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 ...
74 Phase behavior of coarse-grained lipid bilayers No interdigitation was found for the chosen value of the repulsion parameter between the headgroups, a hh=35. Also, an increase of a hh up to 55 does not lead to any interdigitation (data not shown). This result is consistent with the experimentally observed structure of symmetric PC’s bilayers, for which no spontaneous interdigitation is found. The transition temperature was derived from the inflection points A L 1.8 1.6 1.4 1.2 1.0 0.1 0.3 0.5 0.7 T* 0.9 1.1 (a) S tail 1.0 0.8 0.6 0.4 0.2 D c 6.0 5.5 5.0 4.5 4.0 3.5 0.0 0.1 0.3 0.5 0.7 T* 0.9 1.1 (c) 3.0 0.1 0.3 0.5 0.7 T* 0.9 1.1 Figure 5.15: Area per lipid AL (a), bilayer thickness Dc (b), and tail order parameter, Stail (c), as function of reduced temperature T ∗ for lipid type h3(t5)2. The error bars are smaller than the symbol size. of the shown curves. The system undergoes a main transition at a reduced temperature T∗ m=0.425. Above the reduced temperature T∗ m, the lipid chains are in the melted state (hence a low value of the bilayer thickness and of the tail order parameter) and the system is in the Lα fluid phase. The snapshot in figure 5.16(c) shows a typical configuration of the system in the fluid phase. At very low temperatures the system is in the Lβ ′ gel phase, which is characterized by having ordered chains, hence a high value of the bilayer thickness and of the tail order parameter. While single-tail lipids are not tilted in the gel phase, for the (b)
5.3 Double-tail lipid bilayers 75 (a) L β ′ (b) P β ′ (c) Lα Figure 5.16: Snapshots of typical configurations of the h3(t5)2 bilayer simulated at reduced temperatures: (a) T ∗ < 0.35, corresponding to the gel phase, or Lβ ′; (b) 0.35 ≤ T∗ < 0.425 corresponding to the ripple-like ’striated’ phase, or Pβ ′; and (c) T∗ > 0.425 corresponding to the fluid phase, or Lα. The lipid headgroups are represented by black lines and the lipid tails by gray lines, with the terminal tail beads darker gray. The water is not shown. double-tail lipid we observe that the lipid chains are tilted with respect to the bilayer normal. We find a tilt angle of 25 o , which is slightly lower than the value of ≈ 32 o measured experimentally for DMPC lipid bilayers [113]. A typical configuration at this temperature can be see in the snapshot in figure 5.16(a). Between the Lα and the Lβ ′ phases, when the temperature is increased above T∗ =0.35, we observed a third phase. This phase, which disappears again as the temperature reaches the main-transition temperature, is characterized by having striated regions made of lipids in the gel-state intercalated by regions made of lipids in the fluid-state. This modulated structure can be seen in the snapshot in figure 5.16(b). This phase resembles the Pβ ′, or ripple-phase. The ripple-phase occurs in phospholipid bilayers at the so-called pre-transition temperature, and is characterized by a rippling of the bilayer, with a wave length of the order of 150 ˚A [114]. As we have discussed in Chapters 2 and 3, the double-tail lipid h3(t5)2 can be mapped onto DMPC, if a coarse-grained representation is used in which one DPD bead has a volume of 90 ˚A 3 . This correspondence between the lipid h3(t5)2 and DMPC allows us to quantitatively compare the values of structural quantities found in our simulations with experimentally measured values. Besides the unit of length, which is derived, as discussed in Chapter 2, from the volume of one DPD bead, and is equal to Rc = 6.4633˚A, we need to map the reduced temperature onto real temper-
- 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
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- 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 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
