Needle in the haystack: structure-based toxin discovery.
In the current data-rich era, making the leap from sequence data to knowledge is a task that requires an elegant bioinformatics toolset to pinpoint pressing research questions. Therefore, a strategy to expand important protein-family knowledge is required, particularly in cases in which primary sequence identity is low but structural conservation is high. For example, the mono-ADP-ribosylating toxins fit these criteria and several approaches have been used to accelerate the discovery of new family members. The strategy evolved from conduction of PSI-BLAST searches through to the combination of secondary-structure prediction with pattern-based searches. However, a newly developed tactic, in which fold recognition dominates, reduces reliance on sequence similarity and advances scientists toward a true structure-based protein-family expansion methodology.
Fieldhouse
Robert J
RJ
Department of Molecular and Cellular Biology, University of Guelph, ON, Canada.
Merrill
A Rod
AR
D036002:ADP Ribose Transferases / Q000235:genetics / Q000378:metabolism*; D000818:Animals; D001427:Bacterial Toxins / Q000378:metabolism*; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D017510:Protein Folding; D017433:Protein Structure, Secondary; D016415:Sequence Alignment / Q000379:methods; D012984:Software
D001427:Bacterial Toxins; D036002:ADP Ribose Transferases