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 ...
46 Structural characterization of lipid bilayers A L 1.2 1.1 1.0 0.9 0.8 0.7 0.6 4 5 6 7 8 9 10 chain length (n) (a) flexible stiff a hh =15 stiff a hh =35 D c 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 4 5 6 7 8 9 10 chain length (n) (b) flexible stiff a hh =15 stiff a hh =35 Figure 4.4: Effect of the lipid topology (stiffness, chain length, and headgroup interaction) on the bilayer structural properties: (a) average area per lipid, AL, and (b) bilayer hydrophobic thickness, Dc. The data refer to flexible chains (full circles), stiff chains in a non interdigitated bilayer (full triangles), and stiff chains in an interdigitated bilayer (open squares). The lines are only a guide to the eye. For the thickness the error bars are smaller than the symbols size. 3, i.e. π(z) = [PL(z) − PT (z)], where PL(z) and PN(z) are the lateral and normal components of the pressure tensor at position z. To better describe and understand the distribution of lateral pressure, we find it convenient to divide the system in four regions which define three main interfaces, as illustrated in figure 4.5. A similar approach has been proposed earlier by Marrink and Berendsen [93] to describe permeation of water through a lipid membrane studied with MD. The three main interfacial regions are: the water/headgroups interface (WH interface), the headgroups/tails interface (HT interface), and the bilayer center (midplane MP). We investigate the effect of several lipid characteristics on the distribution of the pressure profile. Namely: • the effect of chain stiffness, by comparing flexible and stiff lipids; • the effect of chain packing, by comparing stiff interdigitated and not interdigitated bilayers; • the effect of changes in the head group, by comparing the two repulsion parameters used in the stiff lipids; • the effect of tail length; • the effect of changes in the lipid structure at specific positions along the chain. We start by comparing the model lipids considered in the previous section. The lateral pressure profiles for the three different bilayers are plotted in figure 4.6. The
4.4 Results and discussion 47 WH HT MP Water Headgroups Tails Tails Headgroups Water £££ £££ £££ £££ £££ ££££ ££££ ££££ ££££ £££ ¢£¢£¢£¢ ¤£¤£¤£¤ ¥£¥£¥£¥£¥ ¦£¦£¦£¦ §£§£§£§£§ ¨£¨£¨£¨ ©£©£©£© £££ £££ £££ £££ £££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ ¢£¢£¢£¢ ££££ ££££ ££££ ££££ ££££ ££££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ ££££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ ££££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ £££ Figure 4.5: Schematic representation of the four regions and three interfaces used in the text to characterize the lateral pressure distribution in a lipid bilayer. The three interfaces are the water/headgroups interface (WH), the headgroups/tails interface (HT) and the interface between the two opposing monolayers at the bilayer midplane (MP). The arrows represent the direction, and indicative magnitude, of the lateral pressure. £££ £££ £££ £££ ££££ ££££ contributions to the lateral pressure from different potentials (non-bonded, spring and angles) are also shown. For all lipid types a positive maximum in the pressure profile characterizes the region at the WH interface. The positive lateral pressure indicates that the net force in this region tends to expand the interface, due to steric effects and hydration of the headgroups by the water. The height of this maximum is larger for stiff lipids compared to flexible ones, and between the two stiff types the maximum is higher in the case of the interdigitated bilayer, as a consequence of the higher value of the headgroup repulsion parameter. At the HT interface there is a strong inward (negative) pressure as the system attempts to limit the contact between water and hydrophobic tails. The depth of this minimum shows the same trend as the height of the maximum at the WH interface; i.e. it is deeper for stiff lipids, and slightly deeper in the interdigitated bilayer compared to the non interdigitated one, but broader in the latter case. It is interesting to observe that the contributions to both the described peaks arise mainly from the non-bonded and spring interactions. At the sides of the box the tension goes to zero indicating that water in these regions has the characteristics of a bulk fluid, and that the bilayer is completely hydrated. The presence of the maximum at the WH interface and the minimum at the HT interface are characteristics of the pressure profiles also observed in the atomistic MD simulations of Lindahl and Edholm [77] (see also figure 4.11(b)) and Gullingsrud and Schulten [81]. Such characteristics are also observed in the CG Lennard-Jones models of Groot and Rabone [24] and DPD models of Goetz and Lipowsky [21] and
- Page 1: Mesoscopic models of lipid bilayers
- Page 4 and 5: Promotiecommissie: Promotor: • pr
