You have an appreciation for the complexity of protein structure. As many of you have indicated in your problem set responses, knowledge of DNA sequence can only take us so far. Genomics may have given rise to proteomics, but the two fields really are evolving in parallel as this point. As you probably appreciate from your reading and from exploring the three dimensional protein structures using CN3D, protein biophysics can be very complex. However, there is also an important role for "unfolded" proteins in physiology and disease.
1. Given that protein folding is largely determined by primary structure, what is the role of chaperone proteins? Bukau et al discuss the role of some of the major players, like HSPs, in proper protein folding.
2. Is it beneficial that some proteins do not generate higher order structures? De Simone et al discuss the role and properties of Intrinsically Disordered Protein Regions (IPDs), what is the take home message?
3. What is the role of misfolded proteins in disease? To come full circle, how does protein misfolding fit into our "protein evolution" model? I am offering two perspectives as a starting point for this discussion.