21 - Signaling Scaffolds and Cross-Talk Flashcards
In fibroblasts, what does sustained ERK signaling lead to?
Proliferation
In fibroblasts, what does transient ERK signaling lead to?
Quiescence
In PC12 cells, what does sustained ERK signaling lead to?
Differentiation
In PC12 cells, what does transient ERK signaling lead to?
Proliferation
In yeast, what does sustained ERK signaling lead to?
Filamentous growth
In yeast, what does transient ERK signaling lead to?
Mating
How does cAMP function in the ERK pathway?
It inhibits Raf-1 and activates B-raf
Does cAMP lead to sustained or transient ERK activation?
Sustained ERK activation
What is MP1?
A signaling scaffold protein bound on the signaling endosome
Where is MP1 found?
At the endosome
Which proteins bind to MP1?
MEK, ERK, and p14
What is KSR?
A signaling scaffold protein bound at the cell membrane
Where is KSR found?
At the cell membrane
Which proteins bind to KSR?
Raf-1, MEK, and ERK
What type of signaling is MP1 associated with?
Sustained ERK signaling
What type of signaling is KSR associated with?
Transient ERK signaling
Which scaffolding protein works on cytosolic targets?
KSR
Which scaffolding protein works on nuclear targets?
MP1
What is the advantage of KSR?
Brings Raf, MEK, and ERK together at the cell surface in proximity of Ras for specific signaling
Where is Ras found in the cell?
At the cell surface
True or false: signaling scaffolds allow for signal amplification
True: they can amplify the signal, even in the presence of phosphatases
How can signaling scaffolds lead to signal amplification?
They can block the proteins from being inactivated (blocking phosphatases)
How does ERK interact with KSR?
It can phosphorylate the site where Raf binds, preventing it from binding to the scaffold
What is the significance of the ERK interaction with KSR?
Allows for a timer function of the scaffolding system to turn on or off
What happens if KSR is mutated to not have pERK sites?
There will be sustained ERK signaling
How come mutation of KSR to the pERK sites leads to sustained ERK signaling?
There is no timer function to stop Raf from signaling to ERK
What happens to 14-3-3 in non-stimulated cells?
They keep KSR and Raf in the cytoplasm, and block the catalytic A and C units
What happens to 14-3-3 in stimulated cells?
They displace, allowing KSR and Raf to localize to the cell membrane, and allow the A and C units to lead to MEK/ERK signaling
What is 14-3-3?
A scaffold protein for KSR and Raf
What does the PH domain bind to?
PIP3
What proteins are brought together by PH domains?
PDK1 and Akt
True or false: PIP3 is not a second messenger
False: it is a structural organizing center
How does Akt get activated?
By binding to PIP3, exposing Thr308, which can be phsophorylated by PDK1
Which enzyme turns PIP2 into PIP3?
PI3K
Which enzyme turns PIP3 into PIP2?
PTEN
What happens if PH domains are disrupted?
This can lead to oncogenic activation of Akt
What is Gab1?
An organizing molecule (similar to PIP3)
What molecules can bind to Gab1?
PLC-gamma, PI3K, SOS, GRB2, and the receptor
What effects can be mediated by Gab1?
Cell proliferation, adhesion, motility, and survival pathways
What pathways can be mediated by Gab1?
Ras/Ref/MEK/ERK, Ras/Rac/PAK, FAK, and Akt/mTOR
True or false: Gab1 can only mediate sustained MAPK activation
False: it can also mediate transient MAPK activation through Ras
True or false: Gab1 can only mediates transient MAPK activation
False: it can also mediate sustained MAPK activation through SRC and PLC-gamma
How does Gab1 create a positive feedback loop?
It recruits more PI3K, leading to more PIP3, leading to more recruitment of Gab1
What were the first anchoring proteins described?
AKAPs
What does AKAP stand for?
A kinase anchoring protein
What proteins binds to all AKAPs?
PKA
What is the purpose of the many isoforms of AKAPs?
They localize at different areas of the cell
What are some examples of subcellular locations where AKAPs can localize PKA?
Nuclear membrane, centrosome, golgi, etc.
Besides PKA, what can AKAPs localize?
Different signaling components downstream or upstream of that specific PKA
What is the relationship between AKAPs and cAMP?
Each AKAP has a specific regulation on a local loop of cAMP
How can AKAPs bind many different signaling components together?
They have different binding sites for effectors, PDEs, and PKA
True or false: there are few diseases that involve a mutated AKAP
False: there are a variety of diseases associated with mutated AKAPs
How specific are diseases involving AKAP mutations?
Tissue specific and substrate specific
How can AKAP mutations in cardiomyocytes lead to cardiovascular disease?
This can prevent the cardiomyocyte from releasing calcium properly, reducing the effectiveness
How can AKAPs lead to convergence of signaling?
AKAPs can bind to both PKA and PKC, leading to a convergence of signaling
How can AKAPs lead to crosstalk?
