PROTEIN FOLDING AND DEGRADATION

Kanokporn Boonsirichai

Proteins must fold up into their unique 3-D conformation To be able to perform their

specific function To assemble correctly with

other proteins To bind with small-molecule

cofactors that are required for their activity

To be appropriately modified by protein kinases or other protein-modifying enzymes

When a protein folds:

Most of its hydrophobic residues are buried into an interior core.

A large number of noncovalent interactions are formed.

The final conformation is usually of the lowest free energy.

Proteins begin to fold as they exit from the ribosome

Secondary structures are formed and aligned roughly within a few seconds

“Molten globule”

Side-chain adjustment (slow) to form the appropriate tertiary structure

Cytochrome b562

By the time it is released from the ribosome, much of the folding has already been completed.

Molecular Chaperones

A class of proteins which mediate protein folding

Heat-Shock Proteins (Hsp)

Firstly identified in E. coli

Increased synthesis at elevated temperature (42oC)

What happens at elevated temperature? Why does the cell need more chaperones?

Heat-Shock Proteins (Hsp)in Eucaryotes

Two major families: Hsp60 and Hsp70

Members are organelle-specific: cytosolic, ER-associated, mitochondrial

Work with their own set of assiciated proteins

Show an affinity for exposed hybrophobic patches

Hydrolyze ATPs

Hsp70

• Works with Hsp40

• Performs its function as the target protein is being translated

• Binds to a string of seven hydrophobic amino acids

• Hydrolyzes an ATP as it binds; releases ADP and rebinds ATP as it dissociates

Hsp60 (Chaperonin)

•Acts after its target protein has been fully synthesized.•Provides a favorable environment for the target protein to refold.•Binding of ATP and GroES may transiently stretch the misfolded protein.•ATP hydrolysis triggers the release of the target protein.

Choices of Protein Quality Control

Proteasome A machinery for protein destruction An abundant ATP-dependent protease (= 1% of

cellular proteins) Found in the cytosol and the nucleus

Only marked proteins are targeted to the proteasome

Ubiquitin•A 76-amino-acid tag•Activated through a high-energy thioester linkage to a cysteine residue•Is transferred to the lysine residue of the target protein

biology.caltech.edu/Members/Deshaies

~ 30 distinct kinds

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100

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ds•E3 recognizes specific degradation signals in the target proteins.•Multiubiquitin chain is recognized by the proteasome.

Targets

•Denatured/ misfolded proteins

•Proteins with oxidized/ abnormal amino acids

Regulated Destruction of Proteins

Some proteins turn over rapidly at all time.

Some proteins are stable most of the time but become unstable under a certain condition.

Mechanisms

•Activation of specific E3

•Activation/ exposure of the degradation signal in within the target protein

Activation of Ubiquitin Ligase

Activation of Degradation Signal

Abnormally folded proteins may form protease-resistant aggregates

•Some protein aggregates form a fibril structure

•Cross-beta filaments: layered of polypeptide chains with continuous stacks of beta sheets

Prion disease

Protein-aggregates-induced Diseases

Huntinton’s disease Alzheimer’s disease

Creutzfeldt-Jacob disease (CJD) in humans

Bovine spongiform encephalopathy (BSE) in cattle (i.e. mad cow disease)

Prion diseases

Regulation of cellular protein levels can occur at many different points

•Transcription

•RNA processing

•RNA transport

•Translation

•Protein degradation