What is the relationship between secondary structures, motifs, domains, and tertiary structure in protein folding?
Protein folding is hierarchical: Polypeptide first folds into secondary structures (α-helices, β-strands). Secondary structures combine into motifs (distinct 3D structures, e.g., Helix-Turn-Helix, Zinc Finger, EF-hand). Motifs group into domains (functionally or structurally distinct regions, e.g., Domain III AAA+ ATPase of DnaA). Domains form the tertiary structure, which is the overall 3D conformation.
What are unstructured regions in proteins?
Regions without a fixed structure that are flexible; most proteins contain them.
Example: DnaA.
What motifs exist in DnaA Domain III and IV?
Domain III: Walker A, Walker B, and other motifs for ATP binding and hydrolysis. Domain IV: Helix-Turn-Helix and Basic loop motifs for DNA binding.
How does proline influence protein folding?
Proline can isomerize between cis and trans configurations, which can dramatically alter protein structure and affect activity. Peptidyl-proline isomerases (PPIases) speed up this process.
What drives hydrophobic residues to be buried in the protein core?
The hydrophobic effect: water molecules form constrained cages around hydrophobic residues; burying them reduces entropy loss, driving folding. Misfolded proteins often expose hydrophobic patches.
What is the function of chaperones?
Chaperones assist folding of newly made or misfolded proteins, prevent aggregation, and refold proteins. If refolding fails, proteins may be degraded.
What are the 5 steps of the Hsp70 ATPase cycle?
- Protein Binding (Open, ATP-bound): Substrate binds Hsp70 at substrate-binding site. 2. ATP Hydrolysis → ADP + Pi: Hydrolysis drives conformational change. 3. Clamping/Folding (Closed, ADP-bound): Hsp70 clamps tightly on substrate; misfolding blocked; substrate explores conformations. 4. Nucleotide Exchange (ADP out, ATP in): Hsp70 returns to open form. 5. Protein Release / Reset: Substrate released to fold independently; cycle repeats if folding incomplete.
What is the general architecture of GroEL/GroES?
GroEL: two stacked rings (7 subunits each); GroES: lid (7 subunits); creates central upper and lower chambers for protein folding.
What are the 4 steps of the GroEL/GroES cycle?
- Protein Entry & ATP Binding / Lid Exchange: Unfolded protein enters upper chamber; bottom chamber capped by GroES; ATP enters; bottom lid detaches; ADP + Pi released. 2. Upper Chamber Closure & Folding: ATP enters; GroES lid closes upper chamber; protein folds inside. 3. ATP Hydrolysis (Slow Step) / Opposite Chamber Activation: ATP hydrolyzed → Pi released; protein remains inside; ATP binds opposite chamber; new GroES lid attaches → both chambers capped. 4. Lid Release & Protein Exit: ADP leaves; upper chamber lid detaches; folded/partially folded protein exits; cycle repeats if needed.
What triggers protein degradation?
Proteins that cannot be properly refolded by chaperones/chaperonins are tagged for degradation.
What is ubiquitin?
Small protein (76 aa, 8.6 kDa) that becomes covalently linked to lysine residues of target proteins.
What is the ubiquitin conjugation process?
- Ubiquitin carboxyl terminus activated. 2. Transferred to E3 ubiquitin ligase, which recognizes specific cytosolic target proteins (~600 E3 in humans). 3. Polyubiquitinylation: multiple ubiquitins attached (≥4) at exposed hydrophobic residues. 4. Polyubiquitin-tagged proteins recognized by proteasome Ub receptors. 5. Deubiquitinases (DUBs) recycle ubiquitin. 6. ATPase-driven auxiliary proteins unfold protein and feed into proteasome.
How are proteins digested inside the proteasome?
Polypeptides cleaved into 2–24 aa fragments; fragments further degraded to single amino acids; peptide bonds of hydrophobic, acidic, and basic residues are cleaved.
When does protein aggregation occur?
If proteins are misfolded and the degradation system is imperfect, aggregates form. Aggregates can be amorphous or organized (e.g., amyloid fibrils).
What are amyloid fibrils?
Long filaments formed by short β-strand segments (6–12 residues) stacked perpendicular to the fibril axis; often associated with Alzheimer’s, Parkinson’s, and prion diseases.