- Page 6 and 7: ii CONTENTS 5.3 Double-tail lipid b
- Page 8 and 9: 2 Introduction 1.1 The cell membran
- Page 10 and 11: 4 Introduction between the beads, a
- Page 12 and 13: 6 Introduction whether the preferre
- Page 14 and 15: 8 Simulation method for coarse-grai
- Page 16 and 17: 10 Simulation method for coarse-gra
- Page 18 and 19: 12 Simulation method for coarse-gra
- 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
- Page 31 and 32: 3.2 Method of calculation of surfac
- 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
- Page 39 and 40: 3.4 Surface tension in lipid bilaye
- Page 41 and 42: 3.4 Surface tension in lipid bilaye
- 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: 4.4 Results and discussion 45 one l
- Page 55 and 56: 4.4 Results and discussion 49 Shill
- Page 57 and 58: 4.4 Results and discussion 51 chain
- Page 59 and 60: 4.4 Results and discussion 53 4.4.4
- 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
- Page 68 and 69: 62 Phase behavior of coarse-grained
- Page 70 and 71: 64 Phase behavior of coarse-grained
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- Page 80 and 81: 74 Phase behavior of coarse-grained
- Page 82 and 83: 76 Phase behavior of coarse-grained
- Page 85 and 86: VI Interaction of small molecules w
- Page 87 and 88: 6.2 Computational details 81 For re
- Page 89 and 90: 6.3 Results and Discussion 83 withi
- Page 91 and 92: 6.3 Results and Discussion 85 ρ(z)
- 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
- Page 97 and 98: 6.3 Results and Discussion 91 π(z)
- Page 99: 6.3 Results and Discussion 93 the l
4.4 Results <strong>and</strong> discussion 47<br />
WH<br />
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MP<br />
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Figure 4.5: Schematic representation <strong>of</strong> the four regions <strong>and</strong> three interfaces used in the text<br />
to characterize the lateral pressure distribution in a <strong>lipid</strong> bilayer. The three interfaces are the<br />
water/headgroups interface (WH), the headgroups/tails interface (HT) <strong>and</strong> the interface between<br />
the two opposing monolayers at the bilayer midplane (MP). The arrows represent the<br />
direction, <strong>and</strong> indicative magnitude, <strong>of</strong> the lateral pressure.<br />
£££ £££ £££ £££<br />
££££ ££££<br />
contributions to the lateral pressure from different potentials (non-bonded, spring<br />
<strong>and</strong> angles) are also shown. For all <strong>lipid</strong> types a positive maximum in the pressure<br />
pr<strong>of</strong>ile characterizes the region at the WH interface. The positive lateral pressure indicates<br />
that the net force in this region tends to exp<strong>and</strong> the interface, due to steric<br />
effects <strong>and</strong> hydration <strong>of</strong> the headgroups by the water. The height <strong>of</strong> this maximum<br />
is larger for stiff <strong>lipid</strong>s compared to flexible ones, <strong>and</strong> between the two stiff types<br />
the maximum is higher in the case <strong>of</strong> the interdigitated bilayer, as a consequence <strong>of</strong><br />
the higher value <strong>of</strong> the headgroup repulsion parameter. At the HT interface there<br />
is a strong inward (negative) pressure as the system attempts to limit the contact<br />
between water <strong>and</strong> hydrophobic tails. The depth <strong>of</strong> this minimum shows the same<br />
trend as the height <strong>of</strong> the maximum at the WH interface; i.e. it is deeper for stiff <strong>lipid</strong>s,<br />
<strong>and</strong> slightly deeper in the interdigitated bilayer compared to the non interdigitated<br />
one, but broader in the latter case. It is interesting to observe that the contributions<br />
to both the described peaks arise mainly from the non-bonded <strong>and</strong> spring interactions.<br />
At the sides <strong>of</strong> the box the tension goes to zero indicating that water in these<br />
regions has the characteristics <strong>of</strong> a bulk fluid, <strong>and</strong> that the bilayer is completely hydrated.<br />
The presence <strong>of</strong> the maximum at the WH interface <strong>and</strong> the minimum at the HT<br />
interface are characteristics <strong>of</strong> the pressure pr<strong>of</strong>iles also observed in the atomistic<br />
MD simulations <strong>of</strong> Lindahl <strong>and</strong> Edholm [77] (see also figure 4.11(b)) <strong>and</strong> Gullingsrud<br />
<strong>and</strong> Schulten [81]. Such characteristics are also observed in the CG Lennard-Jones<br />
<strong>models</strong> <strong>of</strong> Groot <strong>and</strong> Rabone [24] <strong>and</strong> DPD <strong>models</strong> <strong>of</strong> Goetz <strong>and</strong> Lipowsky [21] <strong>and</strong>
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