biochem assignment

Question

predict how changing Trp105 to alanine would affect the ability of CEL-I to interact with GalNAc. A complete answer will describe the chemical role of Trp105 in GalNAc binding, how Trp and Ala differ on a chemical level, and the chemical details of how ligand binding changes when Ala is substituted (Make assumptions, state facts and justify prediction with clear conclusion). Concise writing of about 2 paraphraphs needed.

Answer 1

So the main thing you should be thinking about with these types of site-specific mutagenesis problems, is the change in physical properties. Each enzyme has specific physical properties based on the functional groups present on the amino acids, & the order that these amino acids are arranged. If you swap one amino acid for another, with different functional groups (Different R groups) you will get a new enzyme, with different properties.

Now that we got that out of the way, think about the structures of tryptophan & alanine. The difference lies in the R groups. Alanine is small, & hydrophobic, since it just has a methyl group. Tryptophan is large, aromatic & nonpolar.

I did a quick google image search, because I was unfamiliar with this specific enzyme. I cannot share the picture here, but just enter the same search as I did & you should see the same image: CEL-I to interact with GalNAc

Trp105 is on the top left, & it is interacting with GalNAc via Van de waals interaction. This is only possible because of the size of trp. If substituted for an alanine residue, this interaction would occur less frequently, meaning that GalNAc would bind to the active site less often, resulting in an increased Km (Weaker affinity).

I hope this helps.

Best of luck,

Michael G.