Simulationen von Lipidmembranen

Transcription

1 Simulationen von Lipidmembranen Thomas Stockner

2 Molecular biology Molecular modelling

3 Membranes environment Many cellular functions occur in or around membranes: energy productions, protein synthesis, clearance, communication,... Lipids in membranes Number of different types of lipids can exceed 1000 in cell membranes Membranes are fluid: lipid are not covalently bound In membranes, domains (rafts) are formed consisting of particular proteins and lipids

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5 Lipids

6 Lipids: headgroups Phophatidyl-Ethylamine Phophatidyl-Serine Phophatidyl-Choline Phophatidyl-Inositol

7 Lipids: tails Sphingomyeline Phophoglycerides

8 Lipids: tails Saturated fatty acid Unsaturated fatty acid

9 Lipids: tails Saturated Unsaturated

10 Lipids: Chain length dependent properties PC PE Huang C. and Li S. BBA 1999, 1422, 273

11 Cholesterol Martinez-Seara H et al. PloS One 2010, 5, e11162

12 Membrane lipids Lipid types Phospholipids, cholesterol, sphingolipids Variable chain properties Chain length, saturation Head groups Choline, serine, ethanolamine, inositol

13 Setup of a Simulations Requirements Lipids Water Conterions Simulation parameter Starting geometry Macromolecular parameters Results Dynamics: time evolution of a system; e.g. ligand binding to a receptor or conformational changes All properties that depend on coordinates can in principle be calculated E= k (l l i bonds i 2 i,0 ) + k (θ i i θ i,0 ) 2 + angle k (1+ cos(nω δ)) + i dihedral 12 6 σ σ q q ij ij i j 4ε ij r r + 4πε r 0 ij i=1 j= i+1 ij ij N N

14 Membrane Force Fields The choice of the applied force field depends on the question to be answered, the resolution necessary and the computer time available. All atom force fields Charmm Amber United atom force field Berger lipids GROMOS Coarse grained Martini Force field Implicit solvent model

15 System assemply

16 System assemply

17 System assemply

18 System assemply

19 System assemply

20 Periodic boundary conditions Closest image convention Box boundaries distort system behavior Solution: periodic system Approximation of an infinite system No edge effects (e.g. wall) Actual system size can remain relatively small

21 Box Shape Finite system problem On a confined system, most of the atoms are affected by the presence of the wall. Completely fill the volume 5 shapes are available: Cubic, rectangular, rombic, truncated-octahedron, dodecahedron

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24 Box Shape Semi-isotropic pressure scaling to maintain rectangular shape of NPT ensembles

25 Center of mass motion removal The global center of mass motion must be subtracted in order to maintain systems momentum constant = 0. Small rounding errors lead to global translational motion of the system, of its subsystems. The result is a reduction of the system temperature (flying ice-cube problem)

26 Area per lipid ApL= Area of the membrane patch Number of lipids per leaflet

27 Density profile Cournia Z. et al. J. Phys. Chem. B 2007, 111, 1786

28 Membrane thickness Membrane thickness

29 Phase transitions Fluid to gel phase transition of a 1:1 DLPC (18C) DSPC (12C) mixture When a large enough nucleation center has formed, the transition occurs almost irreversible

30 Local pressure profile Pressure tensor p(z) = 2 E V Local pressure profile P local ( z)= mi v i v i 1 F r f ( z,zi,z j ) ΔV i< j ij ij j i RS Cantor. Biochemistry. (1997) E. Lindahl, O Edholm. J. Chem Phys. (2000)

31 Pressure profile

32 Diffusion Diffusion Calculated from the mean square displacement using the Einstein relationship 2 6Dt=lim (r r0 ) t

33 Diffusion Plochberger B.et al. Langmuir 2010, 26, 17322

34 Order parameter Order tensor used to extract order parameter 1 S ij = 3 cos θi cos θ j δij 2 Order parameter of saturated chain 2S xx S yy S = Sat CD

35 Order parameter The order parameter is a measure of the degree of order/disorder at a given position along the aliphatic chain. It is one of the few parameters that can be measured experimentally (NMR) quite accurate. DPPC order parameter determined at two different temperatures:335 and 350 K Leekumjorn S. and Sum AK. Biophys J. 2006, 90, 3951

36 Cholesterol Cholesterol has very strong effect on membranes Used by cells to manipulate/adjust the behavior of their membranes to many needs, as temperature changes, fluidity, rafts formation,.. Schematic diagram of cholesterol position Cholesterol distribution Phenyl ring and tail Cournia Z. et al. J. Phys. Chem. B 2007, 111, 1786 Lipid tail chain ordering caused by 3 different type of cholesterol

37 All atom simulations Formation of a membrane triggered by a transmembrane peptide DPPC lipid, 50 ns System at different timepoints Density profiles Esteban-Martin S. and Salgado J. Biophys J. 2007, 92, 903

38 Coarse grained simulations Vesicle fusion Side view Time course: 0 20 ns Knecht V. and Marrink SJ. Biophys J. 2007, 92, 4254 Top view

39 Example: Simulation studies of oxidized lipids in model membranes

40 Biological activity oxidized lipids Oxidized lipids are recognized by the immune system Danger signal Induce apoptosis Inflammation Foam cell formations athereosclerotic plaques Disease Atherosclerosis, CNS disorder, liver disease, rheumatoid arthritis

41 Lipid oxidation Formation Radical reaction Enzymatic Biophysical properties Membrane fluidity Membrane thickness Stability of rafts Membrane permeability Influence the activity of membrane inserted proteins

42 Lipid whisker model Reversal of oxidized chain Protrution from the membrane surface Recognition by receptors ME. Greenberg et al. J. Biol. Chem. (2008)

43 Membrane size PGPC POVPC

44 Area per lipid

45 Membrane thickness

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47 8% PGPC 8% POVPC

48 8% PGPC 8% POVPC

49 8% PGPC 8% POVPC

50 Order parameter

51 Model of oxidized lipid geometry PGPC POVPC

52 Area per lipid

53 Membrane Thickness

54 Diffusion