Protein Lec #3

Protein Lec #3

1. Anfinsen Paradigm

   • 3D structure of a protein is entirely determined by its amino acid sequence

2. Levinthal Paradox

   • Many proteins fold in seconds or less, but how is this possible if the protein has so many conformations to explore?
   • Flat Folding Landscape
     • Unrealistic

3. Alternative to Levinthal Paradox

   • Conformation options are affected by
     • Limited by unfavourable contacts (Ramachandran plot)
     • Reduced by hydrophobic collapse
     • Local formation of secondary structure
   • Proteins don't fold via a random search - each residue does not act independently
   • Other pathways
     • Tunnel
     • Folding funnel, realistic landscape
       • There is one LOW energy, minimum conformation. But it can be accessed via multiple different folding pathways
         • CONCEPT: there is more than one way to fold a protein
       • molten globule: partially folded state in which hydrophobic collapse has occurred and native secondary structure has developed, but a stable tertiary structure has not yet formed
         • traditional view
         • new view

4. Molecular Chaperones

   • Chaperones do not actively promote folding - they prevent aggreation by binding exposed hydrophobic regions
   • Heat shock proteins
     • Hsp70 binds to unfolded or misfolded proteins via recognition of hydrophobic regions
       • Protects unfolded protein until rest of it is synthesised
     • Hsp 40 binds and promotes ATP hydrolysis, which enhances binding between Hsp70 and unfolded protein (CLOSED FORM of Hsp)
       • Protein finishes synthesising
         • Some proteins spontaneously fold into native conformation others ferried to chaperonins
           • NEF protein: helps Hsp70 eject ADP and the bound protein
   • Chaperonins
     • Required for folding of proteins that cannot fold spontaneously in cell
     • GroEL/GroEs complex (E. Coli)
       • Humans: Hsp60/Hsp10
       • 2 large heptameric rings form a chamber
         • "Private folding room" allows 1 protein at time
         • Single protein folds alternately
           • new protein binding signals release of other
         • 7 molecules ATP
           • ATP hydrolysis, conformational change in GroEl, so protein enters chamber
         • 10 seconds to fold

5. Disease

   • Failure of chaperones to rescue misfolfed proteins --> protein folding diseases
   • Formation of amyloid plaque in Alzheimer's disease