A spectrophotometric assay for conjugation of ubiquitin and ubiquitin-like proteins

Christopher E. Berndsen, Cynthia Wolberger

Research output: Contribution to journalArticle

Abstract

Ubiquitination is a widely studied regulatory modification involved in protein degradation, DNA damage repair, and the immune response. Ubiquitin is conjugated to a substrate lysine in an enzymatic cascade involving an E1 ubiquitin-activating enzyme, an E2 ubiquitin-conjugating enzyme, and an E3 ubiquitin ligase. Assays for ubiquitin conjugation include electrophoretic mobility shift assays and detection of epitope-tagged or radiolabeled ubiquitin, which are difficult to quantitate accurately and are not amenable to high-throughput screening. We have developed a colorimetric assay that quantifies ubiquitin conjugation by monitoring pyrophosphate released in the first enzymatic step in ubiquitin transfer, the ATP-dependent charging of the E1 enzyme. The assay is rapid, does not rely on radioactive labeling, and requires only a spectrophotometer for detection of pyrophosphate formation. We show that pyrophosphate production by E1 is dependent on ubiquitin transfer and describe how to optimize assay conditions to measure E1, E2, and E3 activity. The kinetics of polyubiquitin chain formation by Ubc13-Mms2 measured by this assay are similar to those determined by gel-based assays, indicating that the data produced by this method are comparable to methods that measure ubiquitin transfer directly. This assay is adaptable to high-throughput screening of ubiquitin and ubiquitin-like conjugating enzymes.

Original languageEnglish (US)
Pages (from-to)102-110
Number of pages9
JournalAnalytical Biochemistry
Volume418
Issue number1
DOIs
StatePublished - Nov 1 2011

Fingerprint

Ubiquitins
Ubiquitin
Assays
Ubiquitin-Conjugating Enzymes
Ubiquitin-Activating Enzymes
Screening
Polyubiquitin
Throughput
Ubiquitin-Protein Ligases
Ubiquitination
Electrophoretic mobility
Electrophoretic Mobility Shift Assay
Spectrophotometers
DNA Repair
Enzymes
Proteolysis
Lysine
DNA Damage
Epitopes
Labeling

Keywords

  • Ubc13-Mms2
  • Ubiquitin conjugation
  • Ubiquitin-activating enzyme
  • Ubiquitin-like proteins

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology
  • Cell Biology

Cite this

A spectrophotometric assay for conjugation of ubiquitin and ubiquitin-like proteins. / Berndsen, Christopher E.; Wolberger, Cynthia.

In: Analytical Biochemistry, Vol. 418, No. 1, 01.11.2011, p. 102-110.

Research output: Contribution to journalArticle

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