The Chemical Biology of Reversible Lysine Post-translational Modifications

Abstract

Lysine (Lys) residues in proteins undergo a wide range of reversible post-translational modifications (PTMs), which can regulate enzyme activities, chromatin structure, protein-protein interactions, protein stability, and cellular localization. Here we discuss the "writers," "erasers," and "readers" of some of the common protein Lys PTMs and summarize examples of their major biological impacts. We also review chemical biology approaches, from small-molecule probes to protein chemistry technologies, that have helped to delineate Lys PTM functions and show promise for a diverse set of biomedical applications.

Keywords: acetylation; acetyltransferase; bromodomain; deacetylase; enzyme; methylation; ubiquitination.

Figure 1:

Structures and locations of various Lys PTMs in eukaryotic cells. Modifications include mono-, di-, and tri-methylation (K_Me1,2,3); acetylation (K_Ac), propionylation (K_Pr), butyrylation (K_Bu), crotonylation (K_Cro), malonylation (K_Mal), succinylation (K_Succ), glutarylation (K_Glu), 2-hydroxyisobutyrylation (K_Hib), β-hydroxybutyrylation (K_Bhb), myristoylation (K_Mys), lactylation (K_Lac), benzoylation (K_Bz) and ubiquitination (K_Ub). Note that the cell structure is a cartoon to show the proposed locations of different protein Lys PTMs in the cell.

Fig. 2:

Writer and eraser enzymatic features for Lys acetylation, methylation, and ubiquitination. A. HATs; B. Classical HDACs, showing typical chelating Asp residues and the key Tyr residue; C. Sirtuins, ADP stands for adenosine diphosphate; D. KMTs, showing nucleophilic displacement with SAM; E. LSD1, highlighting the oxidized flavin; F. Jmj demethylase, highlighting the active site iron; G. E1-E2-RING/HECT-E3; H. DUBs, the water molecule/hydrolysis are omitted. Note that the images are cartoons of the stylized enzyme active sites instead of structurally precise crystal structures.

Fig. 3:

Chemical biology approaches for the site-specific installation of Lys PTMs and mimics into proteins. A. ThiaLys analogs generated by Cys modification; B. Introduction of Hydrazide acyl-Lys mimics; C. PTM installation by noncanonical amino acid incorporation, using acetyl-Lys as an example; D. A typical example for the “tag-and-modify” strategy: azidonorleucine (AznL) was first installed by noncanonical amino acid incorporation, followed by traceless-Staudinger ligation reactions with different phosphine reagents to generate acetyl-Lys and succinyl-Lys; E. Expressed protein ligation by chemoselective Cys/thioester reaction; F. Enzyme-catalyzed protein semisynthesis, the cartoon motif recognized by the enzyme is shown as “sequence”.

Fig. 4

Examples of biological investigation facilitated by the chemical preparation of site-specially modified histones. A. The recognition of H2BK120ub leads to H3K79 methylation as activation marker by Dot1L; B. H3K14ac blocks LSD1 of CoREST complex catalyzed demethylation at Lys4.

Fig. 5

Examples of small molecule inhibitors developed for Lys PTM writers, erasers, and readers: A. acetylation writer inhibitors; B. acetylation eraser inhibitors; C. acetylation reader inhibitors; D. methylation writer inhibitors; E. methylation eraser inhibitors; F. methylation reader inhibitors; G. ubiquitination regulators.