23 - Regulated Protein Degradation Flashcards
True or false: protein degradation refers to only ending a process
False: protein degradation can be used as actuators of cell signaling
What is (generally) the most common way to transmit signals in the cell?
Post-translational modifications
What is the most drastic post-translational modification?
Proteolysis
What is proteolysis?
The process of breaking peptide bonds
What are the products of protein degradation (generally)?
Either smaller peptides, or single amino acids
True or false: proteolysis is the only process of breaking peptide bonds
False: protein cleavage can also break peptide bonds
What is protein cleavage?
Breaking peptide bonds at specific sites to create functional domains
True or false: protein cleavage is highly regulated
True: protein cleavage is highly regulated and occurs at very specific locations
What is the typical structure of a cleavage protein?
Long extracellular domain, small transmembrane domain, little or none intracellular domain
What can proteolysis or protein cleavage be used for?
- Degrade proteins to eliminate their activity at specific times and locations
- Generate active enzymes or signaling molecules from longer, inactive precursors
How does proteolysis differ from other post-translational modifications?
It is mostly irreversible
How are other post-translational modifications (besides protein degradation) reversible?
- Ion channels can open / close
- Phosphorylation can be added or removed
- Acetylation of histones can be added or removed
How could protein degradation be “reversed”?
Through translation of the protein
How come protein degradation is called “irreversible”, if it can be reversed by translation?
Translation is a very slow process, so it takes significant time to reverse protein degradation
What are some cell activities that require regulated proteolysis?
Control of the cell cycle, apoptosis, development, growth, survival, etc.
For what types of signaling would protein degradation be the most useful?
When the cell wants to make a committed decision to change its state (instead of reverting back to its starting state)
What are examples of irreversible commitment steps?
Cell cycle, apoptosis, and development/morphogenesis
How is the cell cycle an irreversible commitment step?
It needs to proceed in an orderly fashion from one step to another
How is apoptosis an irreversible commitment step?
It must proceed to completion once initiated
How is development/morphogenesis an irreversible commitment step?
Cells must make irreversible decisions to acquire a specific cell fate
True or false: proteolysis can only be used for irreversible commitment steps
False: it can also be used for reversible commitment steps
How can proteolysis be used for a reversible commitment step?
It can activate signaling or other cellular events, which can be reversible
What family of proteins mediate degradation or cleavage?
Proteases
What do proteases do?
Hydrolyze the peptide bonds of proteins
What are proteases?
Proteins that mediate degradation or cleavage of other proteins
True or false: proteases are evolutionarily conserved
True: they are important for cell function, and thus are highly conserved
What are the functions of proteases?
- Achieve housekeeping functions
- Eliminate proteins no longer needed
- Cleave proteins to create other functional proteins
What is meant by “achieving housekeeping functions” (for proteases)?
Need to break down food for energy and biosynthesis
Why would proteins no longer be needed (for proteases)?
They are damaged or no longer needed in that specific location
How are many signaling proteins generated at the cell surface?
As inactive precursors
How can inactive precursors at the cell surface become active?
Through cleavage (control their activation)
How are proteases classified?
Based on their reaction mechanism
What are the different classifications of proteases?
Metalloproteases, and proteases categorized based on a central amino acid in their active site
What are metalloproteases?
Proteases that contain a metal ion (zinc, cobalt) in their active site
What are some examples of proteases categorized based on a central amino acid in their active site?
Serine proteases, cysteine proteases, and aspartyl proteases
Besides their reaction mechanism, how can proteases be further classified?
By their substrate specificity
How are most proteases synthesized?
As an inactive precursor (zymogen)
What is a zymogen?
An inactive precursor of the protease
Why are proteases synthesized as zymogens?
The cell does not want active proteases running around the cell at all times
How are zymogens activated?
Through protein cleavage
What signals can activate zymogens?
Extracellular signals
True or false: a protease can activate its own zymogen
True: this creates a positive feedback loop for a rapid response
Which steps of protease activation are irreversible?
- Activation of enzymes from inactive zymogens
2. Proteolytic degradation of proteins
True or false: protein degradation offers a unique temporal feature of cell signaling
True: based on its irreversible nature, it offers unique temporal features
What are the unique temporal features of protein degradation in cell signaling?
Degradation occurs rapidly, but translation occurs slowly
How can protein degradation or cleavage be used to sculpt signaling (5 ways)?
- Secretion of an extracellular ligand upon cleavage of a membrane precursor
- Activation of cell-surface receptor upon cleavage
- Removal of cell-surface receptors to down-regulate their signaling
- Degradation of damaged/”old”/inactive proteins (signaling attenuation)
- Degradation of proteins at specific cellular locations to localize signaling
What is an example of secretion of an extracellular ligand upon cleavage of a membrane precursor?
Neurotrophins such as BDNF
How is BDNF (and other neurotrophins) secreted into the extracellular space?
As immature proteins (pro-BDNF)
How is pro-BDNF activated?
By specific cleavage
What is the importance of the signal peptide in pro-BDNF?
