Mesoscopic models of lipid bilayers and bilayers with embedded ...
Mesoscopic models of lipid bilayers and bilayers with embedded ... Mesoscopic models of lipid bilayers and bilayers with embedded ...
52 Structural characterization of lipid bilayers where the tails are already very disordered, does not change the packing structure of the bilayer and has no effect on the pressure profile. As in the case of flexible lipids, a modification in the tail end of stiff lipids (figure 4.9) does not change the pressure profile, while a kink near the headgroup has a large effect. It is interesting to note that, while for flexible lipids the main effect is in the interfacial region, for stiff lipids the main effect is in the hydrophobic core. This difference can be easily explained. The considered bilayers formed by stiff, linear lipids, are largely interdigitated, and interdigitated bilayers are more compact and ordered than bilayers formed by flexible lipids. A kink near the lipids headgroup destabilizes the interfacial region, decreasing the extent of interdigitation and increasing the disorder in the terminal region of the hydrophobic chains. This leads to a pressure profile more similar to the one of fully flexible chains, with a minimum of the lateral pressure at the bilayer center. It is interesting to note that this effect is larger for the shorter chain. Our results are in general agreement with the mean field calculations of Cantor [94]. In [94] the effects of unsaturated bonds was studied by imposing a preference for a 90 o angle between three subsequent sites compared to 180 o used for a saturated chain. Also Cantor found that the largest changes in the lateral pressure distribution are obtained by modifications in the lipid topology close to the head group, and that the changes are more pronounced in short chains than in long ones. π(z) 0.1 0.0 −0.1 −0.2 −7 −5 −3 −1 1 3 5 7 Z (a) ht (L) 4 t ht (L) 3 t(K) t ht (K) t (L) 3 t π(z) 0.1 0.0 −0.1 −0.2 −7 −5 −3 −1 1 3 5 7 Z (b) ht (L) 8 t ht (L) 7 t(K) t ht (K) t (L) 7 t Figure 4.9: Pressure profile, π(z), as function of the distance z from the bilayer center (z=0). Stiff lipids and lipids with a kink near the headgroup or at the tail end are compared for (a) short lipids with 5 tail beads, and (b) long lipids with 9 tail beads.
4.4 Results and discussion 53 4.4.4 Double-tail lipids We have so far investigated the structure of bilayers formed by single-tail lipids. We have shown that lipid stiffness is an important characteristics in order to reproduce the bilayer structure and lipid chain order as displayed in phospholipid bilayers. Furthermore, we have shown that by tuning the interaction parameter between the lipid headgroups we obtain either an interdigitated or a non interdigitated bilayer. To further investigate the dependence of the bilayer structure on the lipid topology we can increase the complexity of the model by considering model lipids with two hydrophobic tails. We will focus the study to lipids with two symmetric tails, i.e. two tails consisting of the same number of hydrophilic beads. Here we consider the lipid denoted as h3(t5)2, i.e. with three head-beads and two tails of five hydrophobic beads each, as already described in the previous Chapters. The lipid tails are made stiffer by introducing a bond-bending potential between each consecutive bond, with bending constant Kθ = 6 and equilibrium angle θo = 180 o . An extra bond-bending potential is defined between the bonds connecting the two lipid tails to the headgroup, with Kθ = 3 and θo = 90 o . We considered a bilayer of 400 lipids, at the condition of zero surface tension, and in the fluid phase. In figure 4.10 we compare the density distribution in the bilayer of double-tail lipids (black lines) with the density distribution in the bilayer of stiff, single-tail lipids (gray lines), with five tail beads, and the headgroup repulsion parameter for which the bilayer is not interdigitated. ρ(z) 4.0 3.0 2.0 1.0 w tot t (1,.,n−1) h h tn 0.0 −6 −4 −2 0 2 4 6 z Figure 4.10: Density distribution in bilayers of single-tail lipids (gray lines) and double-tail lipids (black-lines). The black dashed lines are the density of each of the three head-beads of the double-tail lipid. A noticeable difference between the two bilayers is at the WH interface, where in the case of the double-tail lipids the density of water shows a small plateau, which is not present in the case of single-tail lipids. This plateau corresponds to a thicker re- w
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- Page 10 and 11: 4 Introduction between the beads, a
- Page 12 and 13: 6 Introduction whether the preferre
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- Page 20 and 21: 14 Simulation method for coarse-gra
- Page 22 and 23: 16 Simulation method for coarse-gra
