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Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical & Biomolecular Engineering (BK21 Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea, 2Department of BioSystems, Bioinformatics Research Center, Korea Advanced Institute of Science and Technology, 3Korea Basic Science Institute, 52 Yeoeun-dong, Yuseong-gu, Daejeon 305-333, Republic of Korea Cellular proteases play important roles in protein unfolding, translocation, and turnover. However, proteases released upon cell disruption can cause significant problems in proteome analysis. Here we report that small heat shock proteins (sHsps), including IbpAEc and IbpBEc from E. coli and Hsp26Sc from S. cerevisiae, are
able to protect proteins in vitro from proteolytic degradation. Addition of sHsps during 2DE of human serum or whole cell extracts of E. coli, M. succinciproducens, A. thaliana, and human kidney cells allowed detection of up to 50% more protein spots than those obtainable with currently available protease inhibitors. Furthermore, we identified the low abundance proteins that newly appeared in the gels of sHsps-treated proteome. Thus the use of sHsps during 2-DE significantly improves proteome profiling by generally enabling the detection of many more protein spots that could not be seen previously. [This work was supported by the Korea Science
and Engineering Foundation (KOSEF) grant funded by the Korea government (MOST) (No. M10309020000-03B5002-00000). Further supports by LG Chem Chair Professorship, Microsoft and IBM SUR program are appreciated.].