Abstract
Here, we describe the method for the identification of arginylated proteins by mass spectrometry. This method has been originally applied to the identification of N-terminally added Arg on proteins and peptides and then expanded to the side chain modification which has been recently described by our groups. The key steps in this method include the use of the mass spectrometry instruments that can identify peptides with very high pass accuracy (Orbitrap) and apply stringent mass cutoffs during automated data analysis, followed by manual validation of the identified spectra. These methods can be used with both complex and purified protein samples and, to date, constitute the only reliable way to confirm arginylation at a particular site on a protein or peptide.
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References
Kaji H, Novelli GD, Kaji A (1963) A soluble amino acid-incorporating system from rat liver. Biochim Biophys Acta 76:474–477
Kaji A, Kaji H, Novelli GD (1963) A soluble amino acid incorporating system. Biochem Biophys Res Commun 10:406–409
Kopitz J, Rist B, Bohley P (1990) Post-translational arginylation of ornithine decarboxylase from rat hepatocytes. Biochem J 267(2):343–348
Bohley P, Kopitz J, Adam G (1988) Surface hydrophobicity, arginylation and degradation of cytosol proteins from rat hepatocytes. Biol Chem Hoppe Seyler 369(Suppl):307–310
Bohley P, Kopitz J, Adam G (1988) Arginylation, surface hydrophobicity and degradation of cytosol proteins from rat hepatocytes. Adv Exp Med Biol 240:159–169
Ciechanover A, Ferber S, Ganoth D, Elias S, Hershko A, Arfin S (1988) Purification and characterization of arginyl-tRNA-protein transferase from rabbit reticulocytes. Its involvement in post-translational modification and degradation of acidic NH2 termini substrates of the ubiquitin pathway. J Biol Chem 263(23):11155–11167
Soffer RL (1971) Enzymatic modification of proteins. 4. Arginylation of bovine thyroglobulin. J Biol Chem 246(5):1481–1484
Soffer RL (1975) Enzymatic arginylation of beta-melanocyte-stimulating hormone and of angiotensin II. J Biol Chem 250(7):2626–2629
Zhang N, Donnelly R, Ingoglia NA (1998) Evidence that oxidized proteins are substrates for N-terminal arginylation. Neurochem Res 23(11):1411–1420
Wong CC, Xu T, Rai R, Bailey AO, Yates JR 3rd, Wolf YI et al (2007) Global analysis of posttranslational protein arginylation. PLoS Biol 5(10):e258. https://doi.org/10.1371/journal.pbio.0050258
Rai R, Wong CC, Xu T, Leu NA, Dong DW, Guo C et al (2008) Arginyltransferase regulates alpha cardiac actin function, myofibril formation and contractility during heart development. Development 135(23):3881–3889. https://doi.org/10.1242/dev.022723
Cornachione AS, Leite FS, Wang J, Leu NA, Kalganov A, Volgin D et al (2014) Arginylation of myosin heavy chain regulates skeletal muscle strength. Cell Rep 8(2):470–476. https://doi.org/10.1016/j.celrep.2014.06.019
Lian L, Suzuki A, Hayes V, Saha S, Han X, Xu T et al (2014) Loss of ATE1-mediated arginylation leads to impaired platelet myosin phosphorylation, clot retraction, and in vivo thrombosis formation. Haematologica 99(3):554–560. https://doi.org/10.3324/haematol.2013.093047
Saha S, Wong CC, Xu T, Namgoong S, Zebroski H, Yates JR 3rd et al (2011) Arginylation and methylation double up to regulate nuclear proteins and nuclear architecture in vivo. Chem Biol 18(11):1369–1378. https://doi.org/10.1016/j.chembiol.2011.08.019
Xu T, Wong CC, Kashina A, Yates JR 3rd. (2009) Identification of N-terminally arginylated proteins and peptides by mass spectrometry. Nat Protoc 4(3):325–332. https://doi.org/10.1038/nprot.2008.248
Xu T, Venable JD, Park SK, Cociorva D, Lu B, Liao L, Wohlschlegel J, Hewel J, Yates JR, IIIrd. (2006) ProLuCID, a fast and sensitive tandem mass spectra-based protein identification program. Mol Cell Proteomics 5(10):S174
Shen Y, Tolic N, Hixson KK, Purvine SO, Pasa-Tolic L, Qian WJ et al (2008) Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags. Anal Chem 80(6):1871–1882
Tabb DL, McDonald WH, Yates JR 3rd. (2002) DTASelect and contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res 1(1):21–26
Cociorva D, Tabb DL, Yates JR (2007) Validation of tandem mass spectrometry database search results using DTASelect. Curr Protoc Bioinform. Chapter 13:Unit 13 4
Karakozova M, Kozak M, Wong CC, Bailey AO, Yates JR 3rd, Mogilner A et al (2006) Arginylation of beta-actin regulates actin cytoskeleton and cell motility. Science 313(5784):192–196
Tsaprailis G, Nair H, Somogyi A, Wysocki V, Zhong W, Futrell J et al (1999) Influence of secondary structure on the fragmentation of protonated peptides. J Am Chem Soc 121(22):5142–5154
Dongre A, Jones J, Somogyi A, Wysocki V (1996) Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: evidence for the mobile proton model. J Am Chem Soc 118(35):8365–8374
Wong CCL, Xu T, Rai R, Bailey AO, Yates JR, Wolf YI et al (2007) Global analysis of posttranslational protein Arginylation. PLoS Biol 5(10):e258
Washburn MP, Wolters D, Yates JR (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. 19(3):242–247
Eng JK, McCormack AL, Yates JR 3rd (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976–989
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18):3551–3567
Craig R, Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20(9):1466–1467
Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM et al (2004) Open mass spectrometry search algorithm. J Proteome Res 3(5):958–964
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Kashina, A.S., Yates III, J.R. (2023). Identification of Arginylated Proteins by Mass Spectrometry. In: Kashina, A.S. (eds) Protein Arginylation. Methods in Molecular Biology, vol 2620. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2942-0_19
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DOI: https://doi.org/10.1007/978-1-0716-2942-0_19
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