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

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88 Interaction of small molecules with bilayers the pure bilayer. We consider the parameter ∆Q = Qdb − Qo , (6.1) Qo where Q can be one of the following: bilayer area, bilayer thickness, lipid hydrophobic length (projected along the bilayer normal). Qo and Q db refer to any of these quantities in the pure bilayer and in the bilayer with dumb-bells, respectively. For the definition and method of calculation of these quantities we refer the reader to section 4.2 of Chapter 4. The values of these differences for the different dumb-bells and bilayer types are shown in figure 6.6. By addition of the solute, the bilayer area ∆Q % 15 10 5 0 −5 −10 A D c n Lee A D c n Lee D c dbA dbH dbN (a) ht (L) 6 t A n Lee ∆Q % 15 10 5 0 −5 −10 A n Dc Lee A Dc n Lee n Dc Lee dbA dbH dbN (b) ht (L) t (K) 4 t (L) t A ∆Q % 15 10 5 0 −5 −10 A n Dc Lee A Dc n Lee dbA dbH dbN (c) ht7 Figure 6.6: Difference (as percent), with respect to the pure bilayer, of bilayer structural quantities (Q) by addition of different solute molecules in different bilayer types. The quantities considered are: bilayer area, A (black), bilayer hydrophobic thickness, Dc (black and white), and lipid hydrophobic end-to-end distance projected along the bilayer normal, L n ee (gray). (in black in figures 6.6) increases for all bilayer types, although the increase is much larger when the molecules absorb at the interface (amphiphilic and neutral dumbbells). Because we are considering the total area, and because the bilayers are tensionless, a larger number of molecules in the system results in a larger area compared to the pure bilayer. Moreover, if the solutes adsorb at the headgroup interfacial region this increase is larger. This increase in the bilayer area results in a lower interfacial density of lipids, and in a potential creations of voids in the bilayer core. The rearrangement of the bilayer to compensate for this is very much dependent on the bilayer structure and on the type of solute. We will first consider the case of the ht (L) 6 t bilayer, with either the neutral or the amphiphilic solute molecules, which both absorb at the interface near the lipid headgroups. Since the dumb-bells at the interface are far too short to fill-in the voids created in the bilayer interior by an increase of the surface area, two compensating mechanisms could happen. The lipid tails could become more disordered, or the lipids in each opposing monolayer could interdigitate to fill-in the extra free volume. The decrease in bilayer hydrophobic thickness (and the described shape of the density profiles) show that the latter mechanism is taking A D n cLee
6.3 Results and Discussion 89 S m 0.7 0.6 0.5 0.4 0.3 0.2 1 2 3 4 5 6 7 m (a) pure bilayer dbA dbH dbN P(φ) 0.03 0.02 0.01 0.00 0 20 40 φ 60 80 100 (b) pure bilayer dbA dbH dbN Figure 6.7: Modification of the ordering of the lipids induced by addition of solute dumb-bells in a ht (L) 6 t bilayer. (a) Order parameter Sm between the vector connecting each two consecutive beads in the lipid tail and the bilayer normal, m is the index of the vector (starting from the head group). (b) Distribution of the angle (in degrees) formed by the vector between the head-group and the last bead in the lipid tail with the bilayer normal. place. This conclusion is further supported by the observed increase of the lipid endto-end distance along the bilayer normal. If the two monolayers were well separated, an increase of the lipid tail length would correspond to an increase of the bilayer thickness, while we observe a decrease of the latter quantity. Because of increased interdigitation, the lipid tails are more ordered. This can be seen (figure 6.7(a)) from the increase in the tail order parameters respect to the pure bilayer and to the bilayer with hydrophobic dumb-bells. Also, in the case where the solutes adsorb at the interface, the distribution of the angle between the lipid tail and the bilayer normal (figure 6.7(b)) is less broad, and with the maximum at lower values of the angle. Also in the case of flexible (ht7) and unsaturated (ht (L) t (K) 4 t(L) t) bilayers with added surface-absorbed molecules, to an increase in surface area corresponds a decrease of bilayer thickness. However, this decrease can be accounted for by a shortening of the lipid tails, as can be seen by the decrease of the end-to-end distance. For these more flexible bilayers, the effect of molecules absorbed at the interface is opposite than in the case of the more stiff bilayer, i.e. the lipid chains become more disordered to compensate for the larger volume available due to the increase in surface area. When hydrophobic dumb-bells are added, the increase in surface area is much smaller for all the bilayer types considered, and the bilayer hydrophobic thickness is always larger than the thickness of the pure bilayer. Since the hydrophobic solutes locate in the bilayer center, they increase the bulk volume of the bilayer. The largest increase in thickness is observed for the stiff bilayer. The presence of the solutes in the hydrophobic core disrupts the ordering of the lipids tail (as can be seen
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Mesoscopic models of lipid bilayers
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Promotiecommissie: Promotor: • pr
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ii CONTENTS 5.3 Double-tail lipid b
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2 Introduction 1.1 The cell membran
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4 Introduction between the beads, a
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6 Introduction whether the preferre
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8 Simulation method for coarse-grai
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10 Simulation method for coarse-gra
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III Surface tension in lipid bilaye
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3.2 Method of calculation of surfac
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3.2 Method of calculation of surfac
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3.3 Constant surface tension ensemb
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3.3 Constant surface tension ensemb
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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 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: 6.3 Results and Discussion 87 ρ(z)
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 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
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