Question

The tertiary structure of a protein must also be considered when comparing deamidation rates. Another source of catalytic groups are amino acid side chains such as the ones discussed above that are located in the same vicinity as the labile Asn or Gln. Another consideration is the location of the Asn and Gln with respect to the tertiary structure of the protein. It has been observed that Asn and Gln residues in the interior of a protein are deamidated at a much slower rate than Asn and Gln residues on the surface of the protein. Why is this the case?

Answer 1

# Asparagine and glutamine are the amide form of acidic aminoacids aspartic and glutamic acids. Aspartic and glutamic acids have extra carboxyl groups which are hydrophilic in nature. Asparagine and glutamine are not as hydrophilic as aspartic and gluatmic.

Tertiary structure of a protein is a folded three dimensional structure which kept the hydrophobic aminoacids interior and hydrophilic aminoacids to the outside of the protein. When asparagine and glutamine are deaminated, their hydrophilic carboxyl terminal will be exposed outside. This will create choas if it happens in the interior. That is why such reaction rate is slower in the interior and faster in exterior portion of the protein.