Most proteins fold spontaneously on their own. However, there are some proteins that require help from other proteins known as ‘chaperones' to fold and/or avoid misfolding. One chaperone system is composed of the GroEL and GroES proteins. GroEL is a large protein that contains a hydrophobic cavity within which misfolded proteins can bind. A simplified mechanism for how GroEL/ES helps proteins to fold (or re-fold) follows:

1. Misfolded proteins bind into the hydrophobic cavity of GroEL. GroES then acts as a lid to close the cavity.

2. There is a conformational change in GroEL such that the hydrophobic amino acids initially lining the cavity are rotated out. This conformational change in GroEL changes the cavity from a hydrophobic environment to a hydrophilic environment (i.e. the amino acids now lining the cavity are hydrophilic amino acids).

3. During this conformational transition, the cavity of GroEL first expands to exert a stretching force on the misfolded protein and then contracts to its starting volume.

4. Following this conformational change, the lid to the cavity is opened and the protein is expelled from GroEL into the cytosol.

a. Misfolded proteins will tend to bind to the hydrophobic cavity of GroEL (step 1 in the above mechanism) whereas properly folded proteins will not. Why?

b. Explain how steps 2 and 3 in the above mechanism for GroEL/ES function might help a misfolded protein to re-fold into its proper native structure.

c. Draw a two-dimensional conformational energy landscape (free energy on y-axis, conformational coordinate on x-axis) to show how a protein may become kinetically (not thermodynamically) ‘trapped' in a misfolded conformation.