Site-Specific Proteomic Mapping Identifies Selectively Modified Regulatory Cysteine Residues in Functionally Distinct Protein Networks

Alegre-Cebollada, 2014, S-glutathionylation of cryptic cysteines enhances titin elasticity by blocking protein folding, Cell, 156, 1235, 10.1016/j.cell.2014.01.056 Benhar, 2010, Identification of S-nitrosylated targets of thioredoxin using a quantitative proteomic approach, Biochemistry, 49, 6963, 10.1021/bi100619k Brandes, 2009, Thiol-based redox switches in eukaryotic proteins, Antioxid. Redox Signal., 11, 997, 10.1089/ars.2008.2285 Britto, 2002, The local electrostatic environment determines cysteine reactivity of tubulin, J. Biol. Chem., 277, 29018, 10.1074/jbc.M204263200 Chouchani, 2013, Cardioprotection by S-nitrosation of a cysteine switch on mitochondrial complex I, Nat. Med., 19, 753, 10.1038/nm.3212 Conway, 2004, Roles for cysteine residues in the regulatory CXXC motif of human mitochondrial branched chain aminotransferase enzyme, Biochemistry, 43, 7356, 10.1021/bi0498050 Dalle-Donne, 2007, S-glutathionylation in protein redox regulation, Free Radic. Biol. Med., 43, 883, 10.1016/j.freeradbiomed.2007.06.014 Denu, 1998, Specific and reversible inactivation of protein tyrosine phosphatases by hydrogen peroxide: evidence for a sulfenic acid intermediate and implications for redox regulation, Biochemistry, 37, 5633, 10.1021/bi973035t Doulias, 2010, Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation, Proc. Natl. Acad. Sci. USA, 107, 16958, 10.1073/pnas.1008036107 Doulias, 2013, Mass spectrometry-based identification of S-nitrosocysteine in vivo using organic mercury assisted enrichment, Methods, 62, 165, 10.1016/j.ymeth.2012.10.009 Doulias, 2013, Nitric oxide regulates mitochondrial fatty acid metabolism through reversible protein S-nitrosylation, Sci. Signal., 6, rs1, 10.1126/scisignal.2003252 Finkel, 2011, Signal transduction by reactive oxygen species, J. Cell Biol., 194, 7, 10.1083/jcb.201102095 Groitl, 2014, Thiol-based redox switches, Biochim. Biophys. Acta, 1844, 1335, 10.1016/j.bbapap.2014.03.007 Hagel, 2011, Selective irreversible inhibition of a protease by targeting a noncatalytic cysteine, Nat. Chem. Biol., 7, 22, 10.1038/nchembio.492 Hamnell-Pamment, 2005, Determination of site-specificity of S-glutathionylated cellular proteins, Biochem. Biophys. Res. Commun., 332, 362, 10.1016/j.bbrc.2005.04.130 Hansen, 2009, Quantifying the global cellular thiol-disulfide status, Proc. Natl. Acad. Sci. USA, 106, 422, 10.1073/pnas.0812149106 Huttlin, 2010, A tissue-specific atlas of mouse protein phosphorylation and expression, Cell, 143, 1174, 10.1016/j.cell.2010.12.001 Karisch, 2011, Global proteomic assessment of the classical protein-tyrosine phosphatome and “Redoxome”, Cell, 146, 826, 10.1016/j.cell.2011.07.020 Kislinger, 2006, Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling, Cell, 125, 173, 10.1016/j.cell.2006.01.044 Klatt, 1999, Nitric oxide inhibits c-Jun DNA binding by specifically targeted S-glutathionylation, J. Biol. Chem., 274, 15857, 10.1074/jbc.274.22.15857 Kruger, 2008, SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function, Cell, 134, 353, 10.1016/j.cell.2008.05.033 Lim, 2012, A low pKa cysteine