Phase Separation in Biological Systems Flashcards
Compartmentalisation of Cells
- in eukaryotic cells have many compartments / organelles with specfic functions and provide spatiotemparal control over cell materials / metabolic pathways etc.
- most organelles have a membrane boundary but there are also many membraneless organelles
- these are supramolecular assemblies of proteins and RNA molecules and typically form liquid droplets or hydrogels
Biophysical Assays of Membraneless Compartments
-established liquid nature of some membraneless compartments
Protein Granule Model of Membraneless Compartments
- protein granules are a good model of liquid membraneless compartments
- molecules diffuse freely within protein granule
- two protein granules can fuse into one
- one protein granule can bud of from another
- spherical shape from surface tension
Liquid-Liquid Phase Separation
Description
- entropy of mixing drives spontaneous mixing of components
- there is a predicted entropy increase with mixing and this drive to spontaneous mixing is always there
Liquid-Liquid Phase Separation
Volume Fractions
φ1 = volume fraction of component 1 φ2 = volume fraction of component 2
φ1 + φ2 = 1
Liquid-Liquid Phase Separation
Concentrations
φ = volume fraction υ = molecular volume c = concentration
c = φ/υ
Liquid-Liquid Phase Separation
De-Mixing
Description
-repulsion between components can lead to de-mixing
-two co-existing phases with volume fractions φ1=φs & φ1=φd
-there is no net-flux of molecules across the interface since:
μ1(φs) = μ1(φd)
Liquid-Liquid Phase Separation
De-Mixing
Free Energy of Mixing
F = E - T Smix
Liquid-Liquid Phase Separation
De-Mixing
Interaction Energy
E = χ12 V φ1 (1 - φ1)
-where χ12 is the FLory interaction parameter
Liquid-Liquid Phase Separation
De-Mixing
Chemical Potential
μ1 = υ1 / V dF/dφ1
Liquid-Liquid Phase Separation Surface Tension
Overview
- entails coarsening of the disperse phase (droplets)
- owing to the Laplace pressure one large droplet is favourable over many small droplets
- droplets may coarsen by fusion or Ostwald ripening
Liquid-Liquid Phase Separation Surface Tension
Laplace Pressure
ΔP = Pin - Pout = 2γ/R
-where γ is the surface tension
Liquid-Liquid Phase Separation Surface Tension
Ostwald Ripening
-droplets leave smaller droplet in preference of larger one
2D Compartments
Overview
- compartmentalisation also occurs in 2D
- e.g. in lipid bilayer membranes and polymer brushes
2D Compartments
Lipid Bilayer Membranes
- microdomains within lipid membranes
- same driving mechanisms as 3D
2D Compartments
Polymer Brushes
- glycocalyces may phase separate in 2D
- potentially driven by cross-linking of polysaccaride scaffold
2D Compartments
Perineural Nets
- HA brushes as invitro model of perineural nets
- demonstrate cross-linking by proteins can recapitulate granular and reticular phases
2D Compartments
Phases
- basic priniples are the same as for 3D
- granular and reticular phases represent polymer-rich phase being the dispose and continuous phase respectively
- a change to substrate provides extra effects (e.g. microphase separation if anchors are immobile and cannot move in plane)
Functions of Membraneless Compartments
List
- concentration of biochemical reactions
- sequestering harmful components
- storage of biomolecules
- sieving
- signal amplitude and noise reduction
Functions of Membraneless Compartments
Concentration of Biochemical Reactions
- benefits from concentrated liquid phase where reactants can easily meet
- composition may be dsitinct from surrounding continuous phase leading to different reactions
Functions of Membraneless Compartments
Sequestering Harmful Components
-protein aggregates in disease are harmful but could be the initial rescue mechanism of cells to sequester more toxic protein oligomers
Functions of Membraneless Compartments
Sieving
-nuclear pore permeability barrier controls biomolecule transport between the nucleus and cytoplasm
Functions of Membraneless Compartments
Signal Amplitude and Noise Reduction
- signal pathways amplified by conecntrating receptors in membrane micro domains
- liquid-liquid phase separation decrease protein concentration fluctuations thereby reducing noise in signalling pathways
Phase Separation as a Mechanism to Reduce Noise in Cells
- proteins are produced in the cell cytoplasm by ribosomes, there are many ribosomes but only a small number will be producing any particular protein at any given time
- this can lead to large variations in protein concentration across the cell but for biochemical reactions it is useful to reduce theis noise and acheive a more uniform concentration
- liquid-liquid phase separtion provides a mechanism to reduce this noise by the creation of two phases, the dilute phase of low protein concentration and the dispere phase of high protein concetration
- when total protein concentration changes, the size and number of the droplets changes but the concentrations in both the continuous and disperse phases remains constant