Four-dimensional orthogonal electrophoresis system for screening protein complexes and protein-protein interactions combined with mass spectrometry

Journal of Proteome Research

Volumn 9, Issue 10, 2010, Pages 5325-5334

  Wang, Xiaodong ^a   Chen, Guoqiang ^a   Liu, Hui ^a   Zhao, Zhiyun ^a   Li, Zhili ^a  

^a PEKING UNION MEDICAL COLLEGE   (China)

Author keywords

four dimensional orthogonal electrophoresis; mass spectrometry; protein complex; protein protein interaction; proteomics; thin layer IEF

Indexed keywords

CARBONATE DEHYDRATASE I; CYTOPLASM PROTEIN; HEAT SHOCK PROTEIN 60; HEMOGLOBIN A2; HEMOGLOBIN ALPHA2BETA2; HEMOGLOBIN ALPHA2DELTA2; PEROXIREDOXIN 2; PROTEASOME; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; ELECTROPHORESIS; ERYTHROCYTE; FOUR DIMENSIONAL ORTHOGONAL ELECTROPHORESIS SYSTEM; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; RAJI CELL; STRUCTURAL PROTEOMICS;

CELL LINE, TUMOR; CYTOPLASM; ELECTROPHORESIS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ERYTHROCYTES; HUMANS; MASS SPECTROMETRY; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 77957354900     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr100581x     Document Type: Article

References (44)

