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

More documents

Recommendations

Info

$Learning LATEX by Doing$

98 Mesoscopic model for lipid bilayers with embedded proteins they do not take into full account the three dimensional structure of the bilayer), and, for example, they can not be used to investigate the lipid-induced protein tilting. Simulations on more realistic models, such as all-atom models for lipid bilayers with embedded proteins, have anyway confirmed that, at least within a time of the order of the nanoseconds, a mismatched protein may induce a deformation of the lipid bilayer structure [10, 63, 170], and that the deformation is of the exponential type [11]. The same type of studies have also shown that—although to reduce a possible hydrophobic mismatch synthetic peptides may prefer to deform the lipid bilayer, rather than undergo tilting [171]—tilting may also occur for membrane peptides [7,8]. Incidentally, the results from these studies indicated that the helical-peptides experience a slight bend in the middle of the helix. No matter the huge body of experimental and theoretical studies on lipid bilayers with embedded proteins, issues such as the range of the protein-induced lipid bilayer perturbation, its dependence on protein size, and the occurrence of protein tilting (or even bending) to adjust for hydrophobic mismatch, are still a matter of debate. Here we want to focus on these issues by adopting the DPD simulation method to study the behavior of a mesoscopic model for lipid bilayers with embedded proteins. We have focused our attention on the perturbation caused by a membrane protein on the surrounding lipids, its possible dependence on hydrophobic mismatch, protein size, and on temperature. We have investigated whether and to which extent—due to hydrophobic mismatch and via the cooperative nature of the system—a protein may prefer to tilt (with respect to the normal to the bilayer plane), rather than to induce a bilayer deformation without (or even with) tilting. 7.2 Computational details 7.2.1 Lipid and protein models Within the mesoscopic approach, each molecule of the system (or groups of molecules) is coarse-grained by a set of beads. In particular, to model the bilayer and the embedded proteins, we consider three types of beads: a water-like bead, labeled ’w’; a hydrophilic bead, labeled ’h’, which models a part of the headgroup of either the lipid or the protein; and a hydrophobic bead, labeled either ’tL’ or ’tP’, depending on whether it refers to a portion of the lipid hydrocarbon chain or a portion of the hydrophobic region of protein, respectively. The systems that we have simulated are made of model lipids having three headgroup beads and two tails of five beads each; this corresponds to the case of acyl chains with fourteen carbon atoms, namely to a model for a dimyristoylphosphatidylcholine (DMPC) phospholipid, as illustrated in figure 2.2 of Chapter 2, and in figure 7.1(a). Within the model formulation, a protein is considered as a rod-like object, with no appreciable internal flexibility, and characterized by a hydrophobic length dP. The model for the transmembrane protein is
7.2 Computational details 99 dL o (a) (b) (c) eff dL (r) dP (d) φ tilt Figure 7.1: Schematic representation of a model-lipid (a), and a model protein (NP=43 and ˜dP=41˚A) (b). A typical configuration of the assembled bilayer with embedded a model-protein (as results from the simulations) is shown in the snapshot (c). The drawing in (d) shows to which part of the system the following quantities refer to: the pure lipid bilayer hydrophobic thickness, d o L, the perturbed lipid bilayer hydrophobic thickness, dL(r), the protein hydrophobic length, dP, the tilted-protein hydrophobic length, d eff P , and the tilt-angle, φ tilt . dP
Page 1:
Mesoscopic models of lipid bilayers
Page 4 and 5:
Promotiecommissie: Promotor: • pr
Page 6 and 7:
ii CONTENTS 5.3 Double-tail lipid b
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 18 and 19:
Page 20 and 21:
Page 22 and 23:
Page 24 and 25:
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 39 and 40:
Page 41 and 42:
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 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 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
show all

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

Create successful ePaper yourself

Delete template?

Save as template?