They can bring together various kinds of signaling molecules that have common substrates
What is an example of crosstalk mediated by AKAPs?
PKA and PKC can both interact with calcium/calmodulin or the muscarinic receptor, leading to crosstalk
What does ARMS stand for?
Ankyrin repeat-rich membrane-spanning scaffold protein
Where are ARMS found?
Embedded within the cell surface
What proteins can bind to ARMS?
The cytoskeleton, Trk endosomes, and FRS2 (sustained ERK activation)
How can ARMS regulate synaptic transmission?
By bringing together Trk, ephrin, and AMPAR receptors
What is the structure and function of ARMS?
Large scaffold proteins to bring many things together
What does PSD-95 stand for?
Post synaptic density 95
What is PSD-95?
A scaffold protein found at the post synaptic density
True or false: there are no diseases associated with mutation of PSD-95
False: there are a variety of diseases associated with mutation of PSD-95
What are pleiotropic kinases?
Kinases that have multiple different functions
How can scaffolds interact with pleiotropic kinases?
They can direct them to one specific pathway/function
True or false: a scaffold protein cannot be an activating kinase
False: NIK functions as both an activating kinase and a scaffold protein
What is the importance of the multiple domains in scaffold proteins?
Specificity and modularity
What is meant by signaling pathways converging?
Signals from unrelated receptors can converge to activate a common effector
What is meant by signaling pathways diverging?
Identical signals can diverge to activate a variety of effectors
What is meant by signaling pathways crosstalking?
Signals can be passed back and forth between pathways as a result of crosstalk
What is an example of crosstalk (with EGF and adrenaline)?
EGF and adrenaline can both converge onto CREB, with interactions between the pathways at Raf
How can AC be a source of crosstalk?
In neurons, some AC need calcium to function
What is an example of crosstalk in muscle fibers?
Phosphorylase kinase (activated by the adrenaline pathway) also needs calcium to function
How has modern biology interacted with computational work?
Can be used to understand how large systems function within the cell
What levels of networks are there (from highest to lowest)?
Organ/tissue networks, cellular networks, and molecular networks
What questions (3) can be asked in network biology?
- How does a cell determine the final output?
- How do different cells translate differently?
- What does this imply for pharmacology?
What questions (2) can be asked about drug use and networks?
- How does a cell in a dish translate to a cell in the body?
- How can off target effects be minimized?
What are two strategies to study a molecule in a signaling network?
Looking at all the intermediates, or an input and output (with core processes and system control)
What is the purpose of studying system controls in a network?
Can understand how perturbations of intermediates can affect the entire pathway
True or false: three proteins arranged in the same network will have the same behavior
False: based on rate constants, the behavior can vary widely
What are the different types of behaviors a negative feedback loop can have?
Steady state, drop to zero, oscillating, and dampened oscillations
How does a threshold level affect a network?
Initial conditions below the threshold drop towards zero, while initial conditions above the threshold reach a steady state
What determines the behavior of a negative feedback loop?
The rate constants of how the proteins interact with each other
What is systems biology?
The study of different hierarchies of networks, and the relationships between the different levels of networks
What is at the bottom of the systems biology triangle?
Genes, mRNA, proteins, and metabolites
What is at the top of the systems biology triangle?
Large-scale organization
What is in the middle (closer to the bottom) of the systems biology triangle?
Regulatory motifs and metabolic pathways
What is in the middle (closer to the top) of the systems biology triangle?
Functional modules
As you move up the systems biology triangle, what increases?
Universality
As you move down the systems biology triangle, what increases?
Organism specificity
What are the different (4) viewpoints of analyzing signaling networks?
- View from a particular input and analyzing the entire network as a stand alone system
- View from interactions between similarly acting inputs
- View from a particular signaling component and combining mini-networks of components
- View of the entire system
What is an example of viewing a network as a stand along system with a particular input?
Studying neurotrophins and their pathway in the cell
How can boundaries be established in a stand alone network?
Based on their functionality (PI3K, cytoskeleton, calcium, etc.)
What is an example of viewing a network as interactions between similarly acting inputs?
Studying RTKs and the commonalities between them
What is an example of viewing a network as a particular signaling component and combining mini-networks?
Studying just Rab1 signaling, and every interaction that it is involved in (inflow and outflow)
What is an example of viewing a network as an entire system?
Studying hairballs that represent cellular signaling pathways
What are hairballs?
Big tangled networks of signaling components
What is the controversy surrounding hairballs?
They may be interesting computationally, but not biologically
What is the goal of studying hairballs?
Create global networks that can take into account time and space differences
What is the consequence of having nonlinear functions between proteins, genes, the environment, etc.
The relationships need to be simplified
What is a diseasome?
An overlap between a gene network and a disease phenotype network
What is the purpose of a diseaseome?
See how different genes and proteins interact in different diseases
