Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2016 Mar 25

PMID 27011181

Citations 3

Authors

Putty-Reddy Sudhir

Chung-Hsuan Chen

Affiliations

Soon will be listed here.

Abstract

A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.

Citing Articles

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References

Salwinski L, Miller C, Smith A, Pettit F, Bowie J, Eisenberg D . The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2003; 32(Database issue):D449-51. PMC: 308820. DOI: 10.1093/nar/gkh086. View

Liang J, Shang Y . Estrogen and cancer. Annu Rev Physiol. 2012; 75:225-40. DOI: 10.1146/annurev-physiol-030212-183708. View

Nassa G, Tarallo R, Ambrosino C, Bamundo A, Ferraro L, Paris O . A large set of estrogen receptor β-interacting proteins identified by tandem affinity purification in hormone-responsive human breast cancer cell nuclei. Proteomics. 2010; 11(1):159-65. DOI: 10.1002/pmic.201000344. View

Ho L, Ronan J, Wu J, Staahl B, Chen L, Kuo A . An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc Natl Acad Sci U S A. 2009; 106(13):5181-6. PMC: 2654396. DOI: 10.1073/pnas.0812889106. View

Musso G, Zhang Z, Emili A . Experimental and computational procedures for the assessment of protein complexes on a genome-wide scale. Chem Rev. 2007; 107(8):3585-600. DOI: 10.1021/cr0682857. View

Kaboord B, Perr M . Isolation of proteins and protein complexes by immunoprecipitation. Methods Mol Biol. 2008; 424:349-64. DOI: 10.1007/978-1-60327-064-9_27. View

Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G . CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res. 2009; 38(Database issue):D497-501. PMC: 2808912. DOI: 10.1093/nar/gkp914. View

Stadtfeld M, Hochedlinger K . Induced pluripotency: history, mechanisms, and applications. Genes Dev. 2010; 24(20):2239-63. PMC: 2956203. DOI: 10.1101/gad.1963910. View

Zhu W, Smith J, Huang C . Mass spectrometry-based label-free quantitative proteomics. J Biomed Biotechnol. 2009; 2010:840518. PMC: 2775274. DOI: 10.1155/2010/840518. View

10.

Tarallo R, Bamundo A, Nassa G, Nola E, Paris O, Ambrosino C . Identification of proteins associated with ligand-activated estrogen receptor α in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/MS. Proteomics. 2010; 11(1):172-9. DOI: 10.1002/pmic.201000217. View

11.

Le Naour F, Andre M, Greco C, Billard M, Sordat B, Emile J . Profiling of the tetraspanin web of human colon cancer cells. Mol Cell Proteomics. 2006; 5(5):845-57. DOI: 10.1074/mcp.M500330-MCP200. View

12.

Steen H, Mann M . The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol. 2004; 5(9):699-711. DOI: 10.1038/nrm1468. View

13.

Baldwin R, Bejide M, Trinkle-Mulcahy L, Cote J . Identification of the PRMT1v1 and PRMT1v2 specific interactomes by quantitative mass spectrometry in breast cancer cells. Proteomics. 2015; 15(13):2187-97. DOI: 10.1002/pmic.201400209. View

14.

Snel B, Lehmann G, Bork P, Huynen M . STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 2000; 28(18):3442-4. PMC: 110752. DOI: 10.1093/nar/28.18.3442. View

15.

Puig O, Caspary F, Rigaut G, Rutz B, Bouveret E, Wilm M . The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods. 2001; 24(3):218-29. DOI: 10.1006/meth.2001.1183. View

16.

Wisniewski J, Ostasiewicz P, Dus K, Zielinska D, Gnad F, Mann M . Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol Syst Biol. 2012; 8:611. PMC: 3472694. DOI: 10.1038/msb.2012.44. View

17.

Hofener M, Heinzlmeir S, Kuster B, Sewald N . Probing SH2-domains using Inhibitor Affinity Purification (IAP). Proteome Sci. 2014; 12:41. PMC: 4110944. DOI: 10.1186/1477-5956-12-41. View

18.

Ding J, Xu H, Faiola F, Maayan A, Wang J . Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Res. 2011; 22(1):155-67. PMC: 3252465. DOI: 10.1038/cr.2011.179. View

19.

Foerster S, Kacprowski T, Dhople V, Hammer E, Herzog S, Saafan H . Characterization of the EGFR interactome reveals associated protein complex networks and intracellular receptor dynamics. Proteomics. 2013; 13(21):3131-44. DOI: 10.1002/pmic.201300154. View

20.

Sudhir P, Chen C, Kumari M, Wang M, Tsou C, Sung T . Label-free quantitative proteomics and N-glycoproteomics analysis of KRAS-activated human bronchial epithelial cells. Mol Cell Proteomics. 2012; 11(10):901-15. PMC: 3494152. DOI: 10.1074/mcp.M112.020875. View