BMB Reports

생화학분자생물학회 (Korean Society for Biochemistry and Molecular Biology)
권호 표지
DOI QR코드

DOI QR Code

Nutriproteomics: Identifying the Molecular Targets of Nutritive and Non-nutritive Components of the Diet

  • Barnes, Stephen (Departments of Pharmacology and Toxicology, University of Alabama at Birmingham) ;
  • Kim, Helen (Departments of Pharmacology and Toxicology, University of Alabama at Birmingham)
  • 발행 : 2004.01.31
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

The study of whole patterns of changes in protein expression and their modifications, or proteomics, presents both technological advances as well as formidable challenges to biological researchers. Nutrition research and the food sciences in general will be strongly influenced by the new knowledge generated by the proteomics approach. This review examines the different aspects of proteomics technologies, while emphasizing the value of consideration of "traditional" aspects of protein separation. These include the choice of the cell, the subcellular fraction, and the isolation and purification of the relevant protein fraction (if known) by protein chromatographic procedures. Qualitative and quantitative analyses of proteins and their peptides formed by proteolytic hydrolysis have been substantially enhanced by the development of mass spectrometry technologies in combination with nanoscale fluidics analysis. These are described, as are the pros and cons of each method in current use.

키워드

참고문헌

  1. Adamczyk, M, Gebler, J. C. and Wu, J. (2001) Selective analysis of phosphopeptides within a protein mixture by chemical modification, reversible biotinylation and mass spectrometry. Rapid Commun. Mass Spectrom. 15, 1481-1488. https://doi.org/10.1002/rcm.394
  2. Adkins, J. N., Varnum, S. M., Auberry, K. J., Moore, R. J., Angell, N. H., Smith, R. D., Springer, D. L. and Pounds, J. G. (2002) Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell. Proteomics 1, 947-955. https://doi.org/10.1074/mcp.M200066-MCP200
  3. Anderson, N. G., Matheson, A. and Anderson, N. L. (2001) Back to the future: the human protein index (HPI) and the agenda for post-proteomic biology. Proteomics 1, 3-12. https://doi.org/10.1002/1615-9861(200101)1:1<3::AID-PROT3>3.0.CO;2-T
  4. Aulak, K. S., Miyagi, M., Yan, L., West, K. A., Massillon, D., Crabb, J. W. and Stuehr, D. J. (2001) Proteomic method identify proteins nitrated in vivo during inflammatory challenge. Proc. Nail. Acad. Sci. USA 98, 12056-12061. https://doi.org/10.1073/pnas.221269198
  5. Barnes, S. (1995) Effects of genistein in in vivo and in vitro models of cancer growth. J. Nutr. 125, 777-783.
  6. Barnes, S. (1997) The chemopreventive properties of soy isoflavonoids in animal models of breast cancer. Breast Cancer Res. Treatment 46, 169-179. https://doi.org/10.1023/A:1005956326155
  7. Barnes, S. (1998) Evolution of the history of soy and genistein. Proc. Soc. Exp. Biol. Med. 217, 386-392. https://doi.org/10.3181/00379727-217-44249
  8. Bienvenut, W. V., Deon, C., Pasquarello, C., Campbell, J. M., Sanchez, J. C., Vestal, M. L. and Hochstrasser, D. F. (2002) Matrix-assisted laser desorption/ionization-tandem mass spectrometry with high resolution and sensitivity for identification and characterization of proteins. Proteomics 2, 868-876. https://doi.org/10.1002/1615-9861(200207)2:7<868::AID-PROT868>3.0.CO;2-D
  9. Boersma, B. J., Patel, R. P., Benton, M. R., Kirk, M., Wilson, L. S., Botting, N. P., Barnes, S. and Darley-Usmar, V. M. (2003) Neutrophil myeloperoxidase chlorinates soy isoflavones and enhances their antioxidant properties. Free Radical Biol. Med. 35, 1417-1430. https://doi.org/10.1016/j.freeradbiomed.2003.08.009
  10. Brookes, P. S., Pinner, A., Ramachandran, A., Coward, L., Barnes, S., Kim, H. and Darley-Usmar, V. M. (2002) High throughput 2D blue-native electrophoresis a tool for functional proteomics of mitochondria and signaling complexes. Proteomics 2, 969-977. https://doi.org/10.1002/1615-9861(200208)2:8<969::AID-PROT969>3.0.CO;2-3
  11. Camacho-Carvajal, M. M., Wollscheld, B., Aebersold, R., Steimle, V. and Schamel, W. W. A. (2003) Two-dimensional blue native/SDS gel electrophoresis of multi-protein complexes from whole cellular lysates a proteomics approach. Molecular Cellular Proteomics, in press.
  12. Carr, S. A., Huddleston, M. J. and Annan, R. S. (1996) Selective detection and sequencing of phosphopeptides at the femtomole level by mass spectrometry. Anal. Biochem. 239, 180-192. https://doi.org/10.1006/abio.1996.0313
