Question

The following schemes show the design of a peptide-based chemical probe and the proposed mechanism of its activity-based labeling of protein tyrosine phosphatase, an enzyme that is responsible for removing the phosphate from the tyrosine residue(s) of a peptide in a peptide-sequence specific mamer. Based your understanding of the schemes, identify the key structural components of this probe that are responsible for (a) binding, (b) covalently modifying, and (c) reporting 2 FMPT
I know reporting is the fluorescent tag (I think) but I'm not sure what would be responsible for binding to the active site and covalently modifying

Answer 1

Hi! Let's start analyzing what is going on and then we answer the questions.

1) The Peptides are covalently bonding with the tyrosine. Remember the peptide bond. The goal of doing this is to make sure that the reaction doesn't include the functional groups -COOH and -NH3.

2) According to the machanism proposed, in the first reaction the aromaticy of the ring is broken, to be regained in the last step. This will have a consequence in the fluorescence of the peptide.

3) The phospate and the F- are good leaving groups, but the intermediate not aromatic will be more reactive since it is less stable, and that is where the enzyme appears, and makes a covalent bond between the Nu (nucleophile) and the alquene. I don't see very well the picture but think the enzyme has no role in the first reaction.

So:

a) Binding:

• First the peptidic bond: -NH3 and -COOH. Not sure if it asks directly from the scheme.
• The nucleophile and the alquene carbon.

b) Covalently modifying:

• F- and PO3-
• Nu and C=O
• And again the peptide but I don't think they are asking about it

c) Reporting:

Fluorecence, the second structure loses the tyrosine fluorescence, and the last one will have a fluorescence different from the tyrosine.

Hope to have been helpful!