Question -

Asparagine (Asn) and glutamine (Gln) residues in proteins will sometimes be nonenzymatically hydrolytically deamidated to aspartate (Asp) and glutamate (Glu) residues, respectively. An exhaustive study of proteins known to undergo deamidation has revealed that the rate of deamidation is influenced by the amino acids preceding and following the amide amino acids in primary sequence. Other amino acids that might be far apart in primary sequence to the deamidated amino acids, but close in terms of tertiary structure, might also influence the deamidation process. 

1. Write the balanced chemical equations for the deamidation of asparagine or glutamine in an aqueous solution to yield aspartate or glutamate, respectively, and ammonium. 

2. The primary amino acid sequences were examined for proteins known to undergo hydrolytic deamidation of their Asn residues. The results are shown in the figure below.

What statements can you make concerning the kinds of amino acids you would expect to find before and after the labile Asn? 

3. A proposed mechanism of the deamidation of an amide side chain in a protein is shown below.  

a. State the type of catalysis that is occurring and in which step.  

b. In which step is the transition state intermediate created? Draw the intermediate.

c. What amino acid side chains might participate in stabilizing this structure? Be specific about the kinds of noncovalent interactions involved. 

5. Since the deamidation of Asn and Gln residues is known to be non-enzymatic, the catalyst cannot be provided by an enzyme. Instead, the catalytic groups are believed to be provided by neighboring amino acids in the protein undergoing deamidation. Refer to your answer to Question 2 and examine the mechanism.   Describe how amino acid side chains that either precede or follow the labile Asn could serve as catalytic groups in the deamidation process. 

6. Draw a labeled reaction coordinate diagram of the reaction.