References
- Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. (1997). Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402 https://doi.org/10.1093/nar/25.17.3389
- Andres-Mateos, E., Perier, C., Zhang, L., Blanchard-Fillion, B., Greco, T.M., Thomas, B., Ko, H.S., Sasaki, M., Ischiropoulos, H., Przedborski, S., et al. (2007). DJ-1 gene deletion reveals that DJ-1 is an atypical peroxiredoxin-like peroxidase. Proc. Natl. Acad. Sci. USA 104, 14807-14812
- Attwood, T.K., Bradley, P., Flower, D.R., Gaulton, A., Maudling, N., Mitchell, A.L., Moulton, G., Nordle, A., Paine, K., Taylor, P., et al. (2003). PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res. 31, 400-402 https://doi.org/10.1093/nar/gkg030
- Azevedo, D., Tacnet, F., Delaunay, A., Rodrigues-Pousada, C., and Toledano, M.B. (2003). Two redox centers within Yap1 for H2O2 and thiol-reactive chemicals signaling. Free Radic. Biol. Med. 35, 889-900 https://doi.org/10.1016/S0891-5849(03)00434-9
- Beeby, M., O'Connor, B.D., Ryttersgaard, C., Boutz, D.R., Perry, L.J., and Yeates, T.O. (2005). The genomics of disulfide bonding and protein stabilization in thermophiles. PLoS Biol. 3, e309 https://doi.org/10.1371/journal.pbio.0030309
- Biswas, S., Chida, A.S., and Rahman, I. (2006). Redox modifications of protein-thiols: emerging roles in cell signaling. Biochem. Pharmacol. 71, 551-564 https://doi.org/10.1016/j.bcp.2005.10.044
- Bock, A., Forchhammer, K., Heider, J., and Baron, C. (1991). Selenoprotein synthesis: An expansion of the genetic code. Trends Biochem. Sci. 16, 463-467 https://doi.org/10.1016/0968-0004(91)90180-4
- Calabrese, V., Sultana, R., Scapagnini, G., Guagliano, E., Sapienza, M., Bella, R., Kanski, J., Pennisi, G., Mancuso, C., Stella, A.M., et al. (2006). Nitrosative stress, cellular stress response, and thiol homeostasis in patients with Alzheimer's disease. Antioxid. Redox Signal. 8, 1975-1986 https://doi.org/10.1089/ars.2006.8.1975
- Cammer, S.A., Hoffman, B.T., Speir, J.A., Canady, M.A., Nelson, M.R., Knutson, S., Gallina, M., Baxter, S.M., and Fetrow, J.S. (2003). Structure-based active site profiles for genome analysis and functional family subclassification. J. Mol. Biol. 334, 387-401 https://doi.org/10.1016/j.jmb.2003.09.062
- Castagnetto, J.M., Hennessy, S.W., Roberts, V.A., Getzoff, E.D., Tainer, J.A., and Pique, M.E. (2002). MDB: the metalloprotein database and browser at the scripps research institute. Nucleic Acids Res 30, 379-382 https://doi.org/10.1093/nar/30.1.379
- Chivers, P.T., Laboissiere, M.C., and Raines, R.T. (1996). The CXXC motif: imperatives for the formation of native disulfide bonds in the cell. EMBO J. 15, 2659-2667
- Chivers, P.T., Prehoda, K.E., and Raines, R.T. (1997). The CXXC motif: a rheostat in the active site. Biochemistry 36, 4061-4066 https://doi.org/10.1021/bi9628580
- Collet, J.F., and Bardwell, J.C. (2002). Oxidative protein folding in bacteria. Mol. Microbiol. 44, 1-8 https://doi.org/10.1046/j.1365-2958.2002.02851.x
- Conway, M.E., Poole, L.B., and Hutson, S.M. (2004). Roles for cysteine residues in the regulatory CXXC motif of human mitochondrial branched chain aminotransferase enzyme. Biochemistry 43, 7356-7364 https://doi.org/10.1021/bi0498050
- Dalle-Donne, I., Rossi, R., Giustarini, D., Colombo, R., and Milzani, A. (2007). S-glutathionylation in protein redox regulation. Free Radic. Biol. Med. 43, 883-898 https://doi.org/10.1016/j.freeradbiomed.2007.06.014
- Dalle-Donne, I., Milzani, A., Gagliano, N., Colombo, R., Giustarini, D., and Rossi, R. (2008). Molecular mechanisms and potential clinical significance of S-glutathionylation. Antioxid. Redox Signal. 10, 445-473 https://doi.org/10.1089/ars.2007.1716
