Protein folding, misfolding and degradation

Lecture 4

What is a motif?

the combination of two or more secondary structures that form a distinct 3-D structure

What is a domain?

distinct regions of the proteins structure that represent a particular function, structure or relationship with the rest of the protein

How does a protein fold?

Polypeptide first folds into regions with secondary structures → secondary structure elements group into motifs → then into domains → then tertiary structure

What does an a rotating on its axis allow?

since it can rotate in itself it can create new interactions and folding → can change conformation in primary structure 

How do most amino acid residues orient themselves in the polypeptide chain? Cis or trans? What is the case with proline?

Cis usually → in the case of proline it takes a cis conformation due to its ring 

How does proline help direct protein folding?

Isomerization between the trans and cis configurations can occur spontaneously but its slow

If proline is present it can attract and enzyme that can speed up the process

Isomerization of the proline can dramatically change the structure and activity if the protein

Does protein folding start right away?

Yes - aa can fold on themselves with small changes in orientation of proteins which allow them to twist and turn

In a test tube proteins can fold which shows that the information for structure is within the sequence 

What defines a misfolded protein?

Anything that deferred from the hydrophobic oil drop model

What helps proteins fold and how?

Chaperones - they help guide the folding by recognizing hydrophobic residues that stick out 

Happens during INC temp → fever and inflammation

What else can chaperones do?

they can help disassemble protein aggregates to ensure they don’t continue to fold and become harmful

How do chaperones get the energy to work?

ATP-dependent cycles of binding stabilizes the folding

What is the main chaperone found in humans and how does it work?

Hsp70 → as a new protein emerges from the ribosome it isn’t fully folded → Hsp70 recognizes it and binds to its hyrdophobic stretches which should be buried inside 

the hydrolysis of ATP allows the folding to proceed

The cycle can repeat until the protein is properly folded 

What are chaperonins? 

They are large complexes that isolate unfolded proteins

Explain the chaperonin GroEL

GroEL + GroES combined from a folding chamber where misfolded proteins can fold without aggregating 

How does the GroEL+GroES chamber work?

1. Captures the misfolded protein

2. GroES binds on top closing the chamber to isolate the protein (reduces aggregation)

3. Inside protein folds properly 

*ATP driven cycle 

*proteins can go through multiple rounds but the protein must be caught again

*works for smaller proteins

What happens to proteins if they can’t be folded properly?

they are tagged from degradation

What is the ubiquitin/proteasome system?

poly-ubiquitin takes damaged or misfolded proteins for degradation

What does Ubuquitin link to and how?

it gets covalently linked to the lysine residue of the target protein

Explain the Ubiquitin conjugating system

there are 3 enzymes used in tagging:

E1 - activating enzyme (activates the system by binding to the first tag)

E2 - conjugating enzyme (takes over the place of E1)

E3 - ligase (bring the ubuquitin complex and the protein together - covalently links to the lysine side chain of the target protein)

What does polyubiquitinylation do?

marks proteins for degradation → ubiquintin is added multiple times so the proteosome recognizes that the protein needs to be degraded

Uses ATP to cut up protein into peptides

What are the pathways a protein can take regarding folding

• Folds correctly without help

• Folds correctly with help of chaperone

• Does not fold correctly and is digested by proteasome

• Becomes a protein aggregate because it can’t be degraded or helped by the chaperone

What is protein aggregation?

misfolded proteins or incompletely degraded proteins interact with each other to hide their hydrophobic residues (no specific shape formed)

What are amyloid fibrils?

Amyloid fibrils are made of beta sheets and are highly organized 

When they are misfolded the hydrophobic residues are exposed and can interact to form an aggregate which can cause a lot of diseases and damage like disrupt membranes 

They are resistant to degradation due to their strong structure held by hydrogen bonds