Question

On an atomic scale in a solution of GCN4 leucine zipper proteins one observes that the proteins exist as either unfolded random coils or as dimeric coiled-coils—that is, one does not observe alpha helices existing as folded monomers. Why not? Explain with specific details.

Answer 1

Answer:    The reason goes very simple. As the formation of a protein dimer needs a hydrophobic side on the any of the sides which is going to attach with another hydrophobic side of the other monomer. If we put this single molecule of monomer in water then it is going to collapse or it will bind to some molecule to make its hydrophobic side safe.

Here for GCN4 leucine zipper dimer formation: the hydrophobic side of the helix forms its dimer with itself or another similar helix, keeping the non-polar amino acids away from the solvent. The hydrophilic side of the helix interacts with the water in the solvent.

For unfolded random coils of GCN4 leucine zipper proteins: these are denatured form of GCN4 leucine zipper proteins which have been collapsed to form random strcuture, specifically coils.