Features of reactive cysteines discovered through computation: from kinase inhibition to enrichment around protein degrons

Abstract

Large-scale characterisation of cysteine modification is enabling study of the physicochemical determinants of reactivity. We find that location of cysteine at the amino terminus of an α-helix, associated with activity in thioredoxins, is under-represented in human protein structures, perhaps indicative of selection against background reactivity. An amino-terminal helix location underpins the covalent linkage for one class of kinase inhibitors. Cysteine targets for S-palmitoylation, S-glutathionylation, and S-nitrosylation show little correlation with pKa values predicted from structures, although flanking sequences of S-palmitoylated sites are enriched in positively-charged amino acids, which could facilitate palmitoyl group transfer to substrate cysteine. A surprisingly large fraction of modified sites, across the three modifications, would be buried in native protein structure. Furthermore, modified cysteines are (on average) closer to lysine ubiquitinations than are unmodified cysteines, indicating that cysteine redox biology could be associated with protein degradation and degron recognition.

Proteomic analysis of S-nitrosylated nuclear proteins in rat cortical neurons

“…Lysine motifs for S-nitrosylation have been reported previously; lysine motif 1 (Lys at position −2) was found in a screen for endogenously SNO-Ps in macrophages (38), and lysine motif 2 (Lys at position +6) was identified in a screen on GSNO-treated heart homogenates (25). The mechanisms through which lysine motifs regulate S-nitrosylation of MBD3 and HDAC2 are not currently known; however, a recent bioinformatic analysis suggested that cysteines in close proximity to ubiquitylated lysines are more likely to be modified by S-nitrosylation (39), hinting at a possible interplay between cysteine S-nitrosylation and posttranslational modifications at neighboring residues. Our screen provides targets of nuclear S-nitrosylation in cortical neurons, the site(s) of S-nitrosylation for most identified proteins, and characterization of lysine-containing motifs that regulate cysteine S-nitrosylation.…”

New Factors Enhancing the Reactivity of Cysteines in Molten Globule-Like Structures

“…Therefore, it is of paramount importance that a precise knowledge of the factors that influence the reactivity of these residues is obtained [ 1 , 2 ]. It is a common opinion (universally accepted) that this is mainly controlled by their p K a and by the accessibility of a given reagent [ 1 , 3 , 4 , 5 , 6 , 7 ]. In fact, the sulfhydryl group of cysteines is almost inert in its protonated form (except in free-radical reactions), while the thiolate form is the true reactive form.…”

Structural and mechanistic aspects of S-S bonds in the thioredoxin-like family of proteins

“…In fact, computational studies by Roos and co-workers emphasized that this stabilization is mostly promoted by hydrogen bonds at the N-terminus of α-helices, and it seems to be more pronounced with a larger number of turns in the helix (Roos et al, 2006). In addition, a recent computational study also emphasized that Cys residues closer to the N-terminus of α-helices often exhibit lower pK a s and higher nucleophilicity (Fowler et al, 2017).…”