at the active site of mouse methionine sulfoxide reductase A, J. Biol. Chem., 287, 25596, 10.1074/jbc.M112.369116 Linder, 2003, New insights into the mechanisms of protein palmitoylation, Biochemistry, 42, 4311, 10.1021/bi034159a Marino, 2010, Cysteine function governs its conservation and degeneration and restricts its utilization on protein surfaces, J. Mol. Biol., 404, 902, 10.1016/j.jmb.2010.09.027 Marino, 2010, Structural analysis of cysteine S-nitrosylation: a modified acid-based motif and the emerging role of trans-nitrosylation, J. Mol. Biol., 395, 844, 10.1016/j.jmb.2009.10.042 Marino, 2012, Analysis and functional prediction of reactive cysteine residues, J. Biol. Chem., 287, 4419, 10.1074/jbc.R111.275578 Martin, 2012, Global profiling of dynamic protein palmitoylation, Nat. Methods, 9, 84, 10.1038/nmeth.1769 Martínez-Acedo, 2014, Proteomic analysis of peptides tagged with dimedone and related probes, J. Mass Spectrom., 49, 257, 10.1002/jms.3336 Martínez-Ruiz, 2007, Signalling by NO-induced protein S-nitrosylation and S-glutathionylation: convergences and divergences, Cardiovasc. Res., 75, 220, 10.1016/j.cardiores.2007.03.016 Mertins, 2013, Integrated proteomic analysis of post-translational modifications by serial enrichment, Nat. Methods, 10, 634, 10.1038/nmeth.2518 Mitchell, 2005, Thioredoxin catalyzes the S-nitrosation of the caspase-3 active site cysteine, Nat. Chem. Biol., 1, 154, 10.1038/nchembio720 Pace, 2014, Zinc-binding cysteines: diverse functions and structural motifs, Biomolecules, 4, 419, 10.3390/biom4020419 Passmore, 2004, Getting into position: the catalytic mechanisms of protein ubiquitylation, Biochem. J., 379, 513, 10.1042/bj20040198 Paulsen, 2012, Peroxide-dependent sulfenylation of the EGFR catalytic site enhances kinase activity, Nat. Chem. Biol., 8, 57, 10.1038/nchembio.736 Salsbury, 2008, Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid, Protein Sci., 17, 299, 10.1110/ps.073096508 Schmidt, 2006, Allosteric disulfide bonds, Biochemistry, 45, 7429, 10.1021/bi0603064 Sen, 2012, Hydrogen sulfide-linked sulfhydration of NF-kB mediates its antiapoptotic actions, Mol. Cell, 45, 13, 10.1016/j.molcel.2011.10.021 Seth, 2012, Endogenous protein S-nitrosylation in E. coli: regulation by OxyR, Science, 336, 470, 10.1126/science.1215643 Shi, 2005, Contributions of cysteine residues in Zn2 to zinc fingers and thiol-disulfide oxidoreductase activities of chaperone DnaJ, Biochemistry, 44, 1683, 10.1021/bi0480943 Smith, 2012, Mechanisms of S-nitrosothiol formation and selectivity in nitric oxide signaling, Curr. Opin. Chem. Biol., 16, 498, 10.1016/j.cbpa.2012.10.016 Stewart, 2012, Reactive cysteine in the structural Zn(2+) site of the C1B domain from PKCalpha, Biochemistry, 51, 7263, 10.1021/bi300750w Townsend, 2009, Novel role for glutathione S-transferase pi. Regulator of protein S-Glutathionylation following oxidative and nitrosative stress, J. Biol. Chem., 284, 436, 10.1074/jbc.M805586200 Weerapana, 2010, Quantitative reactivity profiling predicts functional cysteines in proteomes, Nature, 468, 790, 10.1038/nature09472 Wood, 2003, Structure, mechanism and regulation of peroxiredoxins, Trends Biochem. Sci., 28, 32, 10.1016/S0968-0004(02)00003-8