- Delaunay, A., Pflieger, D., Barrault, M.B., Vinh, J. and Toledano, M.B. (2002). A thiol peroxidase is an H2O2 receptor and redoxtransducer in gene activation. Cell 111, 471-481 https://doi.org/10.1016/S0092-8674(02)01048-6
- Fermani, S., Sparla, F., Falini, G., Martelli, P.L., Casadio, R., Pupillo, P., Ripamonti, A., and Trost, P. (2007). Molecular mechanism of thioredoxin regulation in photosynthetic A2B2-glyceraldehyde-3- phosphate dehydrogenase. Proc. Natl. Acad. Sci. USA 104, 11109-11114
- Fetrow, J.S., and Skolnick, J. (1998). Method for prediction of protein function from sequence using the sequence-to-structure-tofunction paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol. 281, 949-968 https://doi.org/10.1006/jmbi.1998.1993
- Fetrow, J.S., Godzik, A., and Skolnick, J. (1998). Functional analysis of the Escherichia coli genome using the sequence-to structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. J. Mol. Biol. 282,703-711 https://doi.org/10.1006/jmbi.1998.2061
- Fetrow, J.S., Siew, N., Di Gennaro, J.A., Martinez-Yamour, M., Dyson, H.J., and Skolnick, J. (2001). Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight? Protein Sci. 10, 1005-1014 https://doi.org/10.1110/ps.49201
- Fomenko, D.E., and Gladyshev, V.N. (2002). CxxS: fold-inependent redox motif revealed by genome-wide searches for thiol/disulfide oxidoreductase function. Protein Sci. 11, 2285-2296 https://doi.org/10.1110/ps.0218302
- Fomenko, D.E., and Gladyshev, V.N. (2003). Identity and functions of CxxC-derived motifs. Biochemistry 42, 11214-11225 https://doi.org/10.1021/bi034459s
- Fomenko, D.E., Xing, W., Adair, B.M., Thomas, D.J., and Gladyshev, V.N. (2007). High-Throughput Identification of Catalytic Redox- Active Cysteine Residues. Science 315, 387-389 https://doi.org/10.1126/science.1133114
- Gattiker, A., Gasteiger, E., and Bairoch, A. (2002). ScanProsite: a reference implementation of a PROSITE scanning tool. Appl. Bioinform. 1, 107-108
- Giles, N.M., Watts, A.B., Giles, G.I., Fry, F.H., Littlechild, J.A., and Jacob, C. (2003). Metal and redox modulation of cysteine protein function. Chem. Biol. 10, 677-693 https://doi.org/10.1016/S1074-5521(03)00174-1
- Gladyshev, V.N., Kryukov, G.V., Fomenko, D.E., and Hatfield, D.L. (2004). Identification of trace element-containing proteins in genomic databases. Annu. Rev. Nutr. 24, 579-596 https://doi.org/10.1146/annurev.nutr.24.012003.132241
- Greco, T.M., Hodara, R., Parastatidis, I., Heijnen, H.F., Dennehy, M.K., Liebler, D.C., and Ischiropoulos, H. (2006). Identification of S-nitrosylation motifs by site-specific mapping of the Snitrosocysteine proteome in human vascular smooth muscle cells. Proc. Natl. Acad. Sci. USA 103, 7420-7425
- Hatfield, D.L., and Gladyshev, V.N. (2002). How selenium has altered our understanding of the genetic code. Mol. Cell. Biol. 22, 3565-3576 https://doi.org/10.1128/MCB.22.11.3565-3576.2002
- Hook, D.W., and Harding, J.J. (1997). Inactivation of glyceraldehyde 3-phosphate dehydrogenase by sugars, prednisolone-21- hemisuccinate, cyanate and other small molecules. Biochim. Biophys. Acta 1362, 232-242 https://doi.org/10.1016/S0925-4439(97)00084-7
- Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., Cuche, B.A., de Castro, E., Lachaize, C., Langendijk-Genevaux, P.S., and Sigrist, C.J. (2008). The 20 years of PROSITE. Nucleic Acids Res. 36, D245-D249 https://doi.org/10.1093/nar/gkm1044
