Membrane Bioinformatics

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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



-
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, Lipid
-
Mediated 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


Contents of Lecture: Membranes

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:

1 nm = 10
-
9
m, bacterial cells 3
-
5
µm = 3
-
5*10
-
6
m

average cell in our body: approx. 50 µm

Length:

Energy:

Thermal energy 1 k
B
T ≈ 0.6 kcal/mol ≈ 0.6 * 4.1868 kJ/mol

= 2.5 kJ/mol (298K)

= 4.1 pN nm


Boltzmann constant k
B
=1.38*10
-
23
JK
-
1



Force:

1 pN = 10
-
12

N

C
-
C bond:

approx. 100 k
B
T stable at room temperature

H
-
bond:


approx. 10 k
B
T

„Kingdoms of Life“

Eubacteria

Archaebacteria

Eukaryotes

Archaebacterium

(5
-
10
µm
)

Eukaryotes: red & white blood cell

Eubacterium: E.coli

(5
-
10
µm
)

First living systems consist of:


information
-
storing molecules
capable of reproduction


catalysts / enzymes able to
enhance reproduction rates


molecules storing energy


boundary forming molecules

O.G. Mouritsen
Life


as a Matter of Fat
Springer (2005)


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

„Molecules of Life“

leucine

adenosine

glucose

phospholipid

(POPC)

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)

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

red blood cell

Major components of the cytoskeleton:


Spectrin


Actin


Ankyrin


Band 4.1


Tropomyosin


Lipowski & Sackmann
Structure & Dynamics of Membranes

Elsevier (1995)

Plasma
-
Membrane: Cytoskeleton

Anthony J. Baines and Jennifer C. Pinder
Frontiers in Bioscience

10

(2005) 3020
-
3033

Spectrin

~106 amino acid units


Flexible protein filament of
100nm total length


Two chains,
α

and
β

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 Bioscience

10

(2005) 3020
-
3033

Plasma
-
Membrane: Cytoskeleton

Composition per cell:

1 x 10
5

spectrin tetramers


3
-
4 x 10
4

actin oligomers


Sufficient to form triangular
network of about 70nm bond
length in a cell with surface of
140
µm
2

2 x 10
5

band 4.1 : facilitates spectrin
-
actin association


≈10
5

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


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

Lipowski & Sackmann
Structure & Dynamics
of Membranes

Elsevier (1995)

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:

single bond

Bonds between un
-
saturated carbon atoms:

double bonds

O.G. Mouritsen
Life


as a Matter of Fat
Springer (2005)

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

Interfacial
region

hydrophobic
region

aqueous
region

fatty acid 14:0

oleic acid 18:1

docosahexaenoic acid (DHA) 22:6

Di
-
acylglycerol (DAG)

Tri
-
acylglycerol

Lipid (di
-
myristoyl phosphatidycholine) DMPC

Lysolipid

Phosphatidic acid

O.G. Mouritsen
Life


as a Matter of Fat
Springer (2005)

Fats & Fatty Acids

Polar head groups:

PC: phosphatidylcholine

PS: phosphatidylserine

PE: phosphatidylethanolamine

PG: phosphatidylglycerol

PI: phosphatidylinositol

PC, PE are neutral (zwitterionic)


PS,PI,PG can be charged

PC

PS

PE

PI

PG

glycolipid

Phospholipids based on
glycerol

O.G. Mouritsen
Life


as a Matter of Fat
Springer (2005)

Fats & Fatty Acids

Phospholipids based on
sphingosine

instead of
glycerol

Simplest version: ceramide (skin)

ceramide

sphingomyelin (SM)

cerebroside

ganglioside

O.G. Mouritsen
Life


as a Matter of Fat
Springer (2005)

Fats & Fatty Acids

Cholesterol is a different kind of lipid:

cholesterol

ergosterol

sitosterol

testosterone

vitamin D

-
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

O.G. Mouritsen
Life


as a Matter of Fat
Springer (2005)

Fats & Fatty Acids

Examples of Strange Lipids:

cardiolipin

di
-
ether lipid

tetra
-
ether lipid, bolalipid

polyisoprenoid lipid

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

O.G. Mouritsen
Life


as a Matter of Fat
Springer (2005)

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

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!

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)

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