Cysteine and CysPTM
In most proteome, cysteine (Cys) residues occur low frequently but high in chemical reactivity. Due to their high reactivity, Cys could react with some electrophilic substrate as the nucleophiles, forming CysPTMs, which can be divided into three categories according to the difference of precursor molecules: oxidation PTM, lipid PTM and metabolite PTM. These PTMs play important roles in regulating protein structures and functions, and relate to a series of diseases.
Chemical proteomics identification
CysPTMs are difficult to directly detect on the proteome-wide scale due to their highly dynamic nature and low abundance. Generally, antibodies for the enrichment of PTM proteins or peptides are useful but difficult to be developed. Alternatively, different strategies have been developed to enrich specific CysPTM. We clustered them into four strategies, according to the their workflows: Thiol Blocking (A), Direct Capture (B), Metabolic Labeling follow by Bioorthogonal Chemistry (MLBC, C) and Thiol Isotope Labeling (TIL, D).
Cells could generate low amounts of ROS, RNS and RSS during normal aerobic metabolism, and increase the amounts under oxidative stress. Cys residues with lower pKa tend to be oxidized by ROS or RNS, occurring reversible S-nitrosylation or S-sulfenylation, respectively. Both types of PTMs could be further oxidized and become irreversible oxidation states like S-sulfinylation and S-sulfonylation. Some modified Cys could also be converted into another reversible oxidation PTM named S-glutathionylation through the direct addition of oxidized glutathione (GSSG). Additionally, some Cysteine residues would be reversibly modified by RSS, forming disulfide or persulfide. These types of reversible oxidations are inter-transformable and such reversible switches regulate protein functions and affect signaling pathways.
Lipid molecules are a large class of hydrophobic molecules widely presenting in all living organisms, which are often involved in the regulation of intracellular life activities, affecting many pathways including energy conversion, signal transduction, cell division, differentiation and so on. Lipid PTM or lipidation of proteins refers to the covalent bonds ( thioester or thioether bonds) of lipid molecules to proteins, which could change their structure and function. The most common ones are S-palmitoylation and S-prenylation.
Metabolism, as the most fundamental feature of living life, can directly meet the material needs for organism growth and development through generating energy and biomolecules. On the other hand, more and more studies have shown that some reactive metabolites such as Lipid-derived electrophiles (LDEs), fumarate, itaconate, coenzymeA and others, can also regulate cell signaling pathways through CysPTM (Figure 5A). Such PTMs could occur at the low levels under physiological conditions, but trigger proteome-wide modifications under abnormal pathological or cellular stress conditions. These modifications are often non-enzymatic and irreversible, reducing the activity of many intracellular proteins thereby contributing to changes in signaling pathways.