. In both cases it causes increasing of helix radius.
But in part, which is near to axis, the radius is (relatively) lowered.
There are virtually no changes in Φ and Ψ angles and during the simulation most
of the time all angles are in most favorable region for α-helices. Also the averages
angle values do not deviate from ideal values for the helix (Table 8.2).
8.5 Changes in the Membrane
The membrane affects the conformation of the peptide due to the difference in the
length of their hydrophobic cores and vice versa the peptide affect the membrane
structural state. In the case of positive difference, lipids could extend around helix
to compensate (at least) part of the difference [8]. We can analyze deuterium order
parameters, fraction of dihedral angles in trans conformation, frequency of changes
between trans and gauche dihedral angles conformation and thickness of membrane
surrounding peptide. All of these parameters are calculated for two cylindrical
shells of lipids. First one is up to 0.8 nm and second one lies between 0.8 till 1.6 nm
from peptide surface, respectively. Tieleman reported that the effect of peptide on
the lipids is negligible at distances surpassing 1.6 nm from the peptide surface [88].
Due to this property we divided lipids into following three groups—1
st
shell, 2
nd
shell and the rest of the lipids. We calculated parameters only for first two groups.