High-stringency tandem affinity purification of proteins conjugated to ubiquitin-like moieties

Filip Golebiowski, Michael H. Tatham, Akihiro Nakamura, Ronald T. Hay

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    15 Citations (Scopus)

    Abstract

    The post-translational modification of proteins with ubiquitin and ubiquitin-like proteins (Ubl) is vital to many cellular functions, and thus the identification of Ubl targets is key to understanding their function. In most cases, only a small proportion of the cellular pool of proteins is found conjugated to a particular Ubl, making identification of Ubl targets technically challenging. For the purposes of proteomic analyses, we have developed a protocol for the large-scale purification of Ubl-linked proteins that minimizes sample contamination with noncovalent interactors and prevents the cleavage of Ubl-substrate bonds catalyzed by Ubl-specific proteases. This is achieved by introducing a denaturing lysis step (in the presence of sodium dodecyl sulfate and alkylating agents that irreversibly inhibit Ubl proteases) before TAP (tandem affinity purification) that allows for efficient purification of putative Ubl-specific substrates in a form suitable for proteomic analysis. The timescale from cell lysis to purified protein sample is 5-6 d.

    Original languageEnglish
    Pages (from-to)873-882
    Number of pages10
    JournalNature Protocols
    Volume5
    Issue number5
    DOIs
    Publication statusPublished - 2010

    Keywords

    • SPECTROMETRY-BASED PROTEOMICS
    • MASS-SPECTROMETRY
    • QUANTITATIVE PROTEOMICS
    • SUMO MODIFICATIONS
    • CELL-CULTURE
    • AMINO-ACIDS
    • DNA-REPAIR
    • IN-VITRO
    • IDENTIFICATION
    • MODIFIER

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