Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

Abstract

Structural genomics is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy that is medically and biologically relevant, of good value, and tractable. As an option to consider, we present the "Pfam5000" strategy, which involves selecting the 5000 most important families from the Pfam database as sources for targets. We compare the Pfam5000 strategy to several other proposed strategies that would require similar numbers of targets. These strategies include complete solution of several small to moderately sized bacterial proteomes, partial coverage of the human proteome, and random selection of approximately 5000 targets from sequenced genomes. We measure the impact that successful implementation of these strategies would have upon structural interpretation of the proteins in Swiss-Prot, TrEMBL, and 131 complete proteomes (including 10 of eukaryotes) from the Proteome Analysis database at the European Bioinformatics Institute (EBI). Solving the structures of proteins from the 5000 largest Pfam families would allow accurate fold assignment for approximately 68% of all prokaryotic proteins (covering 59% of residues) and 61% of eukaryotic proteins (40% of residues). More fine-grained coverage that would allow accurate modeling of these proteins would require an order of magnitude more targets. The Pfam5000 strategy may be modified in several ways, for example, to focus on larger families, bacterial sequences, or eukaryotic sequences; as long as secondary consideration is given to large families within Pfam, coverage results vary only slightly. In contrast, focusing structural genomics on a single tractable genome would have only a limited impact in structural knowledge of other proteomes: A significant fraction (about 30 -40% of the proteins and 40 -60% of the residues) of each proteome is classified in small families, which may have little overlap with other species of interest. Random selection of targets from one or more genomes is similar to the Pfam5000 strategy in that proteins from larger families are more likely to be chosen, but substantial effort would be spent on small families. Proteins 2005;58:166 -179.

Sequence-Based Protein Crystallization Propensity Prediction for Structural Genomics: Review and Comparative Analysis

“…The above provides a strong motivation for further research and development in this area. Several strategies have been proposed to improve the success rate including obtaining one representative structure per protein family and working with multiple orthologues [14,26,27,28].…”

Crystal structure of a novel non-Pfam protein PF2046 solved using low resolution B-factor sharpening and multi-crystal averaging methods

“…Depending on the match, the structure is then searched for motifs or signature catalytic residues in order to narrow down on the function. Such an approach provides a good starting point for designing functional experiments to support the structural evidence in order to determine the function of hypothetical proteins (Brenner and Levitt, 2000;Chandonia and Brenner, 2005).…”

Targeting the Human Cancer Pathway Protein Interaction Network by Structural Genomics

“…This target selection strategy can be applied to any biochemical pathway of interest. Previously reported target selection strategies for structural genomics have focused on family (76,77), whole genome (78 -80), pathways (25,67), and complexes (28,29). The target selection strategy we present here combines the selection strategies that have been proposed for structural genomics of biochemical pathways (25,67) and of protein-protein complexes (28,29).…”