- Jacob, C., Giles, G.I., Giles, N.M., and Sies, H. (2003). Sulfur and selenium: The role of oxidation state in protein structure and function. Angew. Chem. Int. Ed. 42, 4742-4758 https://doi.org/10.1002/anie.200300573
- Jakob, U., Eser, M., and Bardwell, J.C. (2000). Redox switch of hsp33 has a novel zinc-binding motif. J. Biol. Chem. 275, 38302-38310 https://doi.org/10.1074/jbc.M005957200
- Jones, D.T. (1999). Protein secondary structure prediction based on position-specific scoring matrixes. J. Mol. Biol. 292, 195-202 https://doi.org/10.1006/jmbi.1999.3091
- Jones, D.T., and Ward, J.J. (2003). Prediction of disordered regions in proteins from position specific score matrices. Proteins 53, 573-578 https://doi.org/10.1002/prot.10528
- Juarez, J.C., Manuia, M., Burnett, M.E., Betancourt, O., Boivin, B., Shaw, D.E., Tonks, N.K., Mazar, A.P., and Donate, F. (2008). Superoxide dismutase 1 (SOD1) is essential for H2O2-mediated oxidation and inactivation of phosphatases in growth factor signaling. Proc. Natl. Acad. Sci. USA 105, 7147-7152
- Ilbert, M., Horst, J., Ahre16, S., Winter, J., Graf, P.C., Lilie, H., and Jakob, U. (2007). The redox-switch domain of Hsp33 functions as dual stress sensor. Nat. Struct. Mol. Biol. 14, 556-563 https://doi.org/10.1038/nsmb1244
- Iqbalsyah, T.M., Moutevelis, E., Warwicker, J., Errington, N., and Doig, A.J. (2006). The CXXC motif at the N terminus of an alpha-helical peptide. Protein Sci. 15, 1945-1950 https://doi.org/10.1110/ps.062271506
- Kim, H.Y., and Gladyshev, V.N. (2005). Different catalytic mechanisms in mammalian selenocysteine- and cysteine-containing methionine- R-sulfoxide reductases. PLoS Biol. 3, e375 https://doi.org/10.1371/journal.pbio.0030375
- Kim, H.Y., Fomenko, D.E., Yoon, Y.E., and Gladyshev, V.N. (2006). Catalytic advantages provided by selenocysteine in methionine-Ssulfoxide reductases. Biochemistry 45, 13697-13704 https://doi.org/10.1021/bi0611614
- Kortemme, T., and Creighton, T.E. (1995). Ionisation of cysteine residues at the termini of model alpha-helical peptides. Relevance to unusual thiol pha values in proteins of the thioredoxin family. J. Mol. Biol 253, 799-812 https://doi.org/10.1006/jmbi.1995.0592
- Kryukov, G.V., Castellano, S., Novoselov, S.V., Lobanov, A.V., Zehtab, O., Guigo, R., and Gladyshev, V.N. (2003). Characterization of mammalian selenoproteomes. Science 300, 1439-1443 https://doi.org/10.1126/science.1083516
- Martin, J.L. (1995). Thioredoxin - fold for all reasons. Structure 3, 245-250 https://doi.org/10.1016/S0969-2126(01)00154-X
- Mates, J.M., Segura, J.A., Alonso, F.J., and Márquez, J. (2008). Intracellular redox status and oxidative stress: implications for cell proliferation, apoptosis, and carcinogenesis. Arch. Toxicol. 82, 273-299 https://doi.org/10.1007/s00204-008-0304-z
- Moutevelis, E., and Warwicker, J. (2004). Prediction of pKa and redox properties in the thioredoxin superfamily. Protein Sci. 13, 2744-2752 https://doi.org/10.1110/ps.04804504
- Newman, S.F., Sultana, R., Perluigi, M., Coccia, R., Cai, J., Pierce, W.M., Klein, J.B., Turner, D.M., and Butterfield, D.A. (2007). An increase in S-glutathionylated proteins in the Alzheimer's disease inferior parietal lobule, a proteomics approach. J. Neurosci. Res. 85, 1506-1514 https://doi.org/10.1002/jnr.21275
- Pedone, E., Limauro, D., and Bartolucci, S. (2008). The machinery for oxidative protein folding in thermophiles. Antioxid Redox Signal. 10, 157-169 https://doi.org/10.1089/ars.2007.1855
- Rhee, S.G., Bae, Y.S., Lee, S.R., and Kwon, J. (2000). Hydrogen peroxide: a key messenger that modulates protein phosphorylation through cysteine oxidation. Sci. STKE. PE1
