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

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106 Mesoscopic model for lipid bilayers with embedded proteins d L (r) [Å] 45.0 35.0 25.0 15.0 0.0 20.0 40.0 60.0 80.0 (a) NP=4 d L (r) [Å] r [Å] 45.0 35.0 25.0 ∆d=−10 ∆d=−6 ∆d=−1 ∆d= 8 ∆d=17 ∆d=26 d L (r) [Å] 45.0 35.0 25.0 15.0 0.0 20.0 40.0 60.0 80.0 r [Å] (c) NP=43 15.0 0.0 20.0 40.0 60.0 80.0 ∆d=−10 ∆d=−6 ∆d=−1 ∆d= 8 ∆d=17 ∆d=26 (b) NP=7 r [Å] ∆d=−10 ∆d=−6 ∆d=−1 ∆d= 8 ∆d=17 ∆d=26 Figure 7.3: Lipid bilayer hydrophobic thickness profiles, dL(r) as function of the distance r from the protein surface, for different hydrophobic mismatch ∆d = ˜dP − d o L, and for the three protein sizes NP=4, 7 and 43. The data refer to the reduced temperature T ∗ =0.7, which is well above the main-transition temperature of the pure system (T ∗ m=0.425). The calculated pure lipid bilayer hydrophobic thickness at T ∗ =0.7 is d o L =(23.6±0.2) ˚A. The symbols for ∆d refer to the following estimated values of the protein hydrophobic length: the open circle to ˜dP=14 ˚A (negative ∆d), the open triangle to ˜dP=18 ˚A (negative ∆d), the plus to ˜dP=23 ˚A (∆d ≈ 0), the full triangle to ˜dP=32 ˚A (positive ∆d), the full circle to ˜dP=41 ˚A (positive ∆d), and the full diamonds to ˜dP=50 ˚A (positive ∆d).
7.3 Results and discussion 107 ted (see gray and white rectangular areas). The best fit is obtained with the values of the fitting parameters given in Table 7.2, for the three chosen protein sizes, and for varying values of mismatch, i.e. protein hydrophobic thickness. Table 7.2: Values of the decay length, ξP, the pure lipid bilayer hydrophobic thickness d o L (both derived from fitting the thickness profiles dL(r) by using Eq. 7.3), the protein hydrophobic length, dP, and the effective protein hydrophobic length, d eff P (both calculated from the simulations) given for different values of hydrophobic mismatch, ∆d, and for the three protein sizes corresponding to NP=4, 7 and 43. The data refer to simulations made at the reduced temperature T ∗ =0.7, well above the main-transition temperature of the pure lipid bilayer system. The pure lipid bilayer hydrophobic thickness calculated at this temperature is d o L =(23.6±0.2) ˚A. In the case of approximately zero mismatch (∆d=-1 ˚A), the values of ξP and d o L are not calculated. ∆d [˚A] ξP [˚A] d o L [˚A] dP [˚A] d eff P [˚A] Protein fitted fitted computed computed NP=4 -10 9.3 ± 0.3 24.0 ± 0.1 15 ± 1 15 ± 1 -6 11.9 ± 0.3 23.9 ± 0.1 20 ± 1 19 ± 1 -1 * * 24 ± 1 24 ± 1 8 9.6 ± 0.7 23.4 ± 0.1 34 ± 1 32 ± 1 17 9.7 ± 0.7 23.4 ± 0.2 43 ± 1 35 ± 3 26 12.3 ± 0.6 23.2 ± 0.1 53 ± 1 36 ± 3 NP= 7 -10 10.1 ± 0.4 24.2 ± 0.1 15 ± 1 14 ± 1 -6 12.4 ± 0.7 24.0 ± 0.1 19 ± 1 19 ± 1 -1 * * 24 ± 1 23 ± 1 8 9.4 ± 0.8 23.5 ± 0.1 33 ± 1 32 ± 1 17 11.8 ± 0.7 23.2 ± 0.2 42 ± 1 39 ± 2 28 12.4 ± 0.8 23.3 ± 0.2 51 ± 1 39 ± 3 NP= 43 -10 12.8 ± 0.8 24.2 ± 0.1 14 ± 1 14 ± 1 -6 17 ± 2 24.3 ± 0.2 19 ± 1 19 ± 1 -1 * * 24 ± 1 24 ± 1 8 10 ± 1 23.2 ± 0.3 33 ± 1 33 ± 1 17 12 ± 1 22.5 ± 0.6 43 ± 1 43 ± 1 26 12 ± 1 22.1 ± 0.8 52 ± 1 51 ± 2 At negative mismatch, no difference is observed between dP and deff P , as can be seen by looking at figure 7.4(a,c,e). This means that the orientation of the protein is perpendicular to the bilayer plane, hence dP=deff P . However, for a positive mismatch too large to be compensated for by fully stretching the lipids in the vicinity of the protein, another effect can be observed; the peptide tilts in order to decrease its effective hydrophobic length. The effect is much more pronounced in the case of the skinny protein (NP=4) than for the larger protein, as can be seen by comparing figures is much shorter than the ac- 7.4b,d with figure 7.4(f); where in the former cases deff P tual protein hydrophobic length. The values of deff P and dP shown in Table 7.2 confirm
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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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IV Structural characterization of l
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4.2 Structural quantities 39 been r
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4.3 Computational details 41 lipid
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4.4 Results and discussion 43 ρ(z)
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4.4 Results and discussion 45 one l
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4.4 Results and discussion 47 WH HT
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4.4 Results and discussion 49 Shill
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4.4 Results and discussion 51 chain
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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
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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