Purification of phosphoproteins by immobilized metal affinity chromatography and its application to phosphoproteome analysis

Mitsuyo Machida, Hidetaka Kosako, Kyoko Shirakabe, Michimoto Kobayashi, Masato Ushiyama, Junichi Inagawa, Joe Hirano, Tomoyo Nakano, Yasuhiko Bando, Eisuke Nishida, Seisuke Hattori

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Abstract

Prefractionation procedures facilitate the identification of lower-abundance proteins in proteome analysis. Here we have optimized the conditions for immobilized metal affinity chromatography (IMAC) to enrich for phosphoproteins. The metal ions, Ga(III), Fe(III), Zn(II), and Al(III), were compared for their abilities to trap phosphoproteins; Ga(III) was the best. Detailed analyses of the pH and ionic strength for IMAC enabled us to determine the optimal conditions (pH 5.5 and 0.5 m NaCl). When whole cell lysates were fractionated in this way, about one-tenth of the total protein was recovered in the eluate, and the recovery of phosphorylated extracellular signal-regulated kinase (ERK) was more than 90%. Phosphorylated forms of ribosomal S6 kinase (RSK) and Akt were also enriched efficiently under the same conditions. Our Ga(III) IMAC and a commercially available purification kit for phosphoproteins performed similarly, with a slight difference in the spectrum of phosphoproteins. When phosphoproteins enriched from NIH3T3 cells in which ERK was either activated or suppressed were analyzed by two-dimensional fluorescence difference gel electrophoresis, phosphorylated ERK was detected as discrete spots unique to ERK-activated cells, which overlapped with surrounding spots in the absence of prefractionation. We applied the same technique to search for Akt substrates and identified Abelson interactor 1 as a novel potential target. These results demonstrate the efficacy of phosphoprotein enrichment by IMAC and suggest that this procedure will be of general use in phosphoproteome research.

Original languageEnglish
Pages (from-to)1576-1587
Number of pages12
JournalFEBS Journal
Volume274
Issue number6
DOIs
Publication statusPublished - 2007 Mar 1

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Keywords

  • Akt
  • Extracellular signal-regulated kinase (ERK)
  • Immobilized metal affinity chromatography
  • Phosphoproteome
  • Two-dimensional gel electrophoresis

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Machida, M., Kosako, H., Shirakabe, K., Kobayashi, M., Ushiyama, M., Inagawa, J., Hirano, J., Nakano, T., Bando, Y., Nishida, E., & Hattori, S. (2007). Purification of phosphoproteins by immobilized metal affinity chromatography and its application to phosphoproteome analysis. FEBS Journal, 274(6), 1576-1587. https://doi.org/10.1111/j.1742-4658.2007.05705.x