proteostasis Flashcards
regulation of proteostasis largely controlled by
access, since degradative enzymes are sequestered into compartments
why does protein degradation matter? (3)
allows cells to respond to changing conditions or stress, ditch misfolded or mutated proteins, and rapidly turn cellular processes on or off
two examples of processes which are acutely regulated by protein degradation
cell cycle progression, response to stimuli
lysosomal degradation is inhibited by
weak bases (ie chloroquine or ammonium chloride
proteosome specific inhibitors
MG-132, etc
EGFR internalization and degradation pathway
ligand binding, internalization by clathrin-coated vesicles, deliver to lysosome for degradation. Receptor down regulation terminates signal
What happens to internalized receptors between the early endosome and the lysosome?
Internalized receptors are incorporated into multi-vesicular bodies - AKA late endosomes
What are vesicles called within the MVBs?
Intra-lumenal vesicles, which bud inward from the surface to the lumen, away from cytosol
What are the coats for ILV formation?
ESCRT complexes
how does HIV recruit ESCRT for its own purposes?
to exit the cell, gag protein something
autophagy
allows cells to break down its own material and dispose of or re-use obsolete parts of the cell itself
autophagy steps (4)
- Starvation signal
- Formation of a double membrane around cytosolic components to form an autophagosome
- Autophagosome fuses with lysosome
- Lysosomal hydrolases break down autophagic body, allowing recycling
Which E is the ubiquitin ligase?
E3
what results in ubiquitin smear
lots of heterogeneity in MW in targeted proteins
26S proteosome made up of what two major structural components
20S core proteolysis, 19S cap regulatory
20S core structure
four 7 membered rings with alpha and beta subunits, proteolyticaly active sites are on the beta subunits and face inside.
T/F. Unfolded proteins can enter proteolytic channel
False, they must be unfolded and threaded through
19s cap roles (3)
Ub receptor binds ubiquitinated proteins
Unfolds protein and feeds into 20S core
Deubiquitinates substrate to recycle
isopeptide
branched polypeptide, ub is linked to substrates through an isopeptide bond
What is recognized by 19S proteosome cap
K48 chain >4
E1-Ub function
Ubiquitin activating enzyme, ATP dependent rxn. Can transfer Ub to E2
E2-Ub function
receive Ub from E1 and eith help of E3 specificity factor conjugate Ub to target proteins
Specificity factor in Ub cascade
E3-ligase
Two classes of E3s
HECT (covalent intermediate) and RING (no covalent intermediate)
Three ways proteins can be recognized for degradation
- Motifs (PEST, destruction boxes)
- Destabilizing N-terminal residues
- Exposed hydrophobic patch (can bind E3 directly, or indirectly thorugh a chaperone bridge)
Three types of ub chains and their distinct fates
- K48 chains direct a substrate to the proteosome
- K63 chains play a role in DNA repair and autophagy
- Mono-ubiquitin plays trafficking roles, ie endocytosis
SCF E3 ubiquitin ligase
cyclin-dependent kinase inhibitor, target is marked for degradation by phosphorylation
APC/C
involved in separating sister chromatids in anaphase, E3 ligase
how are virally infected cells recognized by cytotoxic T cells
they present fragments of viral proteins on Class I MHC molecules, after antigenic peptides are ubiquitinated and digested by the proteasome
ERAD
ER-associated degradation, where misfolded proteins in ER are retro-translocated from ER to cytosol, where they are ubiquitinated on the cytosolic face of the ER membrane and then degraded by proteasome
Mono-ubiquitin as an endocytosis tag leads to degradation where
lysosome
ubiquitin binding domains
motifs within adapter and receptor proteins that bind Ub on cargoes and link them to downstream effectors
how is monoubiquitination related to lysosomal trafficking
Signal to sort cargo into ILVs of MVB
ubiquitin-like proteins
have structural homology, although often no strong sequence homology - Sumo, APG, etc
sumo
nuclear functions, common beta-grasp fold to ub, can be conjugated to lysine via glycine.
why is Ub and UBLs so good at regulating target activity/localization?
- High info content - diverse surfaces available for interactions
- Mono Ub or topologically distinct chains
- Same site can be modified by distinct Ub or Ubl mods
