Membrane Bioinformatics SoSe 2009 Helms & Böckmann

1. Membrane BioinformaticsSoSe 2009Helms & Böckmann

2. Contents of Lecture: Membranes -Introduction -Physico-Chemical Properties of Membranes (Composition, Chemical Structure, Self-Organisation, Phase Transitions) S.J. Marrink and A.E. Mark JACS 125 (2003) 15233-15242

3. Contents of Lecture: Membranes -Introduction -Physico-Chemical Properties of Membranes (Composition, Chemical Structure, Self-Organisation, Phase Transitions) -Molecular Theory of Membranes (Chain Packing, Elasticity)

4. Contents of Lecture: Membranes -Introduction -Physico-Chemical Properties of Membranes (Composition, Chemical Structure, Self-Organisation, Phase Transitions) -Molecular Theory of Membranes (Chain Packing, Elasticity) -Electrostatic Properties of Membranes (Poisson-Boltzmann Theory) and of Membrane Proteins (KCSA Channel) R.A. Böckmann, A. Hac, T. Heimburg, H. Grubmüller Biophys.J. 85 (2003) 1647-1655

5. Contents of Lecture: Membranes -Introduction -Physico-Chemical Properties of Membranes (Composition, Chemical Structure, Self-Organisation, Phase Transitions) -Molecular Theory of Membranes (Chain Packing, Elasticity) -Electrostatic Properties of Membranes (Poisson-Boltzmann Theory) and of Membrane Proteins (KCSA Channel) -Electroporation of Membranes, Influence of Proteins on Electroporation

6. Contents of Lecture: Membranes -Introduction -Physico-Chemical Properties of Membranes (Composition, Chemical Structure, Self-Organisation, Phase Transitions) -Molecular Theory of Membranes (Chain Packing, Elasticity) -Electrostatic Properties of Membranes (Poisson-Boltzmann Theory) and of Membrane Proteins (KCSA Channel) -Electroporation of Membranes, Influence of Proteins on Electroporation -Interaction between drug molecules and membranes

7. Contents of Lecture: Membranes -Introduction -Physico-Chemical Properties of Membranes (Composition, Chemical Structure, Self-Organisation, Phase Transitions) -Molecular Theory of Membranes (Chain Packing, Elasticity) -Electrostatic Properties of Membranes (Poisson-Boltzmann Theory) and of Membrane Proteins (KCSA Channel) -Electroporation of Membranes, Influence of Proteins on Electroporation -Interaction between drug molecules and membranes -Membrane-Protein Interaction, Lipid-Mediated Protein-Protein Interaction

8. Contents of Lecture: Membranes -Introduction -Physico-Chemical Properties of Membranes (Composition, Chemical Structure, Self-Organisation, Phase Transitions) -Molecular Theory of Membranes (Chain Packing, Elasticity) -Electrostatic Properties of Membranes (Poisson-Boltzmann Theory) and of Membrane Proteins (KCSA Channel) -Electroporation of Membranes, Influence of Proteins on Electroporation -Interaction between alcohols and membranes -Membrane-Protein Interaction, Lipid-Mediated Protein-Protein Interaction -Membrane Properties determined from Molecular Dynamics Simulation

9. Literature on Membranes David Boal Mechanics of the Cell Cambridge Unviversity Press 2002 Ole G. Mouritsen Life – As a Matterof Fat Springer 2005 D. Walz et al. Bioelectrochemistry of Membranes Birkhäuser 2004 Lodish et al. Molecular Cell Biology Freeman 2001 Thomas Heimburg Thermal Biophysics of Membranes Wiley-VCH 2007 R. Lipowski and E. Sackmann Structure and Dynamics of Membranes Elsevier 1995 http://www1.elsevier.com/homepage/sak/hbbiophys/contenthome1.html + further reading will be presented during the lectures

