Target selection for structural genomics: a single genome approach

We describe our strategy for selecting targets for protein structure determination in context of structural genomics of a single genome. In the course of target selection, we have studied two of the smallest microbial genomes, Mycoplasma genitalium and Mycoplasma pneumoniae. To our surprise, we found that only 71 Mycoplasma genes or their orthologues can be considered as easy targets for high-throughput structural studies--far fewer than expected. We discuss the methods and criteria used for target selection and the reasons explaining rarity of easy targets. First, despite the common opinion that protein folds can be predicted for only 30-50% of genes, the number of "truly unknown" structures is less than one-third. Second, due to the different codon usage, two thirds of Mycoplasma proteins cannot be directly expressed in E. coli in high-throughput manner and require substitution by their homologues from other organisms. Third, membrane or large multi-domain proteins are difficult targets because of solubility and size issues and often require identification and structure determination of protein domains. Finally, we propose different approaches to address the difficult targets.