Do you expect a Pro → Gly mutation in a surface-loop region of a globular protein to be stabilizing or destabilizing? Assume the mutant folds to a native-like conformation. Explain your answer in terms of the predicted enthalpic and entropic effects of the mutation on the AG for protein folding compared to AG of folding for the wild-type protein.

The amide hydrogen atoms of peptide bonds within proteins can exchange with protons in the solvent. In general, amide hydrogen atoms in buried regions of proteins and protein complexes exchange more slowly than those on the solvent-accessible surface do. Determination of these rates can be used to explore the proteinfolding reaction, probe the tertiary structure of proteins, and identify the regions of protein–protein interfaces. These exchange reactions can be followed by studying the behavior of the protein in solvent that has been labeled with deuterium ( ²H), a stable isotope of hydrogen. What two methods described in this chapter could be readily applied to the study of hydrogen– deuterium exchange rates in proteins?

Consider the phenolic hydroxyl group of a particular Tyr residue in a protein. Suppose the hydroxyl group in the unfolded protein in aqueous solution, where the group is exposed to H2O, has a pKa of 10.0. If that group is found in a hydrophobic environment in the interior of the protein when the protein is folded into its native tertiary structure, would you expect the pKa of the phenolic hydroxyl to be higher or lower in the folded protein interior than in H2O? Explain your reasoning.

Briefly explain why a "Folding Funnel" is used to represent the kinetics of folding (limit 5-6 sentences)?