10. Typical Length Scales, Energies, Forces, Temperatures: Length: 1 nm = 10-9 m, bacterial cells 3-5 µm = 3-5*10-6 m average cell in our body: approx. 50 µm Energy: Thermal energy 1 kBT ≈ 0.6 kcal/mol ≈ 0.6 * 4.1868 kJ/mol = 2.5 kJ/mol (298K) = 4.1 pN nm Boltzmann constant kB=1.38*10-23JK-1 Force: 1 pN = 10-12 N C-C bond: approx. 100 kBT stable at room temperature H-bond: approx. 10 kBT

11. „Kingdoms of Life“ Eubacteria Archaebacteria Eukaryotes First living systems consist of: • information-storing molecules capable of reproduction • catalysts / enzymes able to enhance reproduction rates • molecules storing energy • boundary forming molecules Archaebacterium (5-10µm) Eubacterium: E.coli (5-10µm) Eukaryotes: red & white blood cell O.G. Mouritsen Life – as a Matter of Fat Springer (2005)

12. „Molecules of Life“ • information-storing molecules capable of reproduction (& energy carriers) nucleotides • catalysts / enzymes able to enhance reproduction rates amino acids • molecules storing energy sugars • boundary forming molecules fatty acids adenosine leucine glucose phospholipid (POPC)

13. Molecules of Life • information-storing molecules capable of reproduction Nucleotides: polynucleotides (DNA, RNA) • catalysts / enzymes able to enhance reproduction rates amino acids: proteins/poly-peptides • molecules storing energy, cell recognition, forming biological fibers, scaffolding sugars: assemble to polysaccharides • boundary forming molecules fatty acids biopolymers loose, macromolecuar assemblies (lipid bilayer)

14. Role of the Membrane Membranes enable formation of compartments! Intracellular space is sub-divided (organelles, cytosol) Distribution of different molecules among the subspaces Membranes allow gradient of composition between nucleus and plasma membrane: directed flow of newly synthesized material from ER to plasma membrane, trafficking of nutrition molecules in opposite direction Membranes allow ionic/pH gradients in organelles: electrochemical gradient, activity control of specialized proteins (lysosomes), accumulation of specific proteins O.G. Mouritsen Life – as a Matter of Fat Springer (2005)

15. Role of the Membrane • Division of intracellular space into sub-spaces: lumina of organelles and cytosol • Different classes of molecules are distributed among different subspaces reducing the number of directly interacting species • Membranes allow gradient of composition between nucleus and plasma membrane: directed flow of newly synthesized material from ER to plasma membrane, trafficking of nutrition molecules in opposite direction • Cell-cell recognition • Membranes allow ionic/pH gradients in organelles: -electrochemical gradient across membranes -activity control of specialized proteins (e.g. lysosomes with low pH) -accumulation of specific proteins • Site for receptor-molecule binding for cell signaling -receptor binds ligand -induces intracellular reactions

16. Architecture of the Plasma-Membrane • Plasma membrane is a three layered, composite system: • glycocalix: film formed by oligosaccharides of glycolipid head groups • 2. center: lipid/protein layer • 3. Intracellular side: cytoskeleton Addison-Wesley 1999

17. Function of the Plasma-Membrane • Bilayer & glycocalix: Filter controlling transfer of ions, molecules, and even of viruses or bacteria • Site for signal transduction (hormones) and amplification; site for energy producing processes • Glycocalix as receptor for extracellular signals, mediates communication between cytosol and exterior • Glycocalix as a connecting link to extracellular matrices • Lipid/protein bilayer together with cytoskeleton responsible for flexibility and stability of the cell Addison-Wesley 1999

18. Plasma-Membrane: Cytoskeleton Major components of the cytoskeleton: • Spectrin • Actin • Ankyrin • Band 4.1 • Tropomyosin red blood cell Lipowski & Sackmann Structure & Dynamics of Membranes Elsevier (1995)

19. Plasma-Membrane: Cytoskeleton Spectrin ~106 amino acid units Flexible protein filament of 100nm total length Two chains, α and β Anthony J. Baines and Jennifer C. Pinder Frontiers in Bioscience10 (2005) 3020-3033

