Protein Folding and Degradation

Post Translational Targeting

Proteins delivered to destination after translation completes. Done for cytosolic proteins and typically have targeting sequences for their destination

Co-Translational Targeting

Proteins are delivered to ER during translation

Note: All translation starts on free ribosomes, but once a specific sequence at the beginning of the mRNA is seen, it will send it to the ER to continue translation

Where is 3D structure info usually found

In the primary sequence

Something (but not molecules) that inhibits renaturation of proteins

Lack of space (due to how crowded the cytoplasm is). Would cause aggregation of proteins

Chaperones

Proteins that assist other proteins in folding, re-folding, and going to the correct place to have correct function. Shields hydrophobic parts of proteins while in cytosol/hydrophilic areas and monitors correct disulfide bond formation + correct glycosylation

Heat Shock Proteins

Type of chaperones that are synthesized more when there are increases in temperature. This is due to the issue that increase in heat means proteins are more likely to be misfolded and to prevent that you want more chaperones

Chaperones are a type of….

ATPase, since they catalyze hydrolysis to change their shape for their activity

First Step in Chaperone Function

ATP binds to Hsp70, opening lid

Second Step in Chaperone Function

Co-chaperone Hsp40 delivers unfolded protein to Hsp70

Third Step in Chaperone Function

Binding of Hsp40 to Hsp70 stimulates ATP hydrolysis, closing the lid

Fourth Step in Chaperone Function

After a bit, NEF exchanges ADP for ATP, re-opening the lid

Fifth Step in Chaperone Function

Resulting protein is either correctly folded or incorrectly folded; NEF leaves

Chaperonins

Larger chaperones that protect and isolate the protein from the crowded cytosol to give it space to fold within its hydrophilic chamber. Uses 2 ATP

GroEL

A chaperonin in bacteria made of heptamers and has two sites to assist protein folding (requires 6-7ATP)

GroES

A co-chaperoning for GroEL that is the lid for the chaperonin

How GroEs and GroEL work

The unfolded protein interacts with the hydrophobic residues of GroEL heptamers to enter the chamber with the use of 6-7 ATP. GroES caps the cylinder and later hydrolysis causes lid to eject the folded protein

Hsp90

A chaperonin in mammals made of two subunits (requires 1 ATP)

How HSP90 works

Unfolded protein enters between the two Hsp90 subunits and ATP binds to the NTD site to “close” the p23 lid. Later ATP hydrolysis causes lid to open and folded protein comes out

BiP

A chaperone in the ER lumen to help protein into lumen during translation and prevent folding until translation is finished and the protein is fully within the lumen

Protein Disulfide Isomerase

A chaperone located in the ER lumen that is both a reductase and isomerase to make the disulfide bridges in the protein. Prefer the ER lumen because of its oxidizing environment that can replenish it after being reduced

ER Oxidoreductin 1

Enzyme in the ER lumen that regenerates Protein Disulfide Isomerase that were reduced

Peptidyl Prolyl Isomerase

A chaperone expressed in multiple places to isomerize proline in proteins

FKBP

A peptidyl prolyl isomerase chaperone found in the ER

Cyclophilin B

A peptidyl prolyl isomerase chaperone found in the ER. Not to be confused with Cyclophilin A

Cyclophilin A

A peptidyl prolyl isomerase chaperone found in the cytosol and is the most abundant peptidyl prolyl isomerase chaperone

Parvulins

A peptidyl prolyl isomerase chaperone found in the cytosol and nucleus

Trait of cis-proline

It is compact

Trait of trans-proline

It has kinks and largely used in collagen. It’s a preference of most molecules because it is more stable than cis-proline

Ubiquitination

Adding a ubiquitin to a protein to signal degradation. Typically for proteins that no matter what were not folded

UPR Pathway

Primary degradation pathway

How UPR Pathway works

Sensors IRE1, ATF6, and PERK, in the ER membrane bind to the excess misfolded proteins, triggering a downstream pathway to suppress genes for translation and activate genes for chaperone synthesis, lipid synthesis to expand ER, and protein degraders (ERAD proteins)

ERAD Pathway

The second pathway if all else fails. Exports misfolded proteins through the retrotranslocon to the 26S proteosome in the cytosol. If there are aggregates of misfolded proteins, it starts autophagy

How autophagy works

A phagophore encapsulates several things at once and fuses with lysosomes to degrade everything inside until the cell is destroyed

Phagophore

A double membrane bilayer used in autophagy

The AA where ubiquitination occurs

Lysine

Components of the Ubiquitin Proteasome

• 19S regulatory particle to control what goes in and out. Delivers misfolded protein to core and unbinds ubiquitin for reuse

• 20S core particle that contains enzymes for digesting the misfolded proteins

E1

Ubiquitin ligase that accepts ubiquitin by hydrolyzing ATP to AMP. Passes ubiquitin to E2

E2

Ubiquitin ligase that holds it and forms complex with E3 to later transfer to the misfolded protein

E3

Ubiquitin ligase that binds to E2 and misfolded proteins