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Submitted on June 4, 2007
Revised on September 10, 2007
Accepted on October 12, 2007
Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697-4560
Corresponding Author: lanhuang{at}uci.edu
Dynamically interacting proteins associate and dissociate with their binding partners at high on/off rates. Although their identification is of great significance to proteomics research, lack of an efficient strategy to distinguish stable and dynamic interactors has hampered the efforts towards this goal. In this work, we have developed a new method, MAP (mixing after purification)-SILAC, to quantitatively investigate the interactions of protein complexes by mass spectrometry. In combination with the original SILAC approach, stable and dynamic components are effectively distinguished by the differences in their relative abundance ratio changes. We applied the newly developed strategies to decipher the dynamics of the human 26S proteasome interacting proteins (PIPs). A total of 67 putative human PIPs are identified by the MAP-SILAC method, among which 14 proteins would have been misidentified as background proteins due to low relative abundance ratios in standard SILAC experiments and 57 proteins have not been previously reported. In addition, 35 of the 67 proteins are classified as stable interactors of the proteasome complex, whereas 16 of them are identified as dynamic ones. The methods reported here provide a valuable expansion of proteomics technologies for identification of important but previously unidentifiable interacting proteins.
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