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A tandem orthogonal proteolysis strategy for high-content chemical proteomics

Academic Article
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Overview

related to degree

  • Speers, Anna, Ph.D. in Chemistry, Scripps Research 2000 - 2005

authors

  • Speers, Anna
  • Cravatt, Benjamin

publication date

  • July 2005

journal

  • Journal of the American Chemical Society  Journal

abstract

  • The field of proteomics aims to assign functions to the numerous protein products encoded by eukaryotic and prokaryotic genomes. Toward this end, chemical strategies have emerged as a powerful means to enrich specific classes of proteins based on shared functional properties, such as catalytic activity [activity-based protein profiling (ABPP)], and post-translational modification state. The theoretical information content in chemical proteomic experiments greatly exceeds the actual data procured, due in large part to limitations in existing analytical technologies. Here, we present a tandem orthogonal proteolysis (TOP) strategy for high-content chemical proteomics that enables the parallel characterization of probe-labeled proteins and sites of probe modification. The TOP approach exploits "click chemistry" to introduce a multifunctional tag onto probe-labeled proteins that contains both a biotin group for protein enrichment and a tobacco etch virus (TEV) protease cleavage site for selective release of probe-modified peptides. Following capture on streptavidin beads, protein targets of probes and their sites of labeling are sequentially identified by a two-step proteolysis strategy (trypsin and TEV, respectively). We apply the TOP method to characterize targets of sulfonate ester ABPP probes in tissue proteomes, resulting in the discovery of numerous active site-labeled enzymes. Enzymes modified on regulatory sites and proteins of unknown function were also identified. These findings indicate that a wide range of functional residues are targeted by sulfonate ester probes and highlight the value of TOP-based chemical proteomics for the characterization of proteins and the residues that regulate their activity.

subject areas

  • Amino Acid Sequence
  • Animals
  • Enzymes
  • Molecular Probe Techniques
  • Molecular Sequence Data
  • Molecular Structure
  • Proteomics
  • Trypsin
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Identity

PubMed Central ID

  • PMC1538546

International Standard Serial Number (ISSN)

  • 0002-7863

Digital Object Identifier (DOI)

  • 10.1021/ja0532842

PubMed ID

  • 16011363
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Additional Document Info

start page

  • 10018

end page

  • 10019

volume

  • 127

issue

  • 28

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