Five years of increasing structural biology throughput - A retrospective analysis

Abstract

The completed sequencing and initial characterization of the human genome in 2001 (Lander et al 2001; Venter et al 2001) and that of other organisms such as Drosophila melanogaster (Adams et al 2000) and the SARS Corona Virus (Marra et al 2003), have educated us on the vast complexity of the proteome. Full genome characterization efforts highlight how critical it is to understand at a molecular level all of the protein products from multiple organisms. An important issue for addressing the molecular characterization challenge is the need to quickly and economically characterize normal and diseased biological processes in order to understand the basic biology and chemistry of the systems and to facilitate the discovery and development of new therapeutic and diagnostic protocols. In order to fully characterize the proteins at the molecular level, three-dimensional protein structure determination has proven to be invaluable, complementing biological and biochemical information from other types of experiments. Structural information is also the ultimate rational drug design tool, with the potential to save an estimated 50% of the cost of drug discovery (Stevens 2004). However, the best means by which to attain structural knowledge is a topic of controversy. The traditional approach was a complex and labor-intensive process in which one protein or complex was studied at a time. The alternative is a high throughput (HT), discovery-oriented approach wherein entire families, pathways or genomes are characterized. Benefits include the economy of scale, the speed of mass production, and a dramatic increase in discovery rates through the systematic collection and analysis of data. Prior to the late 1990's, the technologies and approaches were too slow and unreliable to allow for such larger scale analyses. In the past, we have reviewed some of the technology developments in miniaturizing and streamlining structure determination pipelines (Stevens 2004; Abola et al 2000). For this chapter, we summarize the input and output of several structural genomics efforts that have validated new technology efforts over the first 5 years of the HT structural biology era. These technologies have been used by various HT pipelines that have contributed to the determination of over 1600 new structures, a high percentage of which were novel folds, and 70% had less than 30% identity to any other protein in the Protein Data Bank (PDB) at the time of release. As an example of the implementation of the HT pipeline, we discuss in some detail the specific approach of the Joint Center for Structural Genomics (JCSG) that we have been involved in. © 2007 Springer.