Class notes
Biomolecular Architectures notes part 2
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Detailed notes followed by pictures and tables on all of the lectures for the 'Biomolecular architectures' course
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MEMBRANE-BASED ARCHITECTURES1. lipid bilayer
− functions:
o containment – separating the intracellular from the extracellular environment
o meeting platform – receiving and transducing extracellular signals
o compartmentalization – lipids and proteins are organized in ordered areas to increase
signalling efficiency
o mechanosensing – membrane invaginations are formed or flattened depending on
mechanical stimuli
− composition:
o mix of various lipid types: cholesterol, cardiolipids, sphingolipids…
o type and location of lipids → keep the biological functions of the protein
o asymmetrical bilayer
o mix of proteins with different properties → posttranslational modifications are
responsible for keeping proteins in a lipid environment
o nanoscale architectures and organizations within the cell membrane → not a fluid
mosaic
− phase separation of lipids:
o liquid-ordered state LO – below physiological temperature
o liquid-disordered state LD – above physiological temperature
o LO long chain saturated fatty acids & LD kinked unsaturated fatty acids – at physiological
temperature
o cholesterol likes to fit in
between the ordered
structures (small polar head)
with more complex
glycosylated heads →
ordered domain that will be
between the disordered ones
o phase separation can change
depending on several factors: pH, cholesterol, temperature, chemical modifications of
the components
o cholesterol sulphate has a stabilizing role in cell membranes which can change the
curvature of the membrane (cholesterol vs. cholesterol sulphate change)
− lateral heterogeneity in the plasma membrane:
o saturated lipids, cholesterol, GPI-anchored proteins, transmembrane proteins
(stabilizing the lipid bilayer), cortical actin → a meshwork of short actin polymers
making a grid under the PM, not stress fibers, a network for signalling proteins
o increased lipid packing and ordered
o decreased fluidity due to cholesterol
o asymmetrical distribution
o organization is not binary
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,2. lipid rafts
− modulation of membrane organization
− varying raft coverage: isolated domains → percolating/continuous domains
− raft clustering & declustering:
o nanodomains → raft platforms
o due to signalling and trafficking or addition of clustering agents
o the amount is not increased locally but we have fusion
− lipid and protein interactions drive the lipid rafts architecture:
a) lipid-lipid:
cholesterol likes to
pack between the
tails and it makes
hydrogen bonds
b) lipid-protein:
hydrogen bonds
c) lapidated
proteins: proteins
with lipid tails
inserted into the
membrane where
they start
oligomerizing and
creating local architectures, serve as domain organizers
d) hydrophobic match/mismatch: α-helix must match the thickness of the lipid environment, a
mismatch is not favourable situation
e) transbilayer coupling: GPI-anchored protein interacts with actin through the long chain inner
leaflet lipids and lipid tails
− functions:
o concentrating signalling molecules
o allowing conformational changes
o immune signalling
o host-pathogen interactions
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, 3. caveolae
− made of protein caveolin → 3
isoforms: caveolin 1, 2 & 3
− oligomeric cholesterol-binding
protein
− both the N and the C terminus face
the cytosol
− inserted in the inner leaflet of the
cells at the lipid raft
− hairpin conformation in the
membrane → allows molecule to
insert in the membrane
− domains:
o N-terminus
o conserved scaffolding
domain/CSD → cholesterol-
binding motif
o intramembrane domain
o C-terminus (3 lipid tails)
− caveolae = membrane invaginations
that can also fuse or pinching of the membrane → traditional, grape-like cluster, rosette, tubular
− many more components of caveolae other than caveolin
− caveolins interact with cavins (peripheral membrane proteins)
− caveolin oligomers + cavin trimers → curvature of the membrane
− very specific organization of the components
− functions: endocytosis, signalling, protection from mechanical stress
4. clathrin-coated pits
− made at the cell surface
− clathrin-dependent endocytosis
− 3 heavy + 3 light clathrin chains → 3x triskelion → clathrin
− the triskelion is held together by 3 tripod helices
− 30-40 triskelia assemble → pentagons or hexagons → cage around the invaginating membrane
− adaptins give specificity to one clathrin
− globular heads bind to adaptins which then directly bind to cargo
− AP2 adaptors → between the clathrin coat and the vesicle there are bulky heterotetrameric
AP2s. They bind clathrin on one hand and cargo proteins & membrane lipids on the other hand
→ bridging the vesicle cargo with the clathrin coat
− clathrin-coated pits detaching from the cell membrane: BAR proteins sense or induce the
curvature of the membrane & dynamin forms a ring around the neck of the vesicle until it
pinches of the membrane
− disassembly:
o for every clathrin triskelion removed from the vesicle coat, 1 auxilin molecule and 3
Hsc70 proteins are required
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