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A more recent version of this article appeared on June 1, 2006.
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Submitted on June 1, 2005
Revised on March 10, 2006
Accepted on March 14, 2006

Systematic characterization of nuclear proteome from human T leukemia cells: A quantitative proteomic study during apoptosis by differential extraction and stable isotope labeling

Sun-Il Hwang, Deborah H. Lundgren, Viveka Mayya, Karim Rezaul, Ann E. Cowan, Jimmy K. Eng, and David K. Han

Center for Vascular Biology, Dept. of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030

Corresponding Author: han{at}nso.uchc.edu

Identification and characterization of the nuclear proteome is important for detailed understanding of multiple signaling events in eukaryotic cells. Towards this goal, we have extensively characterized the nuclear proteome of human T leukemia cells by sequential extraction of nuclear proteins with different physiochemical properties using three buffer conditions. This large scale proteomic study also tested the feasibility and technical challenges associated with stable isotope labeling by amino acids in cell culture (SILAC) to uncover quantitative changes during apoptosis. Analyzing proteins from three nuclear fractions extracted from naïve and apoptotic cells generated 780,530 MS/MS spectra that were used for database searching using the SEQUEST algorithm. This analysis resulted in the identification and quantification of 1,174 putative nuclear proteins. A number of known nuclear proteins involved in apoptosis as well as novel proteins not known to be part of the nuclear apoptotic machinery were identified and quantified. Consistent with SILAC-based quantifications, immunofluorescence staining of nucleus, mitochondria, and some associated proteins from both organelles revealed a dynamic recruitment of mitochondria into nuclear invaginations during apoptosis.


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