Positional Scanning Synthetic Combinatorial Libraries for Substrate Profiling

  • Eric L. Schneider
  • Charles S. Craik
Part of the Methods in Molecular Biology™ book series (MIMB, volume 539)


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.

Key words:

Peptide library Substrate profiling Protease specificity PS-SCL ACC 



We thank M. D. Lim, M. Zhao, and Y. Choe for helpful discussions and critical reading of the manuscript. The authors were funded by NIH grants CA108462-04 (E.L.S.) and GM082250 (C.S.C).


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Eric L. Schneider
    • 1
  • Charles S. Craik
  1. 1.Department of Pharmaceutical ChemistryThe University of California, San FranciscoSan FranciscoUSA

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