  13. Celotto, A. M. and Graveley, B. R. (2001) Alternative splicing of the Drosophila Dscam pre-mRNA is both temporally and spatially regulated. Genetics 159, 599-608.
  14. Chong, B. E., Yan, F., Lubman, D. M. and Miller, F. R. (2001) Chromatofocusing nonporous reversed-phase high-performance liquid chromatography/electrospray ionization time-of-flight mass spectrometry of protein s from human breast cancer whole cell lysates: a novel two -dimensional liquid chromatography/mass spectrometry method. Rapid Commun. in Mass Spectrom. 15, 291-296. https://doi.org/10.1002/rcm.227
  15. Coward, L., Kirk, M, Albin, N. and Barnes, S. (1996) Analysis of Plasma Isoflavones by Reversed-Phase HPLC-Multiple Reaction Ion Monitoring-Mass Spectrometry. Clin. Chim. Acta 247, 121-142. https://doi.org/10.1016/0009-8981(95)06242-4
  16. Crow, J., Ye, Y-Z., Strong, M., Barnes, S., Kirk, M. and Beckman, J. (1997) Superoxide dismutase catalyzes nitration of tyrosines by peroxynitrite in the rod and head of neurofilament-L. J. Neurochem. 69, 1945-1953.
  17. Davis, M. T., Beierle, J., Bures, E. T., McGinley, M. D., Mort, J., Robinson, J. H., Spahr, C. S., Yu, W., Luethy, R. and Patterson, S. D. (2001) Automated LC-LC-MS-MS platform using binary ion-exchange and gradient reversed-phase chromatography for improved proteomic analyses. J. Chromatogr. B. Biomed. Sci. Appl. 752, 281-291. https://doi.org/10.1016/S0378-4347(00)00547-8
  18. For the latest information on the human genome, go to http://www.genome.gov/
  19. Gavin, A. C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M., et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147. https://doi.org/10.1038/415141a
  20. Ge, X., Sirich, T. L., Beyer, M. K., Desaire, H. and Leary, J. A. (2001) A strategy for the determination of enzyme kinetics using electrospray ionization with an ion trap mass spectrometer. Anal. Chem. 73, 5078-5082. https://doi.org/10.1021/ac0105890
  21. Geiman, T. M. and Robertson, K. D. (2002) Chromatin remodeling, histone modifications, and DNA methylation - how does it all fit together? J. Cell Biochem. 87, 117-125. https://doi.org/10.1002/jcb.10286
  22. Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W. and Gygi, S. P. (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Nat. Acad. Sci. USA 100, 6940-6945. https://doi.org/10.1073/pnas.0832254100
  23. Gianazza, E., Eberini, I., Arnoldi, A., Wait, R. and Sirtori, C. R. (2003) A proteomic investigation of isolated soy proteins with variable effects in experimental and clinical studies. J. Nutr. 133, 9-14.
  24. Greis, K. D., Hayes, B. K., Comer, F., Hart, G. W., Kirk, M. and Barnes, S. (1996) Selective detection and site analysis of glycopeptides by capillary LC-ESMS. Anal. Biochem. 234, 38-49. https://doi.org/10.1006/abio.1996.0047
  25. Gronborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. S., Ohara, O., Mann, M., Jensen, O. N. and Pandey, A. A. (2002) mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate. Mol. Cell Proteomics 1, 517-527. https://doi.org/10.1074/mcp.M200010-MCP200
  26. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H. and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotech. 17, 994-999. https://doi.org/10.1038/13690
  27. Helbeck, T., McComb, M. E., Lim, A., Schoneich, C., Cohen, R. A. and Costello, C. E. (2003) An affinity labeling method for the identification of nitrotyrosine containing proteins and peptides. 51st Annual Conference of the American Society for Mass spectrometry, Montreal, Canada.
  28. Hsieh, C. Y., Santell, R. C., Haslam, S. Z. and Helferich, W. G. (1998) Estrogenic effects of genistein on the growth of estrogen receptor-positive human breast cancer (MCF-7) cells in vitro and in vivo. Cancer Res. 58, 3833-3888.
  29. Imam-Sghiouar, N., Laude-Lemaire, I., Labas, V., Pflieger, D., Le Caer, J. P. Caron, M. and Nabias, D. K. (2002) Joubert-Caron R. Subproteomics analysis of phosphorylated proteins: application to the study of B-lymphoblasts from a patient with Scott syndrome. Proteomics 2, 828-838. https://doi.org/10.1002/1615-9861(200207)2:7<828::AID-PROT828>3.0.CO;2-T
  30. Kaji, H., Saito, H., Yamauchi, Y., Shinkawa, T., Taoka, M., Hirabayashi, J., Kasai, K., Takahashi, N. and Isobe, T. (2003) Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nature Biotechnol. 21, 667-672. https://doi.org/10.1038/nbt829
  31. Katayama, H., Nagasu, T. and Oda, Y. (2001) Improvement of ingel digestion protocol for peptide mass fingerprinting bymatrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. in Mass Spectrom. 15, 1416-1421.
