HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text (PDF) Submit a response Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Alert me to new issues of the journal Download to citation manager Glossary Citing Articles Citing Articles via Google Scholar Google Scholar Search for Related Content Social Bookmarking                      What's this?

Molecular & Cellular Proteomics 6:S51, 2007.
© 2007 by The American Society for Biochemistry and Molecular Biology, Inc.

---

Abstracts

Session 5

Systems-Wide Analysis of Protein Complexes in Saccharomyces cerevisiae

A.-C. Gavin

European Molecular Biology Laboratory, Heidelberg, Germany

The omics field contributes comprehensive repertoires of the cell building blocks. The next challenge resides in the understanding of how the pieces of this puzzle assemble a coherent entity; a cell. Biology relies on the concerted action of a number interacting proteins and metabolites operationally organized in cellular networks. The current appreciation of the wiring diagram of these networks is scanty. We used tandem-affinity purification and mass spectrometry to achieve a system-wide analysis for protein complexes in a model organism, budding yeast. The study provides one of the largest collections of physically-determined eukaryotic cellular machines; 491 complexes, of which 257 were novel. Beyond the repertoire, the analysis captures the modular nature of proteomes, where protein complexes differentially combine with additional attachment proteins or protein modules to enable a diversification of functions. Support for this organisation comes from integration with available data on expression, localisation, function, evolutionary conservation, protein structure and binary interactions. An innovative scoring system measures the potency of proteins to associate. It represents an attempt to move from static interaction networks to more dynamic maps. This first proteome equation captures some biochemical properties of protein-protein interaction: the likelihood to be in direct physical contact and, weakly, the dissociation constants. In the future, experimental and computational refinements may turn such scoring approaches into suitable parameters for rational modeling of entire systems.

5.2

Degradomics: the Proteolysis of Cell Death

S. Mahrus, J. Trinidad, A. Burlingame, and J. A. Wells

Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA

Apoptosis, or programmed cell death, represents an ultimate fate decision in cell biology. This process is critical for cellular differentiation and remodeling of tissues, and for anti-viral and anti-tumor defense. A distinct molecular feature of apoptosis is the widespread but controlled cellular proteolysis, that is predominantly mediated by the caspase family of cysteine proteases. The study of apoptotic pathways has important ramifications for determining what is critical for cellular homeostasis, and for the development of potential anti-cancer therapeutics. We have developed a robust proteomic method for global profiling of proteolysis ("degradomics") in cells. Key to this is a new method that permits selective labeling and enrichment for the protein N-termini created as a result of proteolysis. Using this approach we have already identified >250 caspase substrates from Jurkat cells that were induced to undergo apoptosis by treatment with the chemotherapeutic agent etoposide. More than 80% of these proteins have not been reported before. These proteins fall into a wide range of functional classes, and reveal much about the molecular components, logic, and timed sequence of events that drive a cell from life to death. We believe this approach will be useful for following the proteolysis of apoptosis induced by various agents or in different cell types, and will be generally useful for dissecting protease signaling pathways.

5.3

Characterization of GSK3 Dependent Circadian Phosphoproteome

K. Kaasik ¹, J. Allen², K. Shokat², L. J. Ptáek¹, and Y.-H. Fu¹

Departments of ¹Neurology and ²Pharmaceutical Chemistry, University of California, San Francisco, CA

Circadian rhythms are an adaptation to the daily solar cycle and are produced by transcriptional feedback loops. Defining features like period length and self sustained oscillations are regulated by protein kinases that phosphorylate clock associated transcription factors. Glycogen synthase kinases (GSK3 and GSK3ß) are among key regulators of circadian rhythms; however the functional significance of GSK3 catalyzed protein phosphorylation in the circadian proteome is poorly understood. GSK3 protein kinase activity itself has a circadian profile. Phosphorylated N-terminus of GSK3 prevents substrate bindings and blocks access to its catalytic center. Therefore we hypothesized that a subset of GSK3 substrates are regulated in a circadian manner. In order to identify direct GSK3 targets we are using chemical genetics approach and we have designed ATP analog-specific (as) kinases, which utilize bulky ATP analogs that are not utilized by wild-type kinases. We have further refined this method to allow antibody based detection and immunoaffinity isolation of kinase substrates. Immunoprecipitation with a thiophosphate-ester specific antibody allows isolation of direct kinase substrates from complex proteomes in the presence of hundreds of other kinases, which is particularly important for GSK3 which often requires a prior phosphorylation priming event to recognize its substrates. We have determined that a subset of GSK3 substrates in liver and brain tissues have a circadian phosphorylation pattern. Furthermore, we are in the process of identifying potentially novel GSK3 targets. Knowing the specificity of GSK3 and GSK3ß substrates and their circadian regulation will assist in design of novel therapies and more efficient use of current GSK3 inhibitors in medical treatment with fewer side effects.

5.4

Interactome Networks

M. Vidal

Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Genetics, Harvard Medical School, Boston, MA

For over half a century it has been conjectured that macromolecules form complex networks of functionally interacting components, and that the molecular mechanisms underlying most biological processes correspond to particular steady states adopted by such cellular networks. However, until recently, systems-level theoretical conjectures remained largely unappreciated, mainly because of lack of supporting experimental data.

To generate the information necessary to eventually address how complex cellular networks relate to biology, we initiated, at the scale of the whole proteome, an integrated approach for modeling protein-protein interaction or "interactome" networks. Our main questions are: How are interactome networks organized at the scale of the whole cell? How can we uncover local and global features underlying this organization, and how are interactome networks modified in human disease, such as cancer?

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This Article Full Text (PDF) Submit a response Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Alert me to new issues of the journal Download to citation manager Glossary Citing Articles Citing Articles via Google Scholar Google Scholar Search for Related Content Social Bookmarking                      What's this?