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Methods Mol Biol. 2009;539:59-78. doi: 10.1007/978-1-60327-003-8_4.

Positional scanning synthetic combinatorial libraries for substrate profiling.

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Department of Pharmaceutical Chemistry, The University of California, San Francisco, San Francisco, CA, USA.


Determining the preferred substrate cleavage sequence of proteases is an important step toward understanding their roles in cancer development and progression. Knowledge of this sequence can aid in the design of new experimental tools for study as well as aid in the identification of endogenous protease substrates and signaling pathways. Various investigators have demonstrated a number of techniques to uncover these sequences, but most can be very time consuming. We have designed and successfully implemented a complete diverse ACC tetrapeptide positional scanning synthetic combinatorial library that allows for the rapid screening of proteases to determine their preferred residues at positions P1-P4. These sequences can be readily verified through kinetic measurements on single peptide substrates and utilized to further knowledge of the role of proteases in cancer.

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