  32. Katta, V., Chow, D. T. and Rohde, M. F. (1998) Applications of in-source fragmentation of protein ions for direct sequence analysis by delayed extraction MALDI-TOF mass spectrometry. Anal. Chem. 70, 4410-4416. https://doi.org/10.1021/ac980034d
  33. Kim, H., Chaves, L., Hall, P., Mills, R., DeSilva, T., Coward, L. and Barnes, S. (2002) The use of proteomics technology to study brain proteins affected by soy isoflavones; in Soy and Health 2002 - clinical evidence - dietetic applications. K. Descheemaeker and I. Debruyne (eds.), pp. 155-166. Garant, Antwerpen.
  34. Kvasnicka, F. (2003) Proteomics: general strategies and application to nutritionally relevant proteins. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 787, 77-89. https://doi.org/10.1016/S1570-0232(02)00212-X
  35. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685. https://doi.org/10.1038/227680a0
  36. Lamartiniere, C. A., Cotroneo, M. S., Fritz, W. A., Wang, J., Mentor-Marcel, R. and Elgavish, A. (2002) Genistein chemoprevention: timing and mechanisms of action in murine mammary and prostate. J. Nutr. 132, 552-558.
  37. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001) International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921. https://doi.org/10.1038/35057062
  38. Lanman, J., Lam, T., Barnes, S., Sakalian, M., Emmett, M. R., Marshall, A. G. and Prevelige, F E. Jr. (2003) Identification of novel interactions in HIV-l capsid protein assembly by high resolution mass spectrometry. J. Mol. Biol. 325, 759-772. https://doi.org/10.1016/S0022-2836(02)01245-7
  39. Lee, C. -L., Hsiao, H. -H., Lin, C. -W., Wu, S. -P., Huang, S. -Y., Wu, C. -Y., Wang, Ah. -J. and Khoo, K. -H. (2003) Strategic shotgun proteomics approach for efficient construction of an expression map of targeted protein families in hepatoma cell lines. Proteomics 3, 2472-2486. https://doi.org/10.1002/pmic.200300586
  40. Marshall, A. G., Hendrickson, C. L. and Jackson, G. S. (1998) Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev. 17, 1-35. https://doi.org/10.1002/(SICI)1098-2787(1998)17:1<1::AID-MAS1>3.0.CO;2-K
  41. Medzihradszky, K. F., Gillece-Castro, B. L., Settineri, C. A., Townsend, R. R., Masiarz, F. R. and Burlingame, A. L. (1990) Structure determination of O-linked glycopeptides by tandem mass spectrometry. Biomed. Environ. Mass Spectrom. 19, 777-781. https://doi.org/10.1002/bms.1200191205
  42. Mortz, E., Vorm, O., Mann, M. and Roepstorff, P. (1994) Identification of proteins in polyacrylamide gels by mass spectrometric peptide mapping combined with database search. Biol. Mass Spectrom. 23, 249-261. https://doi.org/10.1002/bms.1200230503
  43. Noel-Georis, I., Bernard, A., Falmagne, P. and Wattiez, R. (2001) Proteomics as the tool to search for lung disease markers in bronchoalveolar lavage. Dis. Markers 17, 271-284. https://doi.org/10.1155/2001/607263
  44. O'Farrell, P. H. (1975) High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007-4021.
  45. Page, G. P., Edwards, J. W., Barnes, S. and Allison, D. B. (2003) A Design & Statistical Perspective on Microarray Gene. Expression Studies in Nutrition the need for playful creativity and scientific hard-mindedness. Nutrition 19, 997-1000. https://doi.org/10.1016/j.nut.2003.08.001
  46. Pasquali, C., Fialka, I. and Huber, L. A. (1999) Subcellular fractionation, electromigration analysis and mapping of organelles. J. Chromatogr. B Biomed. Sci. Appl. 722, 89-102. https://doi.org/10.1016/S0378-4347(98)00314-4
  47. Pertoft, H. (2000) Fractionation of cells and subcellular particles with Percoll. J. Biochem. Biophys. Methods 44, 1-30. https://doi.org/10.1016/S0165-022X(00)00066-X
  48. Rejtar, T., Hu, P., Juhasz, P., Campbell, J. M., Vestal, M. L., Preisler, J. and Karger, B. L. (2002) Off-line coupling of high-resolution capillary electrophoresis to MALDI-TOF and TOF/TOF MS. J. Proteome Res. 1, 171-179. https://doi.org/10.1021/pr015519o
  49. Reynolds, K. J., Yao, X. and Fenselau, C. (2002) Proteolytic $^18$O labeling for comparative proteomics: evaluation of endoprotease Glu-C as the catalytic agent. J. Proteome Res. 1, 27-33. https://doi.org/10.1021/pr0100016
  50. Roper, J. M., Staversky, R. J., Finkelstein, J. N., Keng, P. C. and O'Reilly, M. A. (2003) Identification and isolation of mouse type II cells on the basis of intrinsic expression of enhanced green fluorescent protein. Am. J. Physiol. Lung Cell Mol. Physiol. 285, 691-700.
  51. Schagger, H. and von Jagow, G. (1991) Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal. Biochem. 199, 223-231. https://doi.org/10.1016/0003-2697(91)90094-A
