Date Published: December 21, 2009
Publisher: Public Library of Science
Author(s): Song Yang, Philip E. Bourne, Robert Belshaw. http://doi.org/10.1371/journal.pone.0008378
Abstract: Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest.
Partial Text: Originally discovered as spatially distinct regions of proteins, protein domains are now considered discrete evolutionary units. One basic physical property–the ability to fold independently–defines the features of protein domains including their evolutionary significance. As stable 3D structures, each covering significant sequence space, with relationships between those sequences perhaps undetectable by sequence methods, domains have much to offer in the study of evolution. Add to that features of domain arrangements  and a limited number relative to the immense possibilities of sequence space  and we have the makings of a powerful method of analysis.