Membrane Bioinformatics
SoSe 2009
Helms & Böckmann
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
Contents of Lecture: Membranes
-Introduction
-Physico-Chemical Properties of Membranes (Composition,
Chemical Structure, Self-Organisation, Phase Transitions)
-Molecular Theory of Membranes (Chain Packing, Elasticity)
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
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
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
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, LipidMediated Protein-Protein Interaction
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
Literature on Membranes
David Boal Mechanics of the Cell Cambridge Unviversity Press 2002
Ole G. Mouritsen Life – As a Matter of 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
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:
H-bond:
approx. 100 kBT stable at room temperature
approx. 10 kBT
„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)
„Molecules of Life“
information-storing molecules capable of reproduction
(& energy carriers)
adenosine
nucleotides
catalysts / enzymes able to enhance reproduction rates
amino acids
molecules storing energy
leucine
glucose
sugars
boundary forming molecules
fatty acids
phospholipid
(POPC)
Molecules of Life
information-storing molecules capable of reproduction
Nucleotides: polynucleotides (DNA, RNA)
catalysts / enzymes able to enhance reproduction rates
biopolymers
amino acids: proteins/poly-peptides
molecules storing energy, cell recognition, forming
biological fibers, scaffolding
sugars: assemble to polysaccharides
boundary forming molecules
fatty acids
loose, macromolecuar
assemblies
(lipid bilayer)
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)
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
Architecture of the Plasma-Membrane
Plasma membrane is a three
layered, composite system:
1. glycocalix: film formed by
oligosaccharides of
glycolipid head groups
2. center: lipid/protein layer
3. Intracellular side:
cytoskeleton
Addison-Wesley 1999
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
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)
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 Bioscience 10 (2005) 3020-3033
Plasma-Membrane: Cytoskeleton
Ankyrin
a cytoskeleton-bilayer coupling
protein
Band 4.1
band 4.1 considered as second
protein anchoring to the membrane
Anthony J. Baines and Jennifer C. Pinder Frontiers in Bioscience 10 (2005) 3020-3033
Plasma-Membrane: Cytoskeleton
Composition per cell:
1 x 105 spectrin tetramers
3-4 x 104 actin oligomers
Sufficient to form triangular
network of about 70nm bond
length in a cell with surface of
140µm2
2 x 105 band 4.1 : facilitates spectrin-actin association
≈105 ankyrin molecules
- Not yet established whether other cells possess similar
membrane coupled cytoskeleta
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
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
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)
Membranes: Protein Composition
4 classes of membrane proteins:
1. Proteins predominantly interacting with the
hydrophobic core
-ion channels (potassium channel,
gramicidin)
-ABC transporter
-reaction center of photosynthetic bacteria
2. Transmembrane proteins anchored by one
hydrophobic stem within the bilayer
-peptide hormone receptors
-membrane bound antibodies
-MHC molecules
3. Proteins attached to the membrane by lipid
anchors
4. Adsorbed proteins
-cytochrome C, myelin basic protein,
spectrin
gramicidin
Fats & Fatty Acids
Saturated hydrocarbon chain
Mono-unsaturated hydrocarbon chain
Bonds between saturated carbon atoms:
Bonds between un-saturated carbon atoms:
single bond
double bonds
O.G. Mouritsen Life – as a Matter of Fat Springer (2005)
Fats & Fatty Acids
aqueous
region
Interfacial
region
Used chain length in plants /
animals: 2 - 36 carbon atoms
hydrophobic
region
fatty acid 14:0
oleic acid 18:1
Most common chain length:
14 – 22 carbon atoms
docosahexaenoic acid (DHA) 22:6
Notation: 18:1 = 18 carbons, 1
double bond
Di-acylglycerol (DAG)
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
Tri-acylglycerol
Lipid (di-myristoyl phosphatidycholine) DMPC
Fatty acid + e.g. Glycerol = lipid
O.G. Mouritsen Life – as a Matter of Fat Springer (2005)
Lysolipid
Phosphatidic acid
Fats & Fatty Acids
PC
Phospholipids based on
glycerol
Polar head groups:
PC: phosphatidylcholine
PS: phosphatidylserine
PE: phosphatidylethanolamine
PG: phosphatidylglycerol
PI: phosphatidylinositol
PS
PE
PI
PG
PC, PE are neutral (zwitterionic)
glycolipid
PS,PI,PG can be charged
O.G. Mouritsen Life – as a Matter of Fat Springer (2005)
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)
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
sitosterol
vitamin D
O.G. Mouritsen Life – as a Matter of Fat Springer (2005)
testosterone
Fats & Fatty Acids
Examples of Strange Lipids:
cardiolipin
Cardiolipin found:
-in inner mitochondrial membrane
-in plant chloroplast membranes
-in some bacterial membranes
di-ether lipid
Ether-bonded lipids:
-found in archaebacterial
membranes
Bolalipids:
-span across bacterial membrane
-basic component of halophilic
archaebacteria
tetra-ether lipid, bolalipid
Poly-isoprenoid lipids
-found in prokaryotic and
eukaryotic membranes
-can act as lipid and sugar
carriers
O.G. Mouritsen Life – as a Matter of Fat Springer (2005)
polyisoprenoid lipid
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 monounsaturated 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
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:
dolphins:
2.1%
1.5%
Animals that evolved at the land-water interface show increased brain-to-body-weight ratio!
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
O.G. Mouritsen Life – as a Matter of Fat Springer (2005) glycocalix
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)
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
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