A phylogenomic reconstruction of the protein world based on a genomic census of protein fold architecture

Minglei Wang, Simina Maria Boca, Rakhee Kalelkar, Jay E. Mittenthal, Gustavo Caetano-Anolles

Research output: Contribution to journalArticle

Abstract

The protein world has a hierarchical and redundant organization that can be specified in terms of evolutionary units of molecular structure, the protein domains. The Structural Classification of Proteins (SCOP) has unified domains into a comparatively small set of folding architectures, the protein fold families and superfamilies, and these have been further grouped into protein folds. In this study, we reconstruct the evolution of the protein world using information embedded in a structural genomic census of fold architectures defined by a phylogenomic analysis of 185 completely sequenced genomes using advanced hidden Markov models and 776 folds described in SCOP release 1.67. Our study confirms the existence of defined evolutionary patterns of architectural diversification and explores how phylogenomic trees generated from folds relate to those reconstructed from fold superfamilies. Evolutionary patterns help us propose a general conceptual model that describes the growth of architectures in the protein world.

Original languageEnglish (US)
Pages (from-to)27-40
Number of pages14
JournalComplexity
Volume12
Issue number1
DOIs
StatePublished - Jan 1 2006

Keywords

  • Architectural diversification
  • Evolutionary funnel
  • Organismal diversification
  • Origins of life
  • Protein fold structure

ASJC Scopus subject areas

  • Computer Science(all)
  • General

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