Mesoscopic models of lipid bilayers and bilayers with embedded ...

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18 Simulation method for coarse-grained lipids takes between 10000 and 20000 time steps for a bilayer to self-assembly, and the bilayer, once formed, is stable and symmetric, i.e. it contains approximately the same number of lipids in each monolayer. A bilayer is the stable structure up to 210 lipids. By further increase in the concentration, the bilayer starts to branch and deforms in a shapeless structure tough still interconnected. For 300 lipids (cs = 0.14) a second, separate, bilayer starts to form, parallel to the first one. In figure 2.4 we show some of the described structures as snapshots taken from the simulations. Our results are in remarkably good agreement with the results by Goetz and Lipowsky [21]. These authors studied the self-assembly of linear CG Lennard-Jones amphiphilic surfactants — with the same topology as our DPD single-tail lipids — by molecular dynamics and Monte Carlo simulations. We find the same self-assembled structures that these authors find, and the same type of structure is formed in the same range of concentrations in the two studies. A small difference between our study and the one in ref. [21] is that in our simulations the transition from one type of structure to the other (like, for example, from spherical micelle to cylindrical micelle) occurs at slightly lower lipid/water ratios than observed by Goetz and Lipowsky. This is likely due to the fact that the amphiphiles in [21] have four beads in the tail and the ones we use have five, while both models have the same headgroup size (one bead). As a consequence, closed spherical structures (like micelles and cylindrical micelles) that contain the same number of molecules become unstable at lower concentrations for amphiphiles with a longer tail. The hydrophilic surface is the same in the two cases, but the hydrophobic volume is larger for amphiphiles with a longer tail. To verify this hypothesis we studied the self-assembly of lipids with four tailbeads (ht4) in the same range of concentrations used for the ones with five tail-beads. We indeed found that, for these shorter chains, the transitions between the different supramolecular aggregates occur at higher concentrations compared to the ones of longer lipids. These concentrations are still slightly lower than the corresponding ones reported in [21]. It is also interesting to compare out results with the recent simulation of Marrink et al. [6] whose work is the first simulation of aggregation of phospholipids into bilayers with atomic details of the structure and interactions. These authors find that a bilayer with an hydrophilic pore, like the one observed in our and Goetz and Lipowsky’s CG simulations, is the intermediate configuration in the formation of the bilayer. The breakdown of the pore is the rate limiting step in the overall process. Although in our simulations the bilayer with a pore is stable and it is observed at concentrations too low for a full bilayer to be formed, the fact that this structure has been produced using such different models and simulation techniques suggests that it could indeed be a fundamental step in the kinetics of bilayer self-assembly.
2.3 Self-assembly 19 (a) (b) (c) (d) (e) Figure 2.4: Snapshots of self-assembled structure of ht5 lipids. Following increasing concentration: large spherical micelle (a), cylindrical micelle (b), flat cylindrical micelle (c), bilayer with a pore (d), and bilayer (side and top view) (e,f). The black beads represent the headgroups, the gray beads the tails, and the dots the water particles.
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 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 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
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68 Phase behavior of coarse-grained
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VI Interaction of small molecules w
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6.2 Computational details 81 For re
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6.3 Results and Discussion 83 withi
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6.3 Results and Discussion 85 ρ(z)
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6.3 Results and Discussion 87 ρ(z)
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6.3 Results and Discussion 89 S m 0
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6.3 Results and Discussion 91 π(z)
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6.3 Results and Discussion 93 the l
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96 Mesoscopic model for lipid bilay
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98 Mesoscopic model for lipid bilay
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100 Mesoscopic model for lipid bila
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References [1] Tanford, C. Science
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7.4 Conclusion 121 [68] Ono, S.; Ko
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7.4 Conclusion 123 [139] Lee, A. Bi
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Summary Biological membranes, as th
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agreement we find gives us confiden
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Samenvatting Biologische membranen,
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de lage temperatuur gel fase of Lβ
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ied dat het dichtst bij het hydrofo
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This thesis is based on the followi
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