  52. Schmidt, F., Donahoe, S., Hagens, K., Mattow, J., Schaible, U. E., Kaufmann, S. H., Aebersold, R. and Jungblut, P. (2003) Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope coded affinity tag technology. Mol. Cell Proteomics, in press.
  53. Schmucker, D., Clemens, J. C., Shu, H., Worby, C. A., Xiao, J., Muda, M., Dixon, J. E. and Zipursky, S. L. (2000) Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell. 101, 671-684. https://doi.org/10.1016/S0092-8674(00)80878-8
  54. Sfakianos, M., WIlson, L., Sakalian, M., Falany, C. N. and Barnes, S. (2002) Conserved Residues in the Putative Catalytic Triad of Human Bile Acid Coenzyme A: Amino Acid Nacyltransferase. J. Biol. Chem. 277, 47270-47275. https://doi.org/10.1074/jbc.M207463200
  55. Shen, Y., Zhao, R. and Berger, S. J. (2002) Anderson GA. Rodriguez N. Smith RD. High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. Anal. Chem. 74, 4235-4249. https://doi.org/10.1021/ac0202280
  56. Spahr, C. S., Davis, M. T., McGinley, M. D., Robinson, J. H., Bures, E. J., Beierle, J., Mort, J., Courchesne, P. L., Chen, K., Wahl, R. C., Yu, W., Luethy, R. and Patterson, S. D. (2001) Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics 1, 93-107. https://doi.org/10.1002/1615-9861(200101)1:1<93::AID-PROT93>3.0.CO;2-3
  57. Unlu, M., Morgan, M. E. and Minden, J. S. (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18, 2071-2077. https://doi.org/10.1002/elps.1150181133
  58. Varnum, S. M., Covington, C. C., Woodbury, R. L., Petritis, K., Kangas, L. J., Abdullah, M. S., Pounds, J. G., Smith, R. D. and Zangar, R. C. (2003) Proteomic characterization of nipple aspirate fluid: identification of potential biomarkers of breast cancer. Breast Cancer Res. Treat. 80, 87-97. https://doi.org/10.1023/A:1024479106887
  59. Venter, J .C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) The sequence of the human genome. Science 291, 1304-1351. https://doi.org/10.1126/science.1058040
  60. Viera, L., Ye, Y. Z., Estevez, A. G. and Beckman, J. S. (1999) Immunohistochemical methods to detect nitrotyrosine. Methods Enzymol. 301, 373-381. https://doi.org/10.1016/S0076-6879(99)01101-5
  61. Wang, Y. K., Ma, Z., Quinn, D. F. and Fu, E. W. (2002) Inverse $^1$N-metabolic labeling /mass spectrometry for comparative proteomics and rapid identification of protein markers/targets. Rapid Commun. Mass Spectrom. 16, 1389-1397. https://doi.org/10.1002/rcm.725
  62. Washburn, M. P., Wolters, D. and Yates, J. R. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247. https://doi.org/10.1038/85686
  63. Wells, L., Vosseller, K., Cole, R. N., Cronshaw, J. M., Matunis, M. J. and Hart, G. W. (2002) Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine posttranslational modifications. Mol. Cell Proteomics 1, 791-804. https://doi.org/10.1074/mcp.M200048-MCP200
  64. Witt, M., Fuchser, J. and Baykut, G. (2003) Fourier transform ion cyclotron resonance mass spectrometry with NanoLC/microelectrospray ionization and matrix-assisted laser desorption/ionization: analytical performance in peptide mass fingerprint analysis. J. Am. Soc. Mass Spectrom. 14, 553-561. https://doi.org/10.1016/S1044-0305(03)00138-7
  65. Yamakawa, K., Huot, Y. K., Haendelt, M. A., Hubert, R., Chen, X. N., Lyons, G. E. and Korenberg, J. R. (1998) DSCAM: a novel member of the immunoglobulin superfamily maps in a Down syndrome region and is involved in the development of the nervous system. Hum. Mol. Genet. 7, 227-237. https://doi.org/10.1093/hmg/7.2.227
  66. Yanagisawa, K., Shyr, Y., Xu, B. J., Massion, P. P., Larsen, P. H., White, B. C., Roberts, J. R., Edgerton, M., Gonzalez, A., Nadaf, S., Moore, J. H., Caprioli, R. M. and Carbone, D. P. (2003) Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet. 362, 433-439. https://doi.org/10.1016/S0140-6736(03)14068-8
  67. Yates, J. R. (1998) Mass spectrometry and the age of the proteome. J. Mass Spectrom. 33, 1-19. https://doi.org/10.1002/(SICI)1096-9888(199801)33:1<1::AID-JMS624>3.0.CO;2-9
  68. Zhang, K. and Tang, H. (2003) Analysis of core histones by liquid chromatography-mass spectrometry and peptide mapping. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 783, 173-179. https://doi.org/10.1016/S1570-0232(02)00631-1
  69. Zhang, L., Eugeni, E. E., Parthun, M. R. and Freitas, M. A. (2003) Identification of novel histone post-translational modifications by peptide mass fingerprinting. Chromosma 112, 77-86. https://doi.org/10.1007/s00412-003-0244-6
  70. Zhou, J., Rusnak, F. and Hathaway, G. (2003) A method for the identification of post-translationally modified peptides by chemical targeting. 51st Annual Conference of the American Society for Mass spectrometry, Montreal, Canada.

