Needle in the haystack: structure-based toxin discovery

Trends Biochem Sci. 2008 Nov;33(11):546-56. doi: 10.1016/j.tibs.2008.08.003. Epub 2008 Sep 22.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • ADP Ribose Transferases / genetics
  • ADP Ribose Transferases / metabolism*
  • Animals
  • Bacterial Toxins / metabolism*
  • Catalytic Domain
  • Computational Biology / methods*
  • Databases, Protein*
  • Protein Folding
  • Protein Structure, Secondary
  • Sequence Alignment / methods
  • Software

Substances

  • Bacterial Toxins
  • ADP Ribose Transferases