The structural genomics experimental pipeline: Insights from global target lists

Abstract

Structural genomics (SG) initiatives are currently attempting to achieve the high-throughput determination of protein structures on a genome-wide scale. Here we analyze the SG target data that have been publicly released over a period of 16 months to assess the potential of the SG initiatives. We use statistical techniques most commonly applied in epidemiology to describe the dynamics of targets through the experimental SG pipeline. There is no clear bottleneck among the key stages of cloning, expression, purification and crystallization. An SG target will progress through each of these steps with a probability of approximately 45%. Around 80% of targets with diffraction data will yield a crystal structure, and 20% of targets with HSQC spectra will yield an NMR structure. We also find the overlaps among SG targets: 61% of SG protein sequences share at least 30% sequence identity with one or more other SG targets. There is no significant difference in average structure quality among SG structures and other structures in the PDB determined by "traditional" methods, but on average SG structures are deposited to the PDB twice as quickly after X-ray data collection.

Progress of Structural Genomics Initiatives: An Analysis of Solved Target Structures

“…In so doing, structural genomics will approach expectations that were conjectured at the outset on the basis of selecting targets not recognisable from sequence. 90 Again considering the 30% sequence identity threshold, there is some overlap between groups, but given the high fraction of published (solved and unsolved) SG targets selected for structure determination that have a close homologue targeted by another consortium, 48,63 it is In all, 20% of CATH nr-SG domains fall into one of these 11 superfamilies. In addition to the number of models, the Table lists the number of sequences for which the CATH nr-SG domains have provided structural information.…”

“…Three proteins have been solved twice by different consortia. Considering all published targets, and not only those that have been solved, O'Toole et al 48 detected 45% target redundancy across consortia at a 30% sequence identity threshold. Thus, despite huge scope for overlap, many duplicated efforts have been avoided at the structure determination stage, although there is still room for improvement.…”

“…Whilst a larger fraction of targets are from "straightforward" archaeal and bacterial genomes such as Escherichia coli and Thermotoga maritima, as many as 19% are eukaryotic. Eukaryotes represent a much higher fraction of all SG targets selected for structural characterisation (53%) 48 but we can expect the two proportions to converge slowly in the coming years as the experimental techniques improve. These dependencies of productivity aside, it is apparent from the final column in Table 2 that output during the year 2004 differs enormously from one consortium to another.…”

ESPRIT: An automated, library-based method for mapping and soluble expression of protein domains from challenging targets

“…The challenges associated with overexpression and purification of monodisperse, soluble, purifiable protein are well-appreciated by any structural biology laboratory. Over the last decade, structural genomics projects have permitted a more quantitative measure of the efficiency of different steps in the structure solution process under a relatively standardised set of conditions (Burley, 2000;O'Toole et al, 2004). Clearly, proteins do not behave uniformly during recombinant expression steps, notably the success rate of a single-domain protein may be very different to a large multi-domain protein when Escherichia coli is used as the preferred production system.…”

Data Management in the Modern Structural Biology and Biomedical Research Environment

“…However, even the modest amount of data available in TargetDB permitted interesting analyses of the overall SG structure determination pipeline [13, 14]. In particular, the overall efficiency of the pipeline—the ratio of solved structures to clones—was found to be below 10 % even in the most productive centers.…”