Protein Folding

Protein Folding

1. Primary

   • LINEAR sequence of AA
     • 1st stage in protein formation

2. Secondary

   • Alpha and beta sheets
     • HYDROGEN BONDING
       • Disrupted by:
         • Urea

3. Tertiary

   • RELATIVE POSITION in folded protein
     • One complete protein chain (single polypeptide)
       • Disrupted by:
         • Beta Mercaptoethanol (BME)
         • Urea
         • DILUTE BME

4. Quaternary

   • ARRANGEMENT OF SUBUNITS
     • Must have two or more subunits
       • Disrupted by:

5. Reagents in protein unfolding

   • BME:
     • Tertiary
     • Interferes with disulfide bonds and hydrogen bonds
     • DILUTE amounts promote folding into something else
   • Urea
     • Backbone and side chains
     • Secondary
     • Tertiary
     • COMEPTES for H-bonds
       • Prevents organization of hydrogen bonds

6. Factors affecting folding

   • Conformational entropy
     • DECREASES in polypeptide (unorganized-> org)
   • Solvent entropy
   • Steric constraints
     • Peptide bond rigid due to partial double bond characteristic
     • Phi angle:
       • N to a-C: angle of H on N and side chain on a-C
     • Psi Angle
       • Angle between carbonyl-C and a-C side chain
     • Ramachandran Chart
       • Energy calculations of Psi and Phi combos
         • most tolerated angles
       • Upper right quadrant = GLY