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

More documents

Recommendations

Info

$Learning LATEX by Doing$

54 Structural characterization of lipid bilayers gion where the lipid headgroup are hydrated by the water, and is due to the fact that double-tail lipids have a larger headgroup (three beads) respect to the one of singletail lipids (one bead). Also, at the HT interface the total density shows more marked minima in the case of double-tail lipids, and a small difference between the two bilayers is observed in the bilayer hydrophobic core where the total density of the tail beads is slightly larger for the single tail lipids. A remarkable fact is that, despite the π(z) 0.1 0.0 −0.1 −0.2 −0.3 −6 −4 −2 0 2 4 6 z (a) (b) Figure 4.11: Figure (a) shows the lateral pressure profile distribution in a bilayer of singletail lipids (gray line) and a bilayer of double-tail lipids (black) line. In figure (b) the pressure profile from atomistic MD simulations of a DPPC bilayer is shown. Figure (b) is reproduced from reference [77] with kind permission of the authors. differences in the density profiles of the two bilayers being not too large, the distribution of lateral pressure in the double-tail lipid bilayer is very different compared with the single-tail lipid bilayer, as shown in figure 4.11(a). In the case of double-tail lipids, the peaks at the WH and HT interface become more pronounced, indicating that the lipids are more densely packed. Also, because of the larger headgroup size of the double-tail lipids, the peak at the WH interface broadens. The central peak (at the bilayer midplane) decreases in size, due to the lower density in the bilayer center. Most noticeably, we observe the appearance of two secondary peaks at the edge of the hydrophobic core, which are not present in the case of the single-tail lipids. These peaks correspond to the region of maximum density for the tail beads (excluded the terminal one). This shape of the pressure profile is remarkably similar to the one calculated by Lindahl and Edholm in atomistic MD simulations of a dipalmitoylphosphatidylcholine bilayer [77], and shown in figure 4.11(b). In Chapter 2 we have shown that, if a DPD bead is chosen to represent three methyl groups, the lipid h3(t5)2 can be mapped onto the DMPC phospholipid. The structure of DPPC is very similar to the one of DMPC, both having a phosphocholine
4.4 Results and discussion 55 headgroup and two saturated hydrocarbon chains, with DPPC having 16 carbons in each tail, and DMPC 14. This result indicates that the coarse-grained model we have developed for double-tail lipids well reproduces the distribution of pressure in a bilayer of saturated phosphocholines. However, care must be used in such a conclusion. We want to point out that, given the differences between the atomistic and the CG representations, and the different way in which the inter-and intra-molecular interactions are implemented in the two models, the remarkable similarity between the pressure profiles in the two model might be fortuitous. To further address this issue, it would be interesting to compare in a more systematic way pressure profiles calculated from MD and CG simulations. Unfortunately, the published pressure profiles in lipid bilayers from MD simulations are still very few.
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: 4.4 Results and discussion 53 4.4.4
Page 64 and 65: 58 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
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:
Page 114 and 115:
Page 116 and 117:
Page 118 and 119:
Page 120 and 121:
Page 122 and 123:
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
Page 131 and 132:
Summary Biological membranes, as th
Page 133 and 134:
agreement we find gives us confiden
Page 135 and 136:
Samenvatting Biologische membranen,
Page 137 and 138:
de lage temperatuur gel fase of Lβ
Page 139:
ied dat het dichtst bij het hydrofo
Page 143:
This thesis is based on the followi
show all

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

Create successful ePaper yourself

Delete template?

Save as template?