Lecture #10 - Membrane-less organelles and Phase Seperation Flashcards
(80 cards)
Question in cell biology
How do molecules find each other and preform important reactions (how are biochemical reactions organized)
Ways that cells compartimentailize Reactions
1 - Membrane bound organelles enclosed by phospholipids (Ex. Lysosomes + ER + mitocondria)
- Membrane bround organelles help organize reactions
- Molecules can’t freely diffuse through
2 - Membrane less organelles (Ex. nucelolus + Cajal bodies)
Discovery of MLO
MLO was found BEFORE membrane bound organelles
Example – Drawing by Ramon y cajal –> looked at the nucleus in neurons and saw electron dense structures in the nucleus (among the electron dense structures is the nucleolus and cajal bodies)
How does MLO form?
How MLO form without enclosure of lipid membrane is NOT completely understood
Membrane less organelles (MLO)
MLO = organelle inside the cell that are not enclosed by membranes
Example - P granuals in C. elegans
- When squeeze C.elegans you can see MLO (P granuals) are flowing = resembles a liquid
Types of MLOs
There are many different MLO in a cell
Diagram on slide = see many kinds of MLO
- Example – Nucleolus inside of nucleus + DNA damage foci in nucleus + stress granusl in cytoplasm + P bodies in cytoplasm
Obervations of MLOs
- MLOs have liquid like properties
- Rapid diffsion of components within MLOs
MLOs have liquid like properties Example #1
Example – germ granuals in C. elegans flow and coalece in response to shear stress
P bodies (germ granuals) in c.elegans can flow on the nucelus when squeeze C.elgans + P bodies can fuse to form larger structures –> MEANS P bodies are NOT solid agregates but instead resemble liquid droplets
MLOs have liquid like properties Example #2
MLOs have liquid like properties in frog egg extra system
2 Spherical nucleoli from Xenopus Laevis fuse and form a larger spherical structure –> means that the nucleolus can ALSO have liquid like properties
Observation #2 – Rapid diffsion of components within MLOs
Used FRAP and watch dynamics of molecules
- FRAP = measures diffusion in cells
Results:
Photobleach a fixed flourecnet sample –> THEN there is no recovery because eveyrthing is statinoary (flourescence never comes back)
FRAP on live sample = see florusnce recovery in bleached area then a stationary end point where it stays filled in
- Can see how quickly things are moving (get a diffision coeficiant)
Example FRAP
FRAP can be used to study the dynamics of material within YAP condensates
- YAP = transcription co-activator ; forms condesates when activly signaling
Experiment - fused GFP to YAP and looked at dynamics to show YAP forms dynamic condensates while actively signaling
- After photobleaching YAP floresnce intensity recovers –> recovery indicates that YAP condesates is a highly dynamic structure where YAP is rapdily diffusing in and out of the condensate (because flouressnce from elsewhere can diffuse into the structure)
END - Shows the condestae is a dynamic structure that is actively and quickly exchanging with the surrounding
FRAP on a solid agregate
FRAP on a solid agregate then the flouresnce recovery would have been much slower
Liquid = faster recovery
Phase of MLO
Based on observation (FRAP and live cell imaging) –> know MLO is liquid like structure
Liquids = have transient bonds that form and break to give dynamic structure –> THIS led to the concept that MLO are formed by weak multi valent interactions
Formation of MLO
Overall – MLO are formed by weak multivalent interactions
What determines how spontenous formation of MLO happens
The balance between entropy and enthalpy determines how spontaneous things happen –> have phase seprpations
Phase separation/MLO formation is probably driven by bond energy (driven by enthalpy that will counteract the increase in entropy)
- Entropy = means there is more space in system
If the MLO rapidly coelece into a define structure then it is probably a bond energy/entropy driven process
What kind of binding/energy interaction takes place in MLO/MLO formation
MLO are NOT high affinity macromolecular complexes that rely on interactions with a fixed ratio of molecules (NO fixed stoichemtry in intrecation)
Interaction with Fixed ratio would be Ribosomes intercation with a 1:1 interaction between the large and small SU to form a defined structure
We know that MLO formation is NOT a interaction with fixed stoichemtry because MLO are NOT stable INSTEAD weak multivalent interactions drives MLO interactions
What drives the weak multi valent interactions
Weak multivalent interactions are driven by:
1. Smaller structure interactions that are repeated many times (multivalent proteins)
2. Interactions between disordered protein domains drives multivalent interactions
- 30% of proteome is constitute of disordered regions
- Disorder regions are implicated in forming MLOs
What drives the weak multi valent interactions #1
Weak multivalent interactions are driven by multivalent proteins (repeated structures interact and form MLO)
Experiment – In a test tube they made synthetic structured domains between SH3-PRM –> mixed repeated domain together
- SH3 and PRM meidate weak interactions in and of itself BUT when mix repeat domain together in test tube they form a droplet like structure
- Formation of droplet structure = indicates weak multivalent interactions can form MLOs
- Droplets ALSO have liquid properties where droplets can fuse with neighboring droplets
What drives the weak multi valent interactions #2
Intrinsically disorder regionsare also implicated in forming MLOs
Intrinsically disordered proteins = proteins that do NOT form defined 3D structures
- Intrinsically disorder domains = noodle like domains
Despite lacking 3D structures these proteins still carry out diverse biologic functions
When mix disordered 3D domains = can form liquid like structures
What interactions might mediate MLO formation (Molecular forces implicated in MLO formation)
Slides = almost all kinds of amino acids interactions might be involved in forming MLOs (DON”T MEMEORIZE)
Example – Cation-pi interactions OR Structured domains such as coil-coil might mediate condensate formation
Looking at different proteins structures –> can allow you to discover new interactions that meidate MLO formation
Implication of MLO having liquid like properties
MLO having liquid like properties implicates there is a phase transition processes occurring
Start -
1. Protein that is diffusely localized in a cell might be a gas like phase (one-phase regime)
2. After gas phase –> when have an increase in concentration of a protein or a specific perterbation put into the cells then you can change the local concentration of the protein –> NOW can have a gas to liquid transition and can now form a liquid MLO (2 phase regime)
- Proteins undergo the gas to liquid transition
- 2 phase regime = co-existing phase of liquid AND gas
3. After 2 phase regime –> IF you further increase the concentration or add a different pertuvation then could enter a liquid like phase (protein enters a liquid like phase?)
Can draw a phase diagram based on in vitro data
Phase diagram
In vitro can make a phase diagram by changing the protein concentration or doing a specific pertuvaion of the protein to cause the protein to go from gas phase a 2 phase regime
- Get 2 phase regime when increase the concentration
Phase seperation helps in thinking about how MLO forms in vitro and in cell (BUT STILL a question if phase sepration is what is forming the MLO inside of a cell)
Answer:
- Free transition of molecules without transporters
- Quick regulation of processes (revrsible)
- STILL have rapid exchange of molecules and if there are reactions you can have fatser export of product in process
Functions of phase separation and forming an MLO
- Bring together enzymes and substrates
- Sequesting
- MLO structures can be an organizational hub that can form a structure that is important for function
- NO role in reactiions ; instead organizational hub