피인용 문헌

  1. A perspective on DNA microarray technology in food and nutritional science vol.8, pp.5, 2005, https://doi.org/10.1097/01.mco.0000179166.33323.c3
  2. The role of proteomics in the study of the influence of climate change on seafood products vol.43, pp.7, 2010, https://doi.org/10.1016/j.foodres.2009.11.012
  3. Nutritional Proteomics: Methods and Concepts for Research in Nutritional Science vol.51, pp.2, 2007, https://doi.org/10.1159/000102101
  4. Identification of Differentially Expressed Proteins in Imatinib Mesylate-resistant Chronic Myelogenous Cells vol.38, pp.6, 2005, https://doi.org/10.5483/BMBRep.2005.38.6.725
  5. Dietary fatty acids affecting hepatic metabolism and atherosclerosis – mechanisms unravelled using a proteomics approach vol.60, pp.1, 2009, https://doi.org/10.3989/gya.086308
  6. Chemopreventive role of food-derived proteins and peptides: A review vol.57, pp.11, 2017, https://doi.org/10.1080/10408398.2015.1057632
  7. Proteomics as a tool for the modelling of biological processes and biomarker development in nutrition research vol.99, pp.S3, 2008, https://doi.org/10.1017/S0007114508006909
  8. Novel omics technologies in nutrition research vol.26, pp.2, 2008, https://doi.org/10.1016/j.biotechadv.2007.11.002
  9. Nutritional Systems Biology: Definitions and Approaches vol.29, pp.1, 2009, https://doi.org/10.1146/annurev-nutr-080508-141138
  10. Proteomic analysis of human plasma and blood cells in nutritional studies: development of biomarkers to aid disease prevention vol.5, pp.6, 2008, https://doi.org/10.1586/14789450.5.6.819