- Ridge, P.G., Zhang, Y., and Gladyshev, V.N. (2008). Comparative genomic analyses of copper transporters and cupropro-teomes reveal evolutionary dynamics of copper utilization and its link to oxygen. PLoS ONE 3, e1378 https://doi.org/10.1371/journal.pone.0001378
- Salmeen, A., Andersen, J.N., Myers, M.P., Meng T.C., Hinks, J.A., Tonks, N.K., and Barford, D. (2003). Redox regulation of protein tyrosine phosphatase 1B involves a sulphenyl-amide intermediate. Nature 423, 769-773 https://doi.org/10.1038/nature01680
- Salsbury, FR. Jr., Knutson, S.T., Poole, L.B., and Fetrow, J.S. (2008). Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid. Protein Sci. 17, 299-312 https://doi.org/10.1110/ps.073096508
- Sanchez, R., Riddle, M., Woo, J., and Momand, J. (2008). Prediction of reversibly oxidized protein cysteine thiols using protein structure properties. Protein Sci. 17, 473-481 https://doi.org/10.1110/ps.073252408
- Stadtman, T.C. (1996). Selenocysteine. Annu. Rev. Biochem. 65, 83-100 https://doi.org/10.1146/annurev.bi.65.070196.000503
- Sun, J., Steenbergen, C., and Murphy, E. (2006). S-nitrosylation: NO-related redox signaling to protect against oxidative stress. Antioxid Redox Signal. 8, 1693-1705 https://doi.org/10.1089/ars.2006.8.1693
- Tu, B.P., and Weissman, J.S. (2004). Oxidative protein folding in eukaryotes: mechanisms and consequences. J. Cell Biol. 164, 341-346 https://doi.org/10.1083/jcb.200311055
- Veal, E.A., Findlay, V.J., Day, A.M., Bozonet, S.M., Evans, J.M., Quinn, J., and Morgan, B.A. (2004). A 2-Cys peroxiredoxin regulates peroxide-induced oxidation and activation of a stressactivated MAP kinase. Mol. Cell 15, 129-139 https://doi.org/10.1016/j.molcel.2004.06.021
- von Mering, C., Jensen, L.J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., Snel, B., and Bork, P. (2007). STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35, D358-D362 https://doi.org/10.1093/nar/gkl825
- Wassef, R., Haenold, R., Hansel, A., Brot, N., Heinemann, S.H., and Hoshi, T. (2007). Methionine sulfoxide reductase A and a dietary supplement S-methyl-L-cysteine prevent Parkinson's-like symptoms. J. Neurosci. 27, 12808-12816 https://doi.org/10.1523/JNEUROSCI.0322-07.2007
- Wessjohann, L.A., Schneider, A., Abbas, M., and Brandt, W. (2007). Selenium in chemistry and biochemistry in comparison to sulfur. Biol. Chem. 388, 997-1006 https://doi.org/10.1515/BC.2007.138
- Wood, Z.A., Poole, L.B., and Karplus, P.A. (2003). Peroxiredoxin evolution and the regulation of hydrogen peroxide signaling. Science 300, 650-653 https://doi.org/10.1126/science.1080405
- Wood, M.J., Storz, G., and Tjandra, N. (2004). Structural basis for redox regulation of Yap1 transcription factor localization. Nature 430, 917-921 https://doi.org/10.1038/nature02790
- Zhang F.L., and Casey P.J. (1996). Protein prenylation: molecular mechanisms and functional consequences. Annu. Rev. Biochem. 65, 241-269 https://doi.org/10.1146/annurev.bi.65.070196.001325
- Zhang, Y., and Gladyshev, V.N. (2005). An algorithm for identifycation of bacterial selenocysteine insertion sequence elements and selenoprotein genes. Bioinformatics 21, 2580-2589 https://doi.org/10.1093/bioinformatics/bti400
- Zhang, Y., and Gladyshev, V.N. (2008a). Trends in selenium utilization in marine microbial world revealed through the analysis of the global ocean sampling (GOS) project. PLoS Genet. 4, e1000095 https://doi.org/10.1371/journal.pgen.1000095
- Zhang, Y., and Gladyshev, V.N. (2008b). Molybdoproteomes and evolution of molybdenum utilization. J. Mol. Biol. 379, 881-899 https://doi.org/10.1016/j.jmb.2008.03.051