Protein folding dynamics, Hydrophobic collapse, hierarchical process, free energy funnel, Assisted Folding, Hsp70, Hsp70, Hsp40 (DnaK, DnaJ) mechanism, Chaperonins, Protein disulfide isomerase, GroEL, GroES

1. Protein Folding

2. As hierarchical process
• Local secondary structures form first
• This is followed by longer-range interactions
• The process continues until complete domains
form and the entire polypeptide is folded

3. Hydrophobic collapse
• Folding is initiated by a spontaneous collapse of
the polypeptide into a compact state, mediated
by hydrophobic interactions among nonpolar
residues
• The state resulting from this “hydrophobic
collapse” may have a high content of secondary
structure
• But many amino acid side chains are not entirely
fixed
• The collapsed state is often referred to as a
molten globule

4. • Most protein fold with the help of both
methods

5. Free energy funnel
• Unfolded states are characterized by a high
degree of conformational entropy and relatively
high free energy
• The narrowing of the funnel represents a
decrease in the number of conformational
species present
• Small depressions along the sides of the free-
energy funnel represent semistable
intermediates that can briefly slow the folding
process
• Ultimately one native conformation or few
possible

6. Assisted Folding
• Molecular chaperones are proteins that
interact with partially folded or improperly
folded polypeptides, facilitating correct
folding pathways or providing
microenvironments in which folding can occur
• Two classes of molecular chaperones have
been well studied
– Hsp70
– chaperonins

7. Hsp70
• Hsp70 proteins bind to regions of unfolded
polypeptides that are rich in hydrophobic
residues, preventing inappropriate aggregation
• These chaperones thus “protect” proteins that
have been denatured by heat and peptides that
are being synthesized and are not yet folded
• Hsp70 proteins also block the folding of certain
proteins that must remain unfolded until they
have been translocated across membranes
• Some chaperones also facilitate the quaternary
assembly of oligomeric proteins

8. Hsp70
Bind unfolded
proteins
Keep protein
unfolded until
translocation
oligomeric
proteins
assembage

9. Hsp70, Hsp40 (DnaK, DnaJ)
mechanism

10. Chaperonins
• GroEL/GroES system in E. coli
• Unfolded proteins are bound within pockets in
the GroEL complex
• The pockets are capped transiently by the
GroES “lid”
GroEL
GroES

11. • GroEL undergoes substantial conformational
changes, coupled to ATP hydrolysis and the
binding and release of GroES
• Which promote folding of the bound
polypeptide
• Then, isomerization

13. • Protein disulfide isomerase (PDI) catalyzes
the interchange or shuffling of disulfide bonds
until the bonds of the native conformation are
formed
• PDI catalyzes the elimination of folding
intermediates with inappropriate disulfide
cross-links

14. • Peptide prolyl cis-trans isomerase (PPI)
catalyzes the interconversion of the cis and
trans isomers of Proline peptide bonds