20. Plasma-Membrane: Cytoskeleton Ankyrin a cytoskeleton-bilayer coupling protein band 4.1 considered as second protein anchoring to the membrane Band 4.1 Anthony J. Baines and Jennifer C. Pinder Frontiers in Bioscience10 (2005) 3020-3033

21. Plasma-Membrane: Cytoskeleton Composition per cell: Sufficient to form triangular network of about 70nm bond length in a cell with surface of 140µm2 1 x 105 spectrin tetramers 3-4 x 104 actin oligomers 2 x 105 band 4.1 : facilitates spectrin-actin association ≈105 ankyrin molecules - Not yet established whether other cells possess similar membrane coupled cytoskeleta

22. Membranes: Lipid Composition • Comparingly few lipids of the enormous variety of lipids are used to build cell membranes • Given type of cell or organism can only synthesize a limited range of lipids (human beings can only synthesize few types of lipids and fats themselves) • Some facts about composition: • cholesterol content 20-50% in plasma membranes of all animals • cholesterol content in membranes of organelles small (except lysosome): mitochondrial membranes <5%, Golgi ≈8%, ER ≈ 10% • Charged lipids: 10% in plasma membranes (only negatively charged) • the longer the fatty acid chain, the more double bonds are present • Lipid asymmetry in the lipid composition of of the two monolayers of the plasma membrane: outer monolayer contains mainly SM, PC, cholesterol, glycolipids; lower monolayer PS, PI, and PE

23. Membranes: Lipid Composition Lipowski & Sackmann Structure & Dynamics of Membranes Elsevier (1995) • Lipid composition of plasma membranes of mammalian cells similar • Distinct differences between plasma membrane and membranes of organelles • 10% charged lipids • Glycolipids almost exclusively in plasma membranes

24. Membranes: Lipid Composition Distribution of most abundant fatty acids among lipids of human erythrocytes: • Phosphatidylcholines are composed of short chains • Sphingomyelin contains high content of long chain lipids • PE has high content of polyunsaturated chains • Charged lipids (PS, PI) have high content of non-saturated lipids Lipowski & Sackmann Structure & Dynamics of Membranes Elsevier (1995)

25. Membranes: Protein Composition 4 classes of membrane proteins: gramicidin • Proteins predominantly interacting with the hydrophobic core • -ion channels (potassium channel, gramicidin) • -ABC transporter • -reaction center of photosynthetic bacteria • Transmembrane proteins anchored by one hydrophobic stem within the bilayer • -peptide hormone receptors • -membrane bound antibodies • -MHC molecules • Proteins attached to the membrane by lipid anchors • 4. Adsorbed proteins • -cytochrome C, myelin basic protein, spectrin

26. Fats & Fatty Acids Saturated hydrocarbon chain Mono-unsaturated hydrocarbon chain Bonds between saturated carbon atoms: single bond Bonds between un-saturated carbon atoms: double bonds O.G. Mouritsen Life – as a Matter of Fat Springer (2005)

27. aqueous region Interfacial region hydrophobic region Fats & Fatty Acids Used chain length in plants / animals: 2 - 36 carbon atoms Most common chain length: 14 – 22 carbon atoms Notation: 18:1 = 18 carbons, 1 double bond Usually even number of carbon atoms Mostly unsaturated or one double bond in plants or animals Short-chain fatty acids can be produced by electrical discharges, long-chain fatty acids only by biochemical synthesis Fatty acid + e.g. Glycerol = lipid fatty acid 14:0 oleic acid 18:1 docosahexaenoic acid (DHA) 22:6 Di-acylglycerol (DAG) Tri-acylglycerol Lipid (di-myristoyl phosphatidycholine) DMPC Lysolipid O.G. Mouritsen Life – as a Matter of Fat Springer (2005) Phosphatidic acid

