Protein-protein interactions: Analysis of a false positive GST pulldown result

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 8, 2011, Pages 2365-2371

  Wissmueller, Sandra ^a   Font, Josep ^a,b   Liew, Chu Wai ^a   Cram, Edward ^a   Schroeder, Thilo ^a,c   Turner, Jeremy ^a   Crossley, Merlin ^a,d   Mackay, Joel P ^a   Matthews, Jacqueline M ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b ROYAL PRINCE ALFRED HOSPITAL   (Australia)

^c UNIVERSITY OF ZURICH   (Switzerland)

^d UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

Binding artifact; Misfolding; NMR spectroscopy; Nucleic acid bridging; Transcription factors

Indexed keywords

DNA; ETHIDIUM BROMIDE; GLUTATHIONE TRANSFERASE; KRUPPEL LIKE FACTOR; KRUPPEL LIKE FACTOR 3; TRANSCRIPTION FACTOR GATA 1; UNCLASSIFIED DRUG;

ARTICLE; DNA BINDING MOTIF; FALSE POSITIVE RESULT; IN VITRO STUDY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION;

ANIMALS; GATA1 TRANSCRIPTION FACTOR; KRUPPEL-LIKE TRANSCRIPTION FACTORS; MICE; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING;

EID: 79960084378     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23068     Document Type: Article

References (25)

1. Mackay JP, Sunde M, Lowry JA, Crossley M, Matthews JM. Protein interactions: is seeing believing? Trends Biochem Sci 2007; 32: 530-531.
2. Fletcher S, Bowden SEH, Marrion NV. False interaction of syntaxin 1A with a Ca2+-activated K+ channel revealed by co-immunoprecipitation and pull-down assays: implications for identification of protein-protein interactions. Neuropharmacology 2003; 44: 817-827.
3. Lai JS, Herr W. Ethidium bromide provides a simple tool for identifying genuine DNA-independent protein associations. Proc Natl Acad Sci USA 1992; 89: 6958-6962.
4. Lee BM, Buck-Koehntop BA, Martinez-Yamout MA, Dyson HJ, Wright PE. Embryonic neural inducing factor churchill is not a DNA-binding zinc finger protein: solution structure reveals a solvent-exposed [beta]-sheet and zinc binuclear cluster. J Mol Biol 2007; 371: 1274-1289.
5. +-binding module. Biochemistry 2001; 40: 5854-5860.
6. Turner J, Crossley M. Mammalian Kruppel-like transcription factors: more than just a pretty finger. Trends Biochem Sci 1999; 24: 236-240.
7. Gamsjaeger R, Liew CK, Loughlin FE, Crossley M, Mackay JP. Sticky fingers: zinc-fingers as protein-recognition motifs. Trends Biochem Sci 2007; 32: 63-70.
8. Martin DI, Orkin SH. Transcriptional activation and DNA binding by the erythroid factor GF-1/NF-E1/Eryf 1. Gene Deve 1990; 4: 1886-1898.
9. Cheng Y, Wu W, Ashok Kumar S, Yu D, Deng W, Tripic T, King DC, Chen K-B, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, Blobel GA, Weiss MJ, Hardison RC. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res 2009; 19: 2172-2184.
10. Tallack MR, Whitington T, Yuen WS, Wainwright EN, Keys JR, Gardiner BB, Nourbakhsh E, Cloonan N, Grimmond SM, Bailey TL, Perkins AC. A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells. Genome Res 2010; 20: 1052-1063.
11. Gregory RC, Taxman DJ, Seshasayee D, Kensinger MH, Bieker JJ, Wojchowski DM. Functional interaction of GATA1 with erythroid Kruppel-like factor and Sp1 at defined erythroid promoters. Blood 1996; 87: 1793-1801.
12. Merika M, Orkin SH. Functional synergy and physical interactions of the erythroid transcription factor GATA-1 with the Kruppel family proteins Sp1 and EKLF. Mol Cell Biol 1995; 15: 2437-2447.
13. Borg J, Papadopoulos P, Georgitsi M, Gutierrez L, Grech G, Fanis P, Phylactides M, Verkerk AJ, van der Spek PJ, Scerri CA, Cassar W, Galdies R, van Ijcken W, Ozgur Z, Gillemans N, Hou J, Bugeja M, Grosveld FG, von Lindern M, Felice AE, Patrinos GP, Philipsen S. Haploinsufficiency for the erythroid transcription factor KLF1 causes hereditary persistence of fetal hemoglobin. Nat Genet 42: 801-805.
14. Zhou D, Liu K, Sun CW, Pawlik KM, Townes TM. KLF1 regulates BCL11A expression and gamma- to beta-globin gene switching. Nat Genet 42: 742-744.
15. Drissen R, von Lindern M, Kolbus A, Driegen S, Steinlein P, Beug H, Grosveld F, Philipsen S. The erythroid phenotype of EKLF-null mice: defects in hemoglobin metabolism and membrane stability. Mol Cell Biol 2005; 25: 5205-5214.
16. Basu P, Lung TK, Lemsaddek W, Sargent TG, Williams DC, Jr, Basu M, Redmond LC, Lingrel JB, Haar JL, Lloyd JA. EKLF and KLF2 have compensatory roles in embryonic beta-globin gene expression and primitive erythropoiesis. Blood 2007; 110: 3417-3425.
17. Eaton SA, Funnell AP, Sue N, Nicholas H, Pearson RC, Crossley M. A network of Kruppel-like Factors (Klfs). Klf8 is repressed by Klf3 and activated by Klf1 in vivo. J Biol Chem 2008; 283: 26937-26947.
18. Funnell APW, Maloney CA, Thompson LJ, Keys J, Tallack M, Perkins AC, Crossley M. Erythroid kruppel-like factor directly activates the basic kruppel-like factor gene in erythroid cells. Mol Cell Biol 2007; 27: 2777-2790.
19. Crossley M, Whitelaw E, Perkins A, Williams G, Fujiwara Y, Orkin SH. Isolation and characterization of the cDNA encoding BKLF/TEF-2, a major CACCC-box-binding protein in erythroid cells and selected other cells. Mol Cell Biol 1996; 16: 1695-1705.
20. Liew CW, Rand KD, Simpson RJY, Yung WW, Mansfield RE, Crossley M, Proetorius-Ibba M, Nerlov C, Poulsen FM, Mackay JP. Molecular analysis of the interaction between the hematopoietic master transcription factors GATA-1 and PU.1. J Biol Chem 2006; 281: 28296-28306.
21. Liew CK, Gamsjaeger R, Mansfield RE, Mackay JP. NMR spectroscopy as a tool for the rapid assessment of the conformation of GST-fusion proteins. Prot Sci 2008; 17: 1630-1635.
22. Simpson R, Cram E, Czjoli R, Matthews JM, Crossley M, Mackay JP. CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions. J Biol Chem 2003; 278: 28011-28018.
23. Crispino JD, Lodish MB, MacKay JP, Orkin SH. Use of altered specificity mutants to probe a specific protein-protein interaction in differentiation: the GATA-1:FOG complex. Mol Cell 1999; 3: 219-228.
24. Dreze M, Monachello D, Lurin C, Cusick ME, Hill DE, Vidal M, Braun P. High-quality binary interactome mapping. Methods Enzymol 2010; 470: 281-315.
25. Crossley M, Tsang AP, Bieker JJ, Orkin, Orkin SH. Regulation of the erythroid Kruppel-like factor (EKLF) gene promoter by the erythroid transcription factor GATA-1. J Biol Chem 1994; 269: 15440-15444.