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

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ii CONTENTS 5.3 Double-tail lipid bilayers . . . . . . . . . . . . . . . . . . . . . . . . . . . 73 5.3.1 Computational details . . . . . . . . . . . . . . . . . . . . . . . . 73 5.3.2 Results and Discussion . . . . . . . . . . . . . . . . . . . . . . . . 73 5.4 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 6 Interaction of small molecules with bilayers 79 6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 6.2 Computational details . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 6.3 Results and Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 6.3.1 Partitioning of the solutes in the bilayer . . . . . . . . . . . . . . 82 6.3.2 Effect on the bilayer properties . . . . . . . . . . . . . . . . . . . 83 6.3.3 Effect on the pressure distribution . . . . . . . . . . . . . . . . . 90 7 Mesoscopic model for lipid bilayers with embedded proteins 95 7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96 7.2 Computational details . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 7.2.1 Lipid and protein models . . . . . . . . . . . . . . . . . . . . . . 98 7.2.2 Method of calculation of statistical quantities . . . . . . . . . . . 101 7.3 Results and discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 7.3.1 Protein-induced bilayer perturbation . . . . . . . . . . . . . . . 105 7.3.2 Lipid-induced protein tilting . . . . . . . . . . . . . . . . . . . . 109 7.3.3 Thermotropic behavior . . . . . . . . . . . . . . . . . . . . . . . . 111 7.4 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 Summary 125 Samenvatting 129 Curriculum Vitae 135 Publications 137 Acknowledgments 139
I Introduction
Page 1: Mesoscopic models of lipid bilayers
Page 4 and 5: Promotiecommissie: Promotor: • pr
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
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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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VI Interaction of small molecules w
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6.2 Computational details 81 For re
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6.3 Results and Discussion 83 withi
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6.3 Results and Discussion 85 ρ(z)
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6.3 Results and Discussion 87 ρ(z)
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6.3 Results and Discussion 89 S m 0
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6.3 Results and Discussion 91 π(z)
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6.3 Results and Discussion 93 the l
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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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