Host–Guest Protein Assembly for Affinity Purification of Methyllysine Proteomes

Abstract

Protein–protein interactions drive self-assembly of biomacromolecules and thus enable important physiological functions at a cellular level. Supramolecular chemists have developed artificial host–guest interactions that are similar with, yet distinct from and orthogonal to, the natural protein–protein interactions. For instance, cucurbit[n]urils are synthetic receptors that can specifically recognize proteins with N-terminal aromatic residues with high affinities, yet this interaction can be reversed by the competition of small molecules such as amantadine. Herein, we develop a site-specific, oriented protein-display method by combining the host–guest interaction based on cucurbit[7]uril and a covalent protein–peptide reaction. A methyllysine-binding protein HP1β chromodomain (CD) is immobilized via host–guest interactions and used as the “bait” to capture methyllysine proteomes from cancer cells. The captured “fish”—methyllysine-containing proteins—can be released via competitive displacement by amantadine in a nondenaturing and traceless manner. This affinity purification method found 73 novel methyllysine sites from 101 identified sites among 66 methylated proteins from 255 HP1β CD-binding proteins in cancer cells via subsequent mass spectrometric analysis. This work thereby presents a new strategy of artificial host–guest protein assembly in affinity purification of methyllysine proteins in coupling to mass spectrometry.