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

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48 Structural characterization of lipid bilayers 0.2 0.1 0.0 −0.1 0.2 0.1 0.0 −0.1 0.2 0.1 0.0 −0.1 WH HT MP −5 −3 −1 1 3 5 Z WH (a) −5 −3 −1 1 3 5 Z WH HT MP HT (c) MP −5 −3 −1 1 3 5 Z (e) w h t (1,..,n−1) t n ρ tot π(z) w h t (1,..,n−1) t n ρ tot π(z) w h t (1,..,n−1) t n ρ tot π(z) p L (z)−p N (z) p L (z)−p N (z) p L (z)−p N (z) 0.8 0.4 0.0 −0.4 −0.8 −5 −3 −1 1 3 5 Z 0.8 0.4 0.0 −0.4 (b) −0.8 −5 −3 −1 1 3 5 Z 0.8 0.4 0.0 −0.4 (d) −0.8 −5 −3 −1 1 3 5 Z (f) total non bonded springs total non bonded springs bending total non bonded springs bending Figure 4.6: Lateral pressure profile π(z) = pL(z) − pT (z), and contributions from the different inter and intra molecular potentials as function of the distance from the bilayer center z = 0. The figures refer to bilayers of fully flexible lipids (top), stiff lipids with headgroup repulsion parameter ahh = 15 (middle), and stiff lipids with headgroup repulsion parameter ahh = 35 (bottom). The density profiles ρ(z) for water (w), head (h), and tail (t) beads, as well as the total density, have been plotted in the same graphs to make clear the location of the maxima and minima of the pressure profile within the bilayer. The interfaces described in the text and shown in figure 4.5 are also indicated. The density profiles have been rescaled to adjust to the pressure scale.
4.4 Results and discussion 49 Shillcock and Lipowsky [50]. Another common characteristic of the pressure profile which was found in the atomistic and CG simulations, and that we also observe in our simulations, is that the absolute value of the peak at HT interface is larger than the one at the WH interface. These similarities in the pressure profiles arise despite the different forces and parameters used in the simulations. For example, Lindahl and Edholm [77] show that the minimum at the HT interface is mainly due to electrostatic interactions, which are not present in our model nor in the CG models in the cited references. It is also worth commenting that Goetz and Lipowsky [21] and Shillcock and Lipowsky [50] consider bilayers of single tail lipids (CG Lennard-Jones MD and CG-DPD, respectively) like the ones we use here, while the results of Lindahl and Edholm [77], Gullingsrud and Schulten [81] and Groot and Rabone [24] refer to double tail lipids (atomistic and CG-DPD, respectively). It is remarkable that different lipid topology, potentials, and parameterizations, produce the same shape of the pressure profiles. This suggests that the distribution of lateral pressure is more sensitive to the local densities and structure of the interfaces, rather than to the details of the forces or of the model. The major difference between the flexible and stiff lipids considered here is in the hydrophobic core of the bilayer. A common feature is that the lateral pressure in this region is positive, showing that an outward pressure is compensating for the inward pressure at the HT interface, and that the chains tend to expand the bilayer. However, the local structure of the pressure profile depends on the lipid characteristics. For flexible lipids first a local maximum and then a local minimum at the center of the bilayer (z=0, MP interface) are present. The local minimum at the bilayer center corresponds to the region where the two monolayers are in contact, and where the density of the tail beads is lower. The shape of the pressure profile for the flexible bilayer looks very similar to the ones obtained by Goetz and Lipowsky [21] and Shillcock and Lipowsky [50] using MD and DPD simulations of coarse-grained lipids, despite the fact that their results refer to stiff (via bond-bending potentials) lipids. In our case, in the bilayer of stiff lipids the pressure profile increases monotonously to a large positive maximum in the bilayer center, which is higher in the non interdigitated bilayer. This is likely due to the fact that, because of interdigitation, the chains are more tightly and orderly packed. As a consequence of this packing order, the thermal collisions, which generate the outward pressure, are damped compared to the the case of a non interdigitated, albeit stiff, bilayer. It is interesting to observe (figures 4.6(d) and 4.6(f)) that, although the additional stiffness gives a negative contribution to the total lateral pressure, at the same time the contribution from the spring potential becomes more positive than in the case of flexible lipids. The net effect of these interactions is an increase in the values of the local pressure. The more positive values of the contribution from the spring potential are due to the fact that stiff lipids have a larger end-to-end distance compared to flexible ones, hence the bonds along the chain are more stretched.
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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: 4.4 Results and discussion 47 WH HT
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 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
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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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