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- 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
- Page 102 and 103: 96 Mesoscopic model for lipid bilay
- Page 104 and 105: 98 Mesoscopic model for lipid bilay
- Page 106 and 107: 100 Mesoscopic model for lipid bila
- Page 108 and 109: 102 Mesoscopic model for lipid bila
- Page 110 and 111: 104 Mesoscopic model for lipid bila
- Page 112 and 113: 106 Mesoscopic model for lipid bila
- Page 114 and 115: 108 Mesoscopic model for lipid bila
- Page 116 and 117: 110 Mesoscopic model for lipid bila
- Page 118 and 119: 112 Mesoscopic model for lipid bila
- Page 120 and 121: 114 Mesoscopic model for lipid bila
- Page 122 and 123: 116 Mesoscopic model for lipid bila
- Page 125 and 126: References [1] Tanford, C. Science
- Page 127 and 128: 7.4 Conclusion 121 [68] Ono, S.; Ko
- Page 129 and 130: 7.4 Conclusion 123 [139] Lee, A. Bi
5.3 Double-tail <strong>lipid</strong> <strong>bilayers</strong> 75<br />
(a) L β ′ (b) P β ′<br />
(c) Lα<br />
Figure 5.16: Snapshots <strong>of</strong> typical configurations <strong>of</strong> the h3(t5)2 bilayer simulated at reduced<br />
temperatures: (a) T ∗ < 0.35, corresponding to the gel phase, or Lβ ′; (b) 0.35 ≤ T∗ < 0.425<br />
corresponding to the ripple-like ’striated’ phase, or Pβ ′; <strong>and</strong> (c) T∗ > 0.425 corresponding to<br />
the fluid phase, or Lα. The <strong>lipid</strong> headgroups are represented by black lines <strong>and</strong> the <strong>lipid</strong> tails<br />
by gray lines, <strong>with</strong> the terminal tail beads darker gray. The water is not shown.<br />
double-tail <strong>lipid</strong> we observe that the <strong>lipid</strong> chains are tilted <strong>with</strong> respect to the bilayer<br />
normal. We find a tilt angle <strong>of</strong> 25 o , which is slightly lower than the value <strong>of</strong> ≈ 32 o<br />
measured experimentally for DMPC <strong>lipid</strong> <strong>bilayers</strong> [113]. A typical configuration at<br />
this temperature can be see in the snapshot in figure 5.16(a).<br />
Between the Lα <strong>and</strong> the Lβ ′ phases, when the temperature is increased above<br />
T∗ =0.35, we observed a third phase. This phase, which disappears again as the temperature<br />
reaches the main-transition temperature, is characterized by having striated<br />
regions made <strong>of</strong> <strong>lipid</strong>s in the gel-state intercalated by regions made <strong>of</strong> <strong>lipid</strong>s<br />
in the fluid-state. This modulated structure can be seen in the snapshot in figure<br />
5.16(b). This phase resembles the Pβ ′, or ripple-phase. The ripple-phase occurs in<br />
phospho<strong>lipid</strong> <strong>bilayers</strong> at the so-called pre-transition temperature, <strong>and</strong> is characterized<br />
by a rippling <strong>of</strong> the bilayer, <strong>with</strong> a wave length <strong>of</strong> the order <strong>of</strong> 150 ˚A [114].<br />
As we have discussed in Chapters 2 <strong>and</strong> 3, the double-tail <strong>lipid</strong> h3(t5)2 can be<br />
mapped onto DMPC, if a coarse-grained representation is used in which one DPD<br />
bead has a volume <strong>of</strong> 90 ˚A 3 . This correspondence between the <strong>lipid</strong> h3(t5)2 <strong>and</strong><br />
DMPC allows us to quantitatively compare the values <strong>of</strong> structural quantities found<br />
in our simulations <strong>with</strong> experimentally measured values. Besides the unit <strong>of</strong> length,<br />
which is derived, as discussed in Chapter 2, from the volume <strong>of</strong> one DPD bead, <strong>and</strong><br />
is equal to Rc = 6.4633˚A, we need to map the reduced temperature onto real temper-
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