28. Fats & Fatty Acids PC Phospholipids based on glycerol PS Polar head groups: PE PC: phosphatidylcholine PS: phosphatidylserine PE: phosphatidylethanolamine PG: phosphatidylglycerol PI: phosphatidylinositol PI PG PC, PE are neutral (zwitterionic) PS,PI,PG can be charged glycolipid O.G. Mouritsen Life – as a Matter of Fat Springer (2005)

29. Fats & Fatty Acids ceramide Phospholipids based on sphingosine instead of glycerol sphingomyelin (SM) Simplest version: ceramide (skin) cerebroside ganglioside O.G. Mouritsen Life – as a Matter of Fat Springer (2005)

30. Fats & Fatty Acids Cholesterol is a different kind of lipid: ergosterol cholesterol -Cholesterol has a steroid ring structure and a simple hydroxyl group as polar head -cholesterol as lipid with bulky and stiff tail and small head testosterone sitosterol vitamin D O.G. Mouritsen Life – as a Matter of Fat Springer (2005)

31. Fats & Fatty Acids Examples of Strange Lipids: cardiolipin Cardiolipin found: -in inner mitochondrial membrane -in plant chloroplast membranes -in some bacterial membranes Ether-bonded lipids: -found in archaebacterial membranes Bolalipids: -span across bacterial membrane -basic component of halophilic archaebacteria Poly-isoprenoid lipids -found in prokaryotic and eukaryotic membranes -can act as lipid and sugar carriers di-ether lipid tetra-ether lipid, bolalipid polyisoprenoid lipid O.G. Mouritsen Life – as a Matter of Fat Springer (2005)

32. Lipids Lipids & Brain All molecular building blocks of our body are supplied from the diet! Animals are able to transform some saturated fatty acids into mono-unsaturated fatty acids with a double bond in position 9, no possibility for other positions! Unsaturated fatty acids are therefore called essential fatty acids since animals need to get them from their diet. essential fatty acids are: C18:2n-6 (linolenic acid, double bonds at positions 9 and 12) and C18:3n-3 (α-linolenic acid, double bonds at positions 9, 12, 15) Human body can slowly produce super-unsaturated fatty acids in the liver from essential fatty acids: arachidonic acid (AA, 20:4), docosapentaenoic (DPA), and docosahexaenoic acid (DHA, 22:6) Sources for AA and DHA: egg yolk, meat and organs of animals, marine algae, cold-water fish, shell fish (e.g.salmon 50% DHA, cow 0.2%) AA and DHA critical for evolution of brain and the human neural system

33. Lipids Lipids & Brain Fatty acids in human brain: 20% DHA, AA+DPA 15% Similar fatty acid contributions in visual system and retina Thesis of Michael Crawford: accessibility of AA/DHA has been a determining factor in the evolution of the human brain Brain-to-body-weight ratio: squirrel, rat, mouse: 2% chimpanzee: 0.5% gorilla: 0.25% rhinoceros,cow: <0.1% human: 2.1% dolphins: 1.5% Animals that evolved at the land-water interface show increased brain-to-body-weight ratio!

34. Brief History of Membrane Models 1925 Gorter & Grendel thin bilayer, two molecules thick 1935 Danielli & Dawson Association of proteins with membranes 1966 Robertson Proteins as layers sandwiching the lipid bilayer 1972 Singer & Nicolson Fluid-mosaic model: integral and peripheral proteins „floating in a fluid sea“ 1978 Israelachvili Includes thickness variations, pore formation 1995 Sackmann Inclusion of cytoskeleton and glycocalix O.G. Mouritsen Life – as a Matter of Fat Springer (2005)

35. Is a New Membrane Model Necessary? • Lipid bilayers are structured on the nanometer-scale • Correlated dynamical phenomena • Protrusions of lipids • Instabilities towards non-lamellar symmetries • Phase transitions in membranes: membrane function may be steered by perturbations by both physical (temperature, pressure) and chemical factors (drugs)

36. Next week: • Self-organization of membranes (self-assembly, stability of lipid bilayers, order parameters) • Phase transitions (fluid, solid) • Elasticity of bilayers (theory, experiment, simulation) • Assignments / Projects