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Target selection for complex structural genomics

workpackage 4.1 of the 3D-Repertoire project

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3D-Repertoire is a European Integrated Project that aims at resolving structures for all amenable protein complexes in the yeast Saccharomyces cerevisiae at the best possible resolution through a combination of electron microscopy, X-ray crystallography and in silico approximations. This will provide valuable information about the biological functions of these cellular machines and details about the interaction interfaces of their protein components.

Despite recent advances in DNA recombination techniques and automation of purification methods, protein production is still challenging for individual proteins and even harder for big macromolecular complexes. Less abundant complexes will need induced overexpression and assembly to obtain the amount of protein necessary for structure determination experiments. The required polycistronic vectors have the disadvantage that they impose certain limits on the number of complex components as well as on their individual size. Another challenge comes from the very dynamic nature of protein complexes which often adopt slightly different compositions (complex isoforms) depending on the cellular conditions. Therefore, the development of clear target selection strategies to rationally select the complexes that should be tackled first is a crucial objective to maximize the return, minimize the costs and prevent experimental difficulties.

In a recent publication in Nature, Anne-Claude Gavin and Patrick Aloy et al. suggested a modular organization within protein complexes: each complex is formed by an invariable core of proteins plus a set of attachment proteins that are only present in certain complex isoforms. Among the attachments they found several instances where two or more proteins were always together and present in more than one complex, which they called modules.

The target selection strategy presented here ranks the set of 491 yeast complexes from Anne-Claude Gavin and Patrick Aloy et al. according to their chances to undergo successful expression, purification and crystallization. In the advanced form, we also let the user choose the weight given to each criterion in the final score so that it can meet his or her particular needs. Furthermore, the complexes are functionally annotated using GO-slim terms, and the orthologs for each complex in the model organisms H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana and E. coli can be displayed. You may also upload and rank your own yeast constructs (i.e. protein complexes of interest).

Please cite the following publication:

Pache RA, Aloy P.
Incorporating high-throughput proteomics experiments into
structural biology pipelines: identification of the low-hanging fruits.
Proteomics. 2008 May;8(10):1959-64.
PMID: 18491310