oligosaccharides are attached to proteins for a variety of reasons. They’re attached to the newly synthesized proteins in the endoplasmic reticulum and golgi apparatus to assign them destination labels, misfolded protein labels, and quality control labels. How does the polarity and charge of these oligosaccharides affect the protein they are bound to?

The α-amylase (α-AM) enzyme secreted by Aspergillus has an isoelectric point of approximately 4.2. If the purification method in problem 1 operates at pH 6.5, would the protein carry a positive charge, negative charge, or net zero charge?

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?

An engineered ligand binds its target with 5 nM affinity at high pH. However, protonation of a histidine residue in the binding site of the ligand renders it unable to bind. Plot the ligand:target complex concentration versus the initial ligand concentration (in protonated or unprotonated form) at pH 4, 5, 6, 7, or 8 (five lines on one plot). Use a total target concentration of 10 nM.