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Summary Biological membranes, as they are found in all living cells, are complex systems. They contain many different molecules and display dynamic and structural properties which span many orders of magnitude, both in length and time scales. The characterization of the structure of lipid bilayers, their thermodynamic and dynamic behavior, the dependence of these properties on the membrane composition, as well as the interaction of the lipid bilayer with other molecules, are key questions in the understanding of how a membrane works and how specific functions are carried out. Different approaches can be adopted to address these questions. Disciplines like biology, biochemistry, physics, have applied different, and complementary, tools to the study of these complex systems. Computer simulations are a relatively new tool that has proved useful in the study of condensed matter systems. From the point of view of a physicist, a membrane is a soft-matter, quasi two-dimensional, aggregate. Due to the non covalent interactions between the lipids forming the bilayer matrix, a membrane is fluid. Lipids and other molecules can diffuse in the bilayer plane, or flip-flop from one monolayer to the other, small ions or molecules can cross it, and proteins can be incorporated. But a membrane is not a fluid in the sense that it constitutes a barrier, thought semi-permeable, which cannot be crossed by large molecules, and which has the properties of an elastic sheet, it can bend, it has a specific rigidity, it can be compressed or stretched. Furthermore, because the lipids of which it is constituted are oriented, a membrane has an internal structure. The lipid hydrophilic headgroups stick into the aqueous environment, and the lipid hydrophobic tails extend in the bilayer core. Computer simulations as a tool to study lipid bilayers The subject of this thesis is the study of lipid bilayers with computer simulations, using a mesoscopic approach. This mesoscopic approach consists in coarse-graining the molecules that form the membrane, i.e. the lipids. Instead of considering an atomistic representations of the lipids, groups of atoms are lumped together to form beads, which are connected by springs to build the lipid molecules. These beads interact via simplified forces, which are described in Chapter 2. In this Chapter we have also introduced the Dissipative Particle Dynamics technique which we use to simulate the movement of these particles. A first, important result of this approach, is that, despite the purely repulsive nature of the interactions between particles of different type, we find that the model lipids can phase separate and form bilayers, and that the formation of the bilayer depends on a single parameter, i.e. on the relative strength of the repulsion between hydrophilic and hydrophobic beads. It is known experimentally, and by thermodynamic considerations, that unconstrained, self-assembled, lipid bilayers are in a tensionless state. To mimic such a
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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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Page 80 and 81: 74 Phase behavior of coarse-grained
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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)
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Page 97 and 98: 6.3 Results and Discussion 91 π(z)
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Page 104 and 105: 98 Mesoscopic model for lipid bilay
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Page 125 and 126: References [1] Tanford, C. Science
Page 127 and 128: 7.4 Conclusion 121 [68] Ono, S.; Ko
Page 129: 7.4 Conclusion 123 [139] Lee, A. Bi
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
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