- Page 24 and 25: 18 Simulation method for coarse-gra
- Page 27 and 28: III Surface tension in lipid bilaye
- Page 29 and 30: 3.2 Method of calculation of surfac
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- Page 33 and 34: 3.3 Constant surface tension ensemb
- Page 35 and 36: 3.3 Constant surface tension ensemb
- Page 37 and 38: 3.4 Surface tension in lipid bilaye
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- Page 43 and 44: IV Structural characterization of l
- Page 45 and 46: 4.2 Structural quantities 39 been r
- Page 47 and 48: 4.3 Computational details 41 lipid
- Page 49 and 50: 4.4 Results and discussion 43 ρ(z)
- Page 51 and 52: 4.4 Results and discussion 45 one l
- Page 53 and 54: 4.4 Results and discussion 47 WH HT
- Page 55 and 56: 4.4 Results and discussion 49 Shill
- Page 57: 4.4 Results and discussion 51 chain
- Page 61: 4.4 Results and discussion 55 headg
- Page 64 and 65: 58 Phase behavior of coarse-grained
- Page 66 and 67: 60 Phase behavior of coarse-grained
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- Page 87 and 88: 6.2 Computational details 81 For re
- Page 89 and 90: 6.3 Results and Discussion 83 withi
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- Page 93 and 94: 6.3 Results and Discussion 87 ρ(z)
- Page 95 and 96: 6.3 Results and Discussion 89 S m 0
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4.4 Results <strong>and</strong> discussion 53<br />
4.4.4 Double-tail <strong>lipid</strong>s<br />
We have so far investigated the structure <strong>of</strong> <strong>bilayers</strong> formed by single-tail <strong>lipid</strong>s. We<br />
have shown that <strong>lipid</strong> stiffness is an important characteristics in order to reproduce<br />
the bilayer structure <strong>and</strong> <strong>lipid</strong> chain order as displayed in phospho<strong>lipid</strong> <strong>bilayers</strong>. Furthermore,<br />
we have shown that by tuning the interaction parameter between the <strong>lipid</strong><br />
headgroups we obtain either an interdigitated or a non interdigitated bilayer. To<br />
further investigate the dependence <strong>of</strong> the bilayer structure on the <strong>lipid</strong> topology we<br />
can increase the complexity <strong>of</strong> the model by considering model <strong>lipid</strong>s <strong>with</strong> two hydrophobic<br />
tails. We will focus the study to <strong>lipid</strong>s <strong>with</strong> two symmetric tails, i.e. two<br />
tails consisting <strong>of</strong> the same number <strong>of</strong> hydrophilic beads.<br />
Here we consider the <strong>lipid</strong> denoted as h3(t5)2, i.e. <strong>with</strong> three head-beads <strong>and</strong><br />
two tails <strong>of</strong> five hydrophobic beads each, as already described in the previous Chapters.<br />
The <strong>lipid</strong> tails are made stiffer by introducing a bond-bending potential between<br />
each consecutive bond, <strong>with</strong> bending constant Kθ = 6 <strong>and</strong> equilibrium angle<br />
θo = 180 o . An extra bond-bending potential is defined between the bonds connecting<br />
the two <strong>lipid</strong> tails to the headgroup, <strong>with</strong> Kθ = 3 <strong>and</strong> θo = 90 o . We considered a<br />
bilayer <strong>of</strong> 400 <strong>lipid</strong>s, at the condition <strong>of</strong> zero surface tension, <strong>and</strong> in the fluid phase.<br />
In figure 4.10 we compare the density distribution in the bilayer <strong>of</strong> double-tail<br />
<strong>lipid</strong>s (black lines) <strong>with</strong> the density distribution in the bilayer <strong>of</strong> stiff, single-tail <strong>lipid</strong>s<br />
(gray lines), <strong>with</strong> five tail beads, <strong>and</strong> the headgroup repulsion parameter for which<br />
the bilayer is not interdigitated.<br />
ρ(z)<br />
4.0<br />
3.0<br />
2.0<br />
1.0<br />
w<br />
tot<br />
t (1,.,n−1)<br />
h h<br />
tn 0.0<br />
−6 −4 −2 0 2 4 6<br />
z<br />
Figure 4.10: Density distribution in <strong>bilayers</strong> <strong>of</strong> single-tail <strong>lipid</strong>s (gray lines) <strong>and</strong> double-tail<br />
<strong>lipid</strong>s (black-lines). The black dashed lines are the density <strong>of</strong> each <strong>of</strong> the three head-beads <strong>of</strong><br />
the double-tail <strong>lipid</strong>.<br />
A noticeable difference between the two <strong>bilayers</strong> is at the WH interface, where in<br />
the case <strong>of</strong> the double-tail <strong>lipid</strong>s the density <strong>of</strong> water shows a small plateau, which is<br />
not present in the case <strong>of</strong> single-tail <strong>lipid</strong>s. This plateau corresponds to a thicker re-<br />
w
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