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

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112 Mesoscopic model for lipid bilayers with embedded proteins ξ P [Å] 25 20 15 10 ∆d0 N P =7 N P =43 5 0.4 0.5 0.6 0.7 0.8 0.9 1.0 T* Figure 7.6: Decay length ξP dependence on reduced temperature T ∗ (T ∗ > T ∗ m), for two values of protein hydrophobic length ˜dP=14 ˚A (a) and ˜dP=41 ˚A (b). These values were chosen to fulfill the condition that either ∆d < 0 (˜dP=14 ˚A) or ∆d > 0 (˜dP=41 ˚A), even if by changing temperature the lipid bilayer hydrophobic thickness may change, and consequently ∆d. The data refer to two protein sizes, NP=7 and 43. The dashed lines are only a guideline for the eye. higher than the ones related to the small protein. These findings are consistent with the results obtained from Monte Carlo simulations on lattice models [167], which predicted that the temperature dependence of the decay length has a dramatic peak at the transition temperature. They are also consistent with results from MD simulations on all-atom models. In fact, data from recent MD simulations on bilayers of fluid POPE and POPC with embedded the membrane channel aquaglycerolporin [11] show that when the hydrophobic length of the protein is shorter than the pure lipid bilayer hydrophobic thickness, the lipids close to the lipid-protein interface compress to favor hydrophobic matching, thus inducing a curvature in the bilayer. Also, the mismatch-induced perturbation is of exponential type, and can be characterized by a decay length around ξP =10 ˚A. Simulations on POPC bilayers with embedded a much smaller protein than aquaglycerolporin, the membrane channel gramicidin A, suggest that this channel induces perturbation having a coherence length that is smaller than that in the case of aquaglycerolporin [181]. At the present stage of experimental development, estimates of the range of the perturbation that proteins such as Bacteriorhodopsin [143, 146], lactose permease [148], and the synthetic alpha-helical peptides [182,183], induce on the surrounding lipids, suggest that the perturbation might be mismatch and protein-size dependent, the larger the protein the more long range the perturbation, consistent with the theo- (b)
7.3 Results and discussion 113 retical predictions discussed here. If the coherence length associated to the proteininduced perturbation is dependent on protein size, one would expect that bilayer activities affected by changes of the coherence length, might be thus be affected by protein sizes. This is indeed the case for the phenomenon of flip-flop of phospholipids in bilayers. In fact, experimental data on flip-flop suggest that the larger the protein size (hence the smaller its curvature at the interface with the lipid chains) the more reduced is the ability of the protein to cause flip-flop [184]. It is worth mentioning that the larger the protein size is, the more the behavior of dL(r) obtained from our DPD simulations differs from the one of the exponential function used for the best fitting. This could already be seen by looking at figure 7.4f (at a temperature well above the main-transition temperature) for NP=43 and in the case of negative mismatch. Figure 7.7 illustrates more in details the non-exponential dependence of the lipid bilayer thickness profile on r. The figure shows the calculated values of dL(r) (open circles) and the fitting ones using expression 7.3 (solid line). The 30.0 d L (r) [Å] 25.0 20.0 15.0 10.0 5.0 0.0 eff dP dP ∆d0 0 10 20 30 40 50 60 70 80 90 r [Å] (b) o dL dL dL fit Figure 7.7: The calculated values of dL(r) (open circles) and the fitting ones using expression 7.3 (solid line) as a function of the distance r from the protein surface. The data refer to a protein size NP=43, and to the following cases: (a) ∆d=-12 ˚A (˜dP=14 ˚A) and T ∗ =0.5, and (b) ∆d=19 ˚A (˜dP=41 ˚A) and T ∗ =1.0, where in both cases the temperature is above the melting temperature of the pure system. The dashed line indicates the value of the pure lipid bilayer hydrophobic thickness d o L at the considered temperature. Also shown are the calculated protein hydrophobic length dP (gray area), and the effective protein hydrophobic length d eff P (white area), which is defined as the projection of dP onto the normal to the bilayer plane. data refer to a protein size NP=43, and to the following two cases: (a) ∆d=-12 ˚A (˜dP=14 ˚A) and T∗ =0.5, and (b) ∆d=19 ˚A (˜dP=41 ˚A) and T∗ =1.0. In the case of positive and large mismatch (dP > do L ) (but low enough to avoid protein tilting), figure 7.7(b) indicates that the lipids in the layers closest to the protein surface are characterized by gellike chain in order to minimize the hydrophobic mismatch; surprisingly, next to this
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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
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4.4 Results and discussion 55 headg
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58 Phase behavior of coarse-grained
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60 Phase behavior of coarse-grained
Page 68 and 69: 62 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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