A Minimal Set of Folds

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Science  21 Jan 2005:
Vol. 307, Issue 5708, pp. 319
DOI: 10.1126/science.307.5708.319d

The application of technologies that allow the collection of large amounts of data (genomic and proteomic, expression and structure) has generated a demand for methods that can be used to interrogate and systematize these data sets—hence large-scale biology has marched arm in arm with sophisticated (and sometimes bordering on the abstruse) computational analysis. In a refreshing departure from this complexity, Yang et al. have used a simple nearest-neighbor kind of approach to overlay a catalog of 174 sequenced genomes with the three-dimensional structures of 1294 protein fold superfamilies.

Surprisingly, they can resurrect the phylogenies of Archaea, Bacteria, and Eukarya quite accurately within each kingdom and pretty well across them. They also find 50 fold superfamilies that are common to all three kingdoms—many, but not all, of these proteins are involved in translation—which, in the authors' view, represents the fossilized metabolic machinery of the last common ancestor of the three major lineages. — GJC

Proc. Natl. Acad. Sci. U.S.A. 102, 373 (2005).

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