Abstract
Protein–protein interactions are essential in various cellular processes including regulation of gene expression, formation of protein complexes, and cellular signaling transduction. In particular, several proteins in the nucleus interact to regulate transcription and RNA splicing. These protein–protein interactions are short and weak and occur through transient processes, making it difficult to identify these interactions. In addition, detection of interacting partners in vitro using cell lysates cannot provide complete information due to the loss of spatial organization and changes in protein modification. Here we describe an in vivo crosslinking technique using disuccinimidyl suberate (DSS), which is useful to capture and stabilize proteins to analyze the interacting proteins.
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References
Veres DV, Gyurko DM, Thaler B, Szalay KZ, Fazekas D, Korcsmaros T, Csermely P (2015) ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis. Nucleic Acids Res 43:D485–D493
Akey CW, Luger K (2003) Histone chaperones and nucleosome assembly. Curr Opin Struct Biol 13(1):6–14
Hillebrand M, Gersting SW, Lotz-Havla AS, Schafer A, Rosewich H, Valerius O, Muntau AC, Gartner J (2012) Identification of a new fatty acid synthesis-transport machinery at the peroxisomal membrane. J Biol Chem 287(1):210–221
Vaschetto LM (2017) Understanding the role of protein interaction motifs in transcriptional regulators: implications for crop improvement. Brief Funct Genomics 16(3):152–155
Watanabe N, Osada H (2016) Small molecules that target phosphorylation dependent protein-protein interaction. Bioorg Med Chem 24(15):3246–3254
Silberberg Y, Kupiec M, Sharan R (2014) A method for predicting protein-protein interaction types. PLoS One 9(3):e90904
Fields S, Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340(6230):245–246
Snider J, Kotlyar M, Saraon P, Yao Z, Jurisica I, Stagljar I (2015) Fundamentals of protein interaction network mapping. Mol Syst Biol 11(12):848
Xing S, Wallmeroth N, Berendzen KW, Grefen C (2016) Techniques for the analysis of protein-protein interactions in vivo. Plant Physiol 171(2):727–758
Kluger R, Alagic A (2004) Chemical cross-linking and protein-protein interactions-a review with illustrative protocols. Bioorg Chem 32(6):451–472
Madler S, Bich C, Touboul D, Zenobi R (2009) Chemical cross-linking with NHS esters: a systematic study on amino acid reactivities. J Mass Spectrom 44(5):694–706
Suchanek M, Radzikowska A, Thiele C (2005) Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells. Nat Methods 2(4):261–267
Gaucher SP, Hadi MZ, Young MM (2006) Influence of crosslinker identity and position on gas-phase dissociation of Lys-Lys crosslinked peptides. J Am Soc Mass Spectrom 17(3):395–405
Merkley ED, Rysavy S, Kahraman A, Hafen RP, Daggett V, Adkins JN (2014) Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances. Protein Sci 23(6):747–759
Shi JM, Pei J, Liu EQ, Zhang L (2017) Bis(sulfosuccinimidyl) suberate (BS3) crosslinking analysis of the behavior of amyloid-beta peptide in solution and in phospholipid membranes. PLoS One 12(3):e0173871
Kim YE, Park C, Kim KE, Kim KK (2018) Histone and RNA-binding protein interaction creates crosstalk network for regulation of alternative splicing. Biochem Biophys Res Commun 499(1):30–36
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This work was supported by Chungnam National University.
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Kim, YE., Kim, K.E., Kim, K.K. (2020). In Vivo Crosslinking of Histone and RNA-Binding Proteins. In: Ørom, U. (eds) RNA-Chromatin Interactions. Methods in Molecular Biology, vol 2161. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0680-3_7
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DOI: https://doi.org/10.1007/978-1-0716-0680-3_7
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