1. Alberts, B. The cell as a collection of protein machines: preparing the next generation of molecular biologists Cell 1998, 92 (3) 291-294
2. Baumeister, W.; Walz, J.; Zuhl, F.; Seemuller, E. The proteasome: paradigm of a self-compartmentalizing protease Cell 1998, 92 (3) 367-380
3. Wang, W. Emergence of a DNA-damage response network consisting of Fanconi anaemia and BRCA proteins Nat. Rev. Genet. 2007, 8 (10) 735-748
4. Yusupova, G.; Jenner, L.; Rees, B.; Moras, D.; Yusupov, M. Structural basis for messenger RNA movement on the ribosome Nature 2006, 444 (7117) 391-394
5. Brosch, G.; Lusser, A.; Goralik-Schramel, M.; Loidl, P. Purification and characterization of a high molecular weight histone deacetylase complex (HD2) of maize embryos Biochemistry 1996, 35 (49) 15907-15914
6. Huber, C. G.; Walcher, W.; Timperio, A. M.; Troiani, S.; Porceddu, A.; Zolla, L. Multidimensional proteomic analysis of photosynthetic membrane proteins by liquid extraction-ultracentrifugation-liquid chromatography-mass spectrometry Proteomics 2004, 4 (12) 3909-3920
7. Yokoyama, R.; Iwafune, Y.; Kawasaki, H.; Hirano, H. Isoelectric focusing of high-molecular-weight protein complex under native conditions using agarose gel Anal. Biochem. 2009, 387 (1) 60-63
8. Claverol, S.; Burlet-Schiltz, O.; Girbal-Neuhauser, E.; Gairin, J. E.; Monsarrat, B. Mapping and structural dissection of human 20 S proteasome using proteomic approaches Mol. Cell. Proteomics 2002, 1 (8) 567-578
9. Froment, C.; Uttenweiler-Joseph, S.; Bousquet-Dubouch, M. P.; Matondo, M.; Borges, J. P.; Esmenjaud, C.; Lacroix, C.; Monsarrat, B.; Burlet-Schiltz, O. A quantitative proteomic approach using two-dimensional gel electrophoresis and isotope-coded affinity tag labeling for studying human 20S proteasome heterogeneity Proteomics 2005, 5 (9) 2351-2363
10. Meetei, A. R.; de Winter, J. P.; Medhurst, A. L.; Wallisch, M.; Waisfisz, Q.; van de Vrugt, H. J.; Oostra, A. B.; Yan, Z.; Ling, C.; Bishop, C. E.; Hoatlin, M. E.; Joenje, H.; Wang, W. A novel ubiquitin ligase is deficient in Fanconi anemia Nat. Genet. 2003, 35 (2) 165-170
11. Puig, O.; Caspary, F.; Rigaut, G.; Rutz, B.; Bouveret, E.; Bragado-Nilsson, E.; Wilm, M.; Seraphin, B. The tandem affinity purification (TAP) method: a general procedure of protein complex purification Methods 2001, 24 (3) 218-229
12. Wittig, I.; Karas, M.; Schagger, H. High resolution clear native electrophoresis for in-gel functional assays and fluorescence studies of membrane protein complexes Mol. Cell. Proteomics 2007, 6 (7) 1215-1225
13. Wittig, I.; Carrozzo, R.; Santorelli, F. M.; Schagger, H. Functional assays in high-resolution clear native gels to quantify mitochondrial complexes in human biopsies and cell lines Electrophoresis 2007, 28 (21) 3811-3820
14. Marzoa, J.; Sanchez, S.; Ferreiros, C. M.; Criado, M. T. Identification of Neisseria meningitidis outer membrane vesicle complexes using 2-D high resolution clear native/SDS-PAGE J. Proteome Res. 2010, 9 (1) 611-619
15. Manabe, T.; Yamaguchi, N.; Mukai, J.; Hamada, O.; Tani, O. Detection of protein-protein interactions and a group of immunoglobulin G-associated minor proteins in human plasma by nondenaturing and denaturing two-dimensional gel electrophoresis Proteomics 2003, 3 (6) 832-846
16. Manabe, T.; Jin, Y.; Yamaguchi, N.; Sugiyama, T.; Ikari, K. Cleavage of fibrinogen alpha chains during isoelectric focusing of human plasma under non-denaturing conditions analyzed by micro two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization mass spectrometry J. Electrophoresis 2007, 51, 27-34
17. Manabe, T.; Jin, Y. Analysis of protein/polypeptide interactions in human plasma using nondenaturing micro-2-DE followed by 3-D SDS-PAGE and MS Electrophoresis 2007, 28 (12) 2065-2079
18. Manabe, T.; Jin, Y. Noncovalent interactions in human plasma proteins analyzed by the comparison of nondenaturing and denaturing micro-2-D gel electrophoresis patterns after polypeptide assignment using matrix-assisted laser desorption/ionization-mass spectrometry and peptide mass fingerprinting Electrophoresis 2008, 29 (12) 2672-2688
19. Jin, Y.; Manabe, T. Performance of agarose IEF gels as the first dimension support for non-denaturing micro-2-DE in the separation of high-molecular-mass plasma proteins and protein complexes Electrophoresis 2009, 30 (6) 939-948
20. Boyum, A. Isolation of leucocytes from human blood. Further observations. Methylcellulose, dextran, and ficoll as erythrocyteaggregating agents Scand. J. Clin. Lab. Invest. 1968, 21, 31-50
21. Boyum, A. Separation of white blood cells Nature 1964, 204, 793-794
