Proteases and Cancer

Volume 539 of the series Methods in Molecular Biology™ pp 93-114


High Throughput Substrate Phage Display for Protease Profiling

  • Boris Ratnikov
  • , Piotr Cieplak
  • , Jeffrey W. SmithAffiliated withCenter on Proteolytic Pathways, Burnham Institute for Medical Research Email author 

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The interplay between a protease and its substrates is controlled at many different levels, including coexpression, colocalization, binding driven by ancillary contacts, and the presence of natural inhibitors. Here we focus on the most basic parameter that guides substrate recognition by a protease, the recognition specificity at the catalytic cleft. An understanding of this substrate specificity can be used to predict the putative substrates of a protease, to design protease activated imaging agents, and to initiate the design of active site inhibitors. Our group has characterized protease specificities of several matrix metalloproteinases using substrate phage display. Recently, we have adapted this method to a semiautomated platform that includes several high-throughput steps. The semiautomated platform allows one to obtain an order of magnitude more data, thus permitting precise comparisons among related proteases to define their functional distinctions.

Key words

Substrate phage display Substrate Protease Specificity Proteolysis Filamentous phage M13 coat protein 3gene protein