Understanding the "horizontal dimension" of Molecular evolution to annotate, classify, and discover proteins with functional domains

Gloria Rendon, Mao Feng Ger, Ruth Kantorovitz, Shreedhar Natarajan, Jeffrey Tilson, Eric Jakobsson

Research output: Contribution to journalArticlepeer-review

Abstract

Protein evolution proceeds by two distinct processes: 1) individual mutation and selection for adaptive mutations and 2) rearrangement of entire domains within proteins into novel combinations, producing new protein families that combine functional properties in ways that previously did not exist. Domain rearrangement poses a challenge to sequence alignment-based search methods, such as BLAST, in predicting homology since the methodology implicitly assumes that related proteins primarily differ from each other by individual mutations. Moreover, there is ample evidence that the evolutionary process has used (and continues to use) domains as building blocks, therefore, it seems fit to utilize computational, domain-based methods to reconstruct that process. A challenge and opportunity for computational biology is how to use knowledge of evolutionary domain recombination to characterize families of proteins whose evolutionary history includes such recombination, to discover novel proteins, and to infer protein-protein interactions. In this paper we review techniques and databases that exploit our growing knowledge of "horizontal" protein evolution, and suggest possible areas of future development. We illustrate the power of the domain-based methods and the possible directions of future development by a case history in progress aiming at facilitating a particular approach to understanding microbial pathogenicity.

Original languageEnglish (US)
Pages (from-to)82-94
Number of pages13
JournalJournal of Computer Science and Technology
Volