Affinity-Based Proteomics Probes; Tools for Studying Carbohydrate-Processing Enzymes

Keith A. Stubbs; David J. Vocadlo

doi:10.1071/CH09140

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Affinity-Based Proteomics Probes; Tools for Studying Carbohydrate-Processing Enzymes

Keith A. Stubbs ^A ^C and David J. Vocadlo ^B

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^A Chemistry M313, School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.

^B Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.

^C Corresponding author. Email: keith.stubbs@uwa.edu.au

Keith A. Stubbs completed his Ph.D. in the laboratory of Bob Stick at the University of Western Australia in 2005. Keith then moved to Canada to take a Post-doctoral position at Simon Fraser University in the laboratory of David J. Vocadlo. In 2008, he moved back to Australia to the University of Western Australia. His research interests include carbohydrates, bioorganic chemistry, and chemical biology.

David J. Vocadlo completed his Ph.D. in the laboratory of Stephen Withers at the University of British Columbia in 2002. Interest in fusing chemistry, enzymology, and biology drew him to the laboratory of Carolyn Bertozzi at the University of California at Berkeley, where he also gained a strong appreciation for cell biology. In 2004, David joined the Department of Chemistry at Simon Fraser University, where he is currently a Scholar of the Michel Smith Health Research Foundation and the Canada Research Chair in Chemical Glycobiology. David is kept busy taking care of his group and growing family but still, on rare occasions, finds time to go rock climbing.

Australian Journal of Chemistry 62(6) 521-527 https://doi.org/10.1071/CH09140
Submitted: 10 March 2009 Accepted: 30 March 2009 Published: 10 June 2009

Abstract

As more information becomes available through the efforts of high-throughput screens, there is increasing pressure on the three main ‘omic’ fields, genomics, proteomics, and metabolomics, to organize this material into useful libraries that enable further understanding of biological systems. Proteomics especially is faced with two highly challenging tasks. The first is assigning the activity of thousands of putative proteins, the existence of which has been suggested by genomics studies. The second is to serve as a link between genomics and metabolomics by demonstrating which enzymes play roles in specific metabolic pathways. Underscoring these challenges in one area are the thousands of putative carbohydrate-processing enzymes that have been bioinformatically identified, mostly in prokaryotes, but that have unknown or unverified activities. Using two brief examples, we illustrate how biochemical pathways within bacteria that involve carbohydrate-processing enzymes present interesting potential antimicrobial targets, offering a clear motivation for gaining a functional understanding of biological proteomes. One method for studying proteomes that has been developed recently is to use synthetic compounds termed activity-based proteomics probes. Activity-based proteomic profiling using such probes facilitates rapid identification of enzyme activities within proteomes and assignment of function to putative enzymes. Here we discuss the general design principles for these probes with particular reference to carbohydrate-processing enzymes and give an example of using such a probe for the profiling of a bacterial proteome.

Acknowledgements

The present manuscript is dedicated to Professor R.V. Stick on the occasion of his retirement. D.J.V. thanks the Natural Sciences and Engineering Research Council of Canada (NSERC) for financial support. D.J.V. is supported as a scholar of the Michael Smith Foundation for Health Research (MSFHR) and is the Canada Research Chair in Chemical Glycobiology.

References

Affinity-Based Proteomics Probes; Tools for Studying Carbohydrate-Processing Enzymes

Abstract

Acknowledgements

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