Design and synthesis of an affinity probe that targets caspases in proteomic experiments

Liau, M.; Panicker, Resmi C.; Yao, Shao Q.

doi:10.1016/s0040-4039(02)02724-7

Cited by 19 publications

(10 citation statements)

References 20 publications

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“…BODIPY labeled epoxide probes have been used for labeling of cysteine proteases in lysates and intact cells [36]. Caspase probes containing the Cy fluorophore have been reported [37]. Because of their superior chemical properties, cyanine dyes have a great potential for use in imaging applications.…”

Section: Structure Of Activity Based Probesmentioning

confidence: 99%

Activity-based probes as a tool for functional proteomic analysis of proteases

Fonović¹,

Bogyo²

2008

Expert Review of Proteomics

213

144

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SUMMARYTraditional proteomics methodology allows global analysis of protein abundance but does not provide information about the regulation of protein activity. Proteases in particular are known for their multilayered posttranslational activity regulation which can lead to a significant difference between protease abundance levels and their enzyme activity. To address those issues, the field of activity based proteomics has been established in order to characterize protein activity and monitor the functional regulation of enzymes in complex proteomes. In this review, we present structural features of activity based probes for proteases and discuss their applications in proteomic profiling of various catalytic classes of proteases.

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Section: Structure Of Activity Based Probesmentioning

confidence: 99%

Activity-based probes as a tool for functional proteomic analysis of proteases

Fonović¹,

Bogyo²

2008

Expert Review of Proteomics

213

144

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“…N-Hydroxysuccinimide (NHS) esters of both Cy3 and Cy5 dyes were synthesized and characterized as previously described [20,24,25]. Briefly, Cy3 (0.44 g, 0.76 mmol), synthesized as described [24], was dissolved in DMF (5 mL) followed by addition of N-hydroxysuccinimide (106 mg, 0.92 mmol) and 1,3-dicyclohexylcarbodiimide (DCC; 190 mg, 0.92 mmol).…”

Section: Dye Synthesismentioning

confidence: 99%

Proteome analysis of Saccharomyces cerevisiae under metal stress by two‐dimensional differential gel electrophoresis

Hu¹,

Wang

Chen

et al. 2003

Electrophoresis

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The defense mechanism by which cells combat metal stress remains poorly understood. By utilizing a newly developed technique - the differential gel electrophoresis (DIGE) - we evaluated the biological alterations of metal stress on Saccharomyces cerevisiae at its translational level. By simultaneously comparing the differential expression profiles of thousands of proteins as results of 15 different metal treatments, we were able to closely examine the response of a large number of proteins within the yeast proteome towards individual metals, as well as the response of the same proteins towards different metals. This, to our knowledge, is the first case which demonstrates the potential of DIGE as a high-throughput tool for large-scale proteome analysis. From our studies, where yeast cells were exhaustively treated with exogenous metals, 20-30% of all proteins detected showed statistically significant changes. According to different effects (up-/downregulation) of protein expression levels observed, we were able to tentatively divide the 15 metals into three groups. By mass spectrometric analysis, more than 50 protein spots were positively identified, both quantitatively and qualitatively. One of the proteins was identified to be Cu/Zn superoxide dismutase (SOD1), and its expression levels as a result of 15 different metal treatments was further examined in greater details. Significant changes in SOD1 expression were observed throughout all 15 DIGE gels.

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“…Recently, the fluoromethylketone electrophile has been incorporated in an ABP containing a racemic aspartate P1 element ( Table 1, entry 2) [9]. Although not tested in complex proteomes, this probe was shown to label a purfied caspase, but not a set of other purified enzymes, including serine and cysteine proteases, illustrating its selectivity for a distinct class of cysteine proteases.…”

Section: Warheads In Abpsmentioning

confidence: 99%

Dissecting Protein Function Using Chemical Proteomic Methods

Verhelst

Bogyo

2005

QSAR Comb. Sci.

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The completion of genome projects of multiple organisms has revealed an enormous number of unknown protein products. The field of proteomics has now become focused on finding ways to elucidate the cellular function of these proteins and their possible role in pathological processes. A relatively new approach to address global protein function has been termed activity-based proteomics or chemical proteomics. This method makes use of small molecules that can covalently attach to catalytic residues in an enzyme active site. The selectivity of the chemically reactive group allows specific proteins or protein subsets to be tagged, purified and analyzed, providing insight in their biochemical roles. As a result this technique has the potential to accelerate the process of identification of new drug targets.

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Design and synthesis of an affinity probe that targets caspases in proteomic experiments

Cited by 19 publications

References 20 publications

Activity-based probes as a tool for functional proteomic analysis of proteases

Activity-based probes as a tool for functional proteomic analysis of proteases

Proteome analysis of Saccharomyces cerevisiae under metal stress by two‐dimensional differential gel electrophoresis

Dissecting Protein Function Using Chemical Proteomic Methods

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