Membrane proteins and membrane proteomics

Proteomics

Volumn 8, Issue 19, 2008, Pages 3924-3932

  Tan, Sandra ^a   Hwee, Tong Tan ^b   Chung, Maxey C M ^a,b  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Biology; Membrane; Methods; Protein

Indexed keywords

BETA2 INTEGRIN; CARBAMAZEPINE; CARRIER PROTEIN; CELL ADHESION MOLECULE; CETUXIMAB; EFALIZUMAB; EPIDERMAL GROWTH FACTOR RECEPTOR; ERLOTINIB; GEFITINIB; GUANOSINE DIPHOSPHATE FUCOSE; INTEGRIN; LAMOTRIGINE; MEMBRANE PROTEIN; NATALIZUMAB; PHENYTOIN; SELECTIN; TRASTUZUMAB; VALPROIC ACID;

CANCER GROWTH; CARCINOGENESIS; CELL FRACTIONATION; CELL MIGRATION; CELL TYPE; CONGENITAL DISORDER OF GLYCOSYLATION TYPE 2C; DRUG BINDING; GENE AMPLIFICATION; GENE MUTATION; GENETIC HETEROGENEITY; HUMAN; LIPID BILAYER; LIPID COMPOSITION; NEOPLASM; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; PROTEOMICS; REVIEW; SEIZURE;

ANIMALS; CELL MEMBRANE; HUMANS; INTRACELLULAR MEMBRANES; MEMBRANE PROTEINS; MODELS, BIOLOGICAL; PROTEOMICS;

EUKARYOTA;

EID: 55749112976     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800597     Document Type: Review

References (70)