It trafficks pro-BDNF to be secreted by the cell
True or false: only mature BDNF can generate signaling
False: pro-BDNF can also generate signaling
What is an example of activation of cell-surface receptors upon cleavage?
Notch-Delta signaling
When is Notch cleaved?
When it binds to its ligand delta
What type of protein is delta?
A cell surface ligand
What happens when Notch is cleaved?
The intracellular domain goes to the nucleus to regulate gene expression
What type of protein is Notch?
A cell surface receptor
What is signaling attenuation?
Reducing the strength of the signal
How can signaling attenuation be achieved?
By down regulating cell surface receptors through proteolysis
Why would a cell use protein degradation for localization?
They may not have other mechanisms, such as scaffold proteins, to accomplish this
How can protein degradation be used for localization?
They can degrade proteins in areas where they shouldn’t be acting, thus restricting their activity to specific locations in the cell
What are the (3) roles of metalloproteases?
- Degrade ECM proteins to regulate migration
- Generate active signaling molecules (ligands) from large precursors
- Cleave receptors for their activation or down regulation
What does MMP stand for?
Matrix metalloprotease
What does ADAM stand for?
A disintegrin and metalloprotease
True or false: MMPs are found at the cell surface
False: they are found in the intracellular space
How come MMPs are not found at the cell surface?
They have no transmembrane and intracellular domain
True or false: ADAMs are found at the cell surface?
True: they are anchored to the cell membrane
How come ADAMs are found at the cell surface?
They have a transmembrane and intracellular domain
For most metalloproteases, which domain is the largest?
The extracellular domain
How are MMPs and ADAMs synthesized?
As inactive precursors (zymogens)
How are MMPs and ADAMs activated?
Through cleavage events
True or false: MMPs are only active during development
False: they are active all throughout life for cell migration
Besides development, what is an example of a process that require MMPs?
Wound healing
Which metalloproteases are anchored at the cell surface?
ADAMs
Which metalloproteases are secreted by the cell?
MMPs
What do ADAMs do?
Cleave membrane-associated proteins at the cell surface (ectodomain shedding)
What is ectodomain shedding?
The cleavage of membrane-associated proteins at the cell surface
How can ADAMs promote signaling?
By releasing an active ligand
How can ADAMs regulate signaling?
By cleaving the extracellular ligand-binding domain of a receptor
What is another name for ADAM-17?
TACE
What is another name for TACE?
ADAM-17
What is one substrate of TACE?
EGF
What does TACE stand for?
Tumor necrosis factor-alpha-converting enzyme
True or false: the only substrate of TACE is EGF
False: TACE has a wide range of substrates
What happened when TACE was deleted in cells?
It had similar phenotypes to EGFR mutations
How does TACE interact with EGFR?
TACE cleaves pro-EGF to release it and allow it to bind to EGFR
In what mechanisms is TACE important for?
Juxtacrine signaling, and establishment of a gradient
Why is the TACE mechanism important for juxtacrine signaling?
It generates localized signaling, so only the cells in the vicinity respond to it
What is juxtacrine signaling?
Signaling to the same or neighboring cells
How can the TACE mechanism lead to a gradient of cues?
Cues can diffuse away from the cell to create a gradient
How is EGF synthesized?
As an inactive cell surface protein
What happens if a protease is absent?
The downstream signaling of that extracellular cue is also absent
What can be done to rescue the deletion of a protease?
Need to activate the pathway genetically or pharmacologically
How do cells influence axon pathfinding?
They can present cell surface ligands to help guide the axon
What axon guidance cues are found on the cell surface?
Ephrins
What receptors bind to ephrins?
Eph receptors
What type of signaling do ephrins mediate?
Repulsive (sometimes attractive) signaling
What is meant by “ephrin bi-directional signaling”?
Ephrins can also act as receptors, and transmit signals when binding to an Eph ligand
What type of proteins are Eph receptors?
RTKs
What are topographic maps?
Precise innervations of axons from specific neurons in one tissue to another
What is the RetinoTectal projection?
The patterning of axons from the retina (eye) to the tectum
What is the tectum?
The part of the brain (in chickens, frogs, and fish) responsible for auditory and visual response)
What brain structure in humans is analogous to the tectum?
The visual cortex
If an axon is anterior in the retina, where will it be found in the tectum?
More posterior
If an axon is posterior in the retina, where will it be found in the tectum?
More anterior
If an axon is posterior in the tectum, where did it originate in the retina?
More anterior
If an axon is anterior in the tectum, where did it originate in the retina?
More posterior
What is the gradient of Eph receptors in the retina?
Lower anterior to higher posterior
What is the gradient of ephrins in the tectum?
Lower anterior to higher posterior
How come axons that start more anterior in the retina end up more posterior in the tectum?
They have less Eph receptors, so they are less affected by ephrin signaling
How come axons that start more posterior in the retina end up more anterior in the tectum?
They have more Eph receptors, so they are more affected by ephrin signaling
Which region of the RetinoTectal projection has a gradient of Eph receptors?
The retina
Which region of the RetinoTectal projection has a gradient of ephrin?
The tectum
What does “anterior” refer to?
Front
What does “posterior” refer to?
Back