22. Chen, G.; Luo, Y.; Wang, X.; Zhao, Z.; Liu, H.; Zhang, H.; Li, Z. A relatively simple and economical protocol for proteomic analyses of human 20S proteasome: Compatible with both scaled-up and scaled-down purifications Electrophoresis 2009, 30 (14) 2422-2430
23. Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 1976, 72, 248-254
24. Elsasser, S.; Schmidt, M.; Finley, D. Characterization of the proteasome using native gel electrophoresis Methods Enzymol. 2005, 398, 353-363
25. Margolis, J.; Kenrick, K. G. 2-dimensional resolution of plasma proteins by combination of polyacrylamide disc and gradient gel electrophoresis Nature 1969, 221 (5185) 1056-1057
26. Wilm, M.; Shevchenko, A.; Houthaeve, T.; Breit, S.; Schweigerer, L.; Fotsis, T.; Mann, M. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry Nature 1996, 379 (6564) 466-469
27. Manabe, T. Combination of electrophoretic techniques for comprehensive analysis of complex protein systems Electrophoresis 2000, 21 (6) 1116-1122
28. OFarrell, P. H. High resolution two-dimensional electrophoresis of proteins J. Biol. Chem. 1975, 250 (10) 4007-4021
29. OFarrell, P. Z.; Goodman, H. M.; OFarrell, P. H. High resolution two-dimensional electrophoresis of basic as well as acidic proteins Cell 1977, 12 (4) 1133-1141
30. Manabe, T.; Mizuma, H.; Watanabe, K. A nondenaturing protein map of human plasma proteins correlated with a denaturing polypeptide map combining techniques of micro two-dimensional gel electrophoresis Electrophoresis 1999, 20 (4-5) 830-835
31. Jin, Y.; Manabe, T. High-efficiency protein extraction from polyacrylamide gels for molecular mass measurement by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry Electrophoresis 2005, 26 (6) 1019-1028
32. Jin, Y.; Manabe, T. Alkaline extraction of human plasma proteins from nondenaturing micro-2-D gels for protein/polypeptide mass measurement and peptide mass fingerprinting using MALDI-TOF MS Electrophoresis 2007, 28 (3) 449-459
33. Voges, D.; Zwickl, P.; Baumeister, W. The 26S proteasome: a molecular machine designed for controlled proteolysis Annu. Rev. Biochem. 1999, 68, 1015-1068
34. Drews, O.; Wildgruber, R.; Zong, C.; Sukop, U.; Nissum, M.; Weber, G.; Gomes, A. V.; Ping, P. Mammalian proteasome subpopulations with distinct molecular compositions and proteolytic activities Mol. Cell. Proteomics 2007, 6 (11) 2021-2031
35. Ducoux-Petit, M.; Uttenweiler-Joseph, S.; Brichory, F.; Bousquet-Dubouch, M. P.; Burlet-Schiltz, O.; Haeuw, J. F.; Monsarrat, B. Scaled-down purification protocol to access proteomic analysis of 20S proteasome from human tissue samples: comparison of normal and tumor colorectal cells J. Proteome Res. 2008, 7 (7) 2852-2859
36. Dahlmann, B.; Ruppert, T.; Kuehn, L.; Merforth, S.; Kloetzel, P. M. Different proteasome subtypes in a single tissue exhibit different enzymatic properties J. Mol. Biol. 2000, 303 (5) 643-653
37. Simplaceanu, V.; Lukin, J. A.; Fang, T. Y.; Zou, M.; Ho, N. T.; Ho, C. Chain-selective isotopic labeling for NMR studies of large multimeric proteins: application to hemoglobin Biophys. J. 2000, 79 (2) 1146-1154
38. Hardison, R. C.; Chui, D. H.; Riemer, C. R.; Miller, W.; Carver, M. F.; Molchanova, T. P.; Efremov, G. D.; Huisman, T. H. Access to a syllabus of human hemoglobin variants (1996) via the World Wide Web Hemoglobin 1998, 22 (2) 113-127 (Pubitemid 28182738)
39. Harris, J. R.; Schroder, E.; Isupov, M. N.; Scheffler, D.; Kristensen, P.; Littlechild, J. A.; Vagin, A. A.; Meissner, U. Comparison of the decameric structure of peroxiredoxin-II by transmission electron microscopy and X-ray crystallography Biochim. Biophys. Acta 2001, 1547 (2) 221-234
40. Habich, C.; Burkart, V. Heat shock protein 60: regulatory role on innate immune cells Cell. Mol. Life Sci. 2007, 64 (6) 742-751
41. Li, S.; Peterson, N. A.; Kim, M. Y.; Kim, C. Y.; Hung, L. W.; Yu, M.; Lekin, T.; Segelke, B. W.; Lott, J. S.; Baker, E. N. Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin J. Mol. Biol. 2005, 346 (4) 1035-1046
42. Braig, K.; Otwinowski, Z.; Hegde, R.; Boisvert, D. C.; Joachimiak, A.; Horwich, A. L.; Sigler, P. B. The crystal structure of the bacterial chaperonin GroEL at 2.8 Å Nature 1994, 371 (6498) 578-586
43. Yuan, Z. A.; Collier, P. M.; Rosenbloom, J.; Gibson, C. W. Analysis of amelogenin mRNA during bovine tooth development Arch. Oral. Biol. 1996, 41 (2) 205-213
44. Matsuda, Y.; Higashiyama, S.; Kijima, Y.; Suzuki, K.; Kawano, K.; Akiyama, M.; Kawata, S.; Tarui, S.; Deutsch, H. F.; Taniguchi, N. Human liver manganese superoxide dismutase. Purification and crystallization, subunit association and sulfhydryl reactivity Eur. J. Biochem. 1990, 194 (3) 713-720