1. Guidotti, G., Membrane proteins. Ann. Rev. Biochem. 1972, 41, 731-752.
2. Singer, S. J., Nicolson, G. L., The fluid mosaic model of the structure of cell membranes. Science 1972, 175, 720-731.
3. Simons, K., van Meer, G., Lipid sorting in epithelial cells. Biochemistry 1988, 27, 6197-6202.
4. Jacobson, K., Dietrich, C., Looking at lipid rafts? Trends Cell Biol. 1999, 9, 87-91.
5. Stevens, T. J., Arkin, I. T., The effect of nucleotide bias upon the composition and prediction of transmembrane helices. Protein Sci. 2000, 9, 505-511.
6. Hopkins, A. L., Groom, C. R., The druggable genome. Nat. Rev. Drug Discovery 2002, 1, 727-730.
7. Kanapin, A., Batalov, S., Davis, M. J., Gough, J. et al., Mouse proteome analysis. Genome Res. 2003, 13, 1335-1344.
8. Alberts, B. (Ed.), Molecular Biology of the Cell, Garland Publishing, Inc, New York 1994, pp. 485-488.
9. Ovchinnikov, Y. A., Structure of rhodopsin and bacteriorhodopsin. Photochem. Photobiol. 1987, 45, 909-914.
10. Lawen, A., Ly, J. D., Lane, D. J., Zarschler, K. et al., Voltage-dependent anion-selective channel 1 (VDAC1) - a mitochondrial protein, rediscovered as a novel enzyme in the plasma membrane. Int. J. Biochem. Cell. Biol. 2005, 37, 277-282.
11. Brown, D., Waneck, G. L., Glycosyl-phosphatidylinositol-anchored membrane proteins. J. Am. Soc. Nephrol. 1992, 3, 895-906.
12. Nakamura, Y., Muguruma, Y., Yahata, T., Miyatake, H. et al., Expression of CD90 on keratinocyte stem/progenitor cells. Br. J. Dermatol. 2006, 154, 1062-1070.
13. Chen, Y. L., Targeting prenylated RAS modifying enzymes in cancer cells. Curr. Signal Transduct. Ther. 2006, 1, 285-293.
14. Bernhard, E. J., McKenna, W. G., Hamilton, A. D., Sebti, S. M. et al., Inhibiting Ras prenylation increases the radiosensitivity of human tumor cell lines with activating mutations of ras oncogenes. Cancer Res. 1998, 58, 1754-1761.
15. Frame, M. C., Src in cancer: Deregulation and consequences for cell behaviour. Biophys. Biochem. Acta 2002, 1602, 114-130.
16. Carter, P., Smith L., Identification and validation of cell surface antigens for antibody targeting in oncology. Endocr. Relat. Cancer 2004, 11, 659-687.
17. Luo, B. H., Carman, C. V., Springer, T. A., Structural basis of integrin regulation and signaling. Ann. Rev. Immunol. 2007, 25, 619-647.
18. Sperandio, M., Selectins and glycosyltransferases in leukocyte rolling in vivo. FEBS J. 2006, 273, 4377-4389.
19. Smith, C. W., Adhesion molecules and receptors. J. Allergy Clin. Immunol. 2008, 121, S375-S379.
20. Malech, H. L., Hickstein, D. D., Genetics, biology and clinical management of myeloid cell primary immune deficiencies: Chronic granulomatous disease and leukocyte adhesion deficiency. Curr. Opin. Hematol. 2007, 14, 29-36.
21. Helmus, Y., Denecke, J., Yakubenia, S., Robinson, P. et al., Leukocyte adhesion deficiency II patients with a dual defect of the GDP-fucose transporter. Blood 2006, 107, 3959-3966.
22. Etzioni, A., Alon, R., Leukocyte adhesion deficiency III: A group of integrin activation defects in hematopoietic lineage cells. Curr. Opin. Allergy Clin. Immunol. 2004, 4, 485-490.
23. Dunehoo, A. L., Anderson, M., Majumdar, S., Kobayashi, N. et al., Cell adhesion molecules for targeted drug delivery. J. Pharm. Sci. 2006, 95, 1856-1872.
24. Sergina, N. V., Moasser, M. M., The HER family and cancer: Emerging molecular mechanisms and therapeutic targets. Trends Mol. Med. 2007, 13, 527-534.
25. Slamon, D. J., Clark, G. M., Wong, S. G., Levin, W. J. et al., Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 1987, 235, 177-182.
26. Ahmed, K., Dasgupta, P., Khan, M. S., Cystine calculi: Challenging group of stones. Postgrad. Med. J. 2006, 82, 799-801.
27. Ryback, R., Bioelectrical modulators and the cell membrane in psychiatric medicine. Psychopharm. Bull. 2001, 35, 5-41.
28. McNamara, J. O. (Ed.), Goodman & Gilman's: The Pharmacological Basis of Therapeutics, McGraw-Hill, New York 1996, pp. 461-486.
29. Macher, B. A., Yen, T. Y., Proteins at membrane surfaces-a review of approaches. Mol. Biosyst. 2007, 3, 705-713.
30. Santoni, V., Molloy, M., Rabilloud, T., Membrane proteins and proteomics: Un amour impossible? Electrophoresis 2000, 21, 1054-1070.
31. Stevens, T. J., Arkin, I. T., Do more complex organisms have a greater proportion of membrane proteins in their genomes? Proteins 2000, 39, 417-420.
32. Wallin, E., von Heijne, G., Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 1998, 7, 1029-1038.
33. Bledi, Y., Inberg, A., Linial, M., Proceed: A proteomic method for analysing plasma membrane proteins in living mammalian cells. Brief Funct Genomics Proteomics 2003, 2, 254-265.
34. Josic, D., Clifton, J. G., Mammalian plasma membrane proteomics. Proteomics 2007, 7, 3010-3029.
35. Brookes, P. S., Pinner, A., Ramachandran, A., Coward, L. et al., High throughput two-dimensional blue-native electrophoresis: A tool for functional proteomics of mitochondria and signaling complexes. Proteomics 2002, 2, 969-977.
36. Krause, F., Detection and analysis of protein-protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (Membrane) protein complexes and supercomplexes. Electrophoresis 2006, 27, 2759-2781.
37. Schägger, H., Pfeiffer, K., The ratio of oxidative phosphorylation complexes I-V in bovine heart mitochondria and the composition of respiratory chain supercomplexes. J. Biol. Chem. 2001, 276, 37861-3787.
38. Wittig, I., Karas, M., Schägger, H., High resolution clear native electrophoresis for in-gel functional assays and fluorescence studies of membrane protein complexes. Mol. Cell. Proteomics 2007, 6, 1215-1225.
39. Zahedi, R. P., Meisinger, C., Sickmann, A., Two-dimensional benzyldimethyl-n-hexadecylammonium chloride/SDS-PAGE for membrane proteomics. Proteomics 2005, 5, 3581-3588.
