Title :
Evolution of protein architectures inferred from phylogenomic analysis of CATH
Author :
Bukhari, S.A. ; Caetano-Anolles, G.
Author_Institution :
Dept. of Crop Sci., Univ. of Illinois, Urbana, IL, USA
Abstract :
Protein architecture refers to similar secondary structural arrangements irrespective of their connectivity. Here we aim to explore the evolution of protein architectures by benchmarking CATH and SCOP annotations. For example, we explore the appearance and diversification of protein architectures such as sandwiches, bundles, barrels, solenoids, ribbons, trefoils, prisms and propellers. Structural phylogenies generated at CATH “A”, “T” and “H” levels of structural abstraction revealed patterns of reductive evolution and three epochs in the evolution of protein world. Although CATH and SCOP differ significantly in their protein domain definitions and in the hierarchical partitioning of fold space, our findings strongly support the fact that both protein structural classification systems classify a protein on a very similar theoretical basis by taking into account their structural, functional and evolutionary roles. The tree of “A” showed that the 3-layer (aba) sandwich (3.40), the orthogonal bundle (1.10) and the alpha-beta complex (3.90) harbor simple secondary structure arrangements that are the most ancient, popular and abundant architectures in the protein world.
Keywords :
evolution (biological); genomics; molecular biophysics; molecular configurations; proteins; 3-layer sandwich; CATH annotation; SCOP annotation; alpha-beta complex; fold space; hierarchical partitioning; orthogonal bundle; phylogenomic analysis; protein architecture; protein domain; protein structural classification system; secondary structure arrangement; structural abstraction; structural phylogenies; Archaea; Genomics; Phylogeny; Protein engineering; Proteins; Vegetation; Last Universal Common Ancestor; Tree of Architectures;
Conference_Titel :
Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference on
Conference_Location :
Atlanta, GA
Print_ISBN :
978-1-4577-1612-6
DOI :
10.1109/BIBMW.2011.6112548