40. Macfarlane, D. E., Two dimensional benzyldimethyl-n-hexadecylammonium chloride-sodium dodecyl sulfate preparative polyacrylamide gel electrophoresis: A high capacity high resolution technique for the purification of proteins from complex mixtures. Anal. Biochem. 1989, 176, 457-463.
41. Hartinger, J., Stenius, K., Högemann, D., Jahn, R., 16-BAC/SDS-PAGE: a two-dimensional gel electrophoresis system suitable for the separation of integral membrane proteins. Anal. Biochem. 1996, 240, 126-133.
42. Rais, I., Karas, M., Schägger, H., Two-dimensional electrophoresis for the isolation of integral membrane proteins and mass spectrometric identification. Proteomics 2004, 4, 2567-2571.
43. Braun, R. J., Kinkl, N., Beer, M., Ueffing, M., Two-dimensional electrophoresis of membrane proteins. Anal. Bioanal. Chem. 2007, 389, 1033-45.
44. Stasyk, T., Huber, L. A., Zooming in: Fractionation strategies in proteomics. Proteomics 2004, 4, 3704-3716.
45. Lawson, E. L., Clifton, J. G., Huang, F., Li, X. et al., Use of magnetic beads with immobilized monoclonal antibodies for isolation of highly pure plasma membranes. Electrophoresis 2006, 27, 2747-2758.
46. Fischer, F., Wolters, D., Rögner, M., Poetsch, A., Toward the complete membrane proteome: High coverage of integral membrane proteins through transmembrane peptide detection. A. Mol. Cell. Proteomics 2006, 5, 444-453.
47. Everberg, H., Leiding, T., Schiöth, A., Tjerneld, F. et al., Efficient and nondenaturing membrane solubilization combined with enrichment of membrane protein complexes by detergent/polymer aqueous two-phase partitioning for proteome analysis. J. Chromatogr. A 2006, 1122, 35-46.
48. Molloy, M. P., Herbert, B. R., Walsh, B. J., Tyler, M. I. et al., Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis 1998, 19, 837-844.
49. Speers, A. E., Wu, C. C., Proteomics of integral membrane proteins-theory and application. Chem. Rev. 2007, 107, 3687-3714.
50. Ghosh, D., Krokhin, O., Antonovici, M., Ens, W. et al., Lectin affinity as an approach to the proteomic analysis of membrane glycoproteins. J. Proteome Res. 2004, 3, 841-850.
51. Fujiki, Y., Hubbard, A. L., Fowler, S., Lazarow, P. B., Isolation of intracellular membranes by means of sodium carbonate treatment: Application to endoplasmic reticulum. J. Cell Biol. 1982, 93, 97-102.
52. Elortza, F., Mohammed, S., Bunkenborg, J., Foster, L. J. et al., Modification-specific proteomics of plasma membrane proteins: Identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment. J. Proteome Res. 2006, 5, 935-943.
53. Wu, C. C., MacCoss, M. J., Howell, K. E., Yates, J. R., III, A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol. 2003, 21, 532-538.
54. Elortza, F., Nuhse, T. S., Foster, L. J., Stensballe, A. et al., Proteomic analysis of glycophosphatidylinositolanchored membrane proteins. Mol. Cell. Proteomics 2003, 2, 1261-1270.
55. Sabarth, N., Hurvitz, R., Schmidt, M., Zimny-Arndt, U. et al., Identification of Helicobacter pylori surface proteins by selective proteinase K digestion and antibody phage display. J. Microbiol. Methods 2005, 62, 345-349.
56. Rodriguez-Ortega, M. J., Norais, N., Bensi, G., Liberatori, S. et al., Characterization and identification of vaccine candidate proteins through analysis of the group a Streptococcus surface proteome. Nat. Biotechnol. 2006, 24, 191-197.
57. Blonder, J., Goshe, M. B., Moore, R. J., Pasa-Tolic, L. et al., Enrichment of integral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry. J. Proteome Res. 2002, 1, 351-360.
58. Han, J., Schey, K. L., Proteolysis and mass spectrometric analysis of an integral membrane: Aquaporin 0. J. Proteome Res. 2004, 3, 807-812.
59. Zhong, H., Marcus, S. L., Li, L., Microwave-assisted acid hydrolysis of proteins combined with liquid chromatography MALDI MS/MS for protein identification. J. Am. Soc. Mass Spectrom. 2005, 16, 471-481.
60. Han, D. K., Eng, J., Zhou, H., Aebersold, R., Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 2001, 19, 946-951.
61. Siuti, N., Kelleher, N. L., Decoding protein modifications using top-down mass spectrometry. Nat. Methods 2007, 4, 817-821.
62. Zabrouskov, V., Whitelegge, J. P., Increased coverage in the transmembrane domain with activated-ion electron capture dissociation for top-down Fourier-transform mass spectrometry of integral membrane proteins. J Proteome Res. 2007, 6, 2205-2210.
63. Liang, X., Zhao, J., Hajivandi, M., Wu, R. et al., Quantification of membrane andmembrane-bound proteins in normal and malignant breast cancer cells isolated from the same patient with primary breast carcinoma. J Proteome Res. 2006, 5, 2632-2641.
64. Ramus, C., Gonzalez de Peredo, A., Dahout, C., Gallagher M. et al., An optimized strategy for ICAT quantification of membrane proteins. Mol. Cell. Proteomics 2006, 5, 68-78.
65. Lu, X., Zhu, H., Tube-gel digestion: A novel proteomic approach for high throughput analysis of membrane proteins. Mol. Cell. Proteomics 2005, 4, 1948-1958.
66. Han, C. L., Chien, C. W., Chen, W. C., Chen, Y. R. et al., A multiplexed quantitative strategy for membrane proteomics: Opportunities for mining therapeutic targets for autosomal-dominant polycystic kidney disease. Mol. Cell. Proteomics 2008, in press.
67. Granseth, E., Seppälä, S., Rapp, M., Daley, D. O. et al., Membrane protein structural biology - how far can the bugs take us? Mol. Membr. Biol. 2007, 24, 329-332.
68. Klammt, C., Schwarz, D., Löhr, F., Schneider, B. et al., Cellfree expression as an emerging technique for the large scale production of integral membrane protein. FEBS J. 2006, 273, 4141-4153.
69. Junge, F., Schneider, B., Reckel, S., Schwarz, D. et al., Largescale production of functional membrane proteins. Cell. Mol. Life Sci. 2008, 65, 1729-1755.
70. Chan, Y. H., Boxer, S. G., Model membrane systems and their applications. Curr. Opin. Chem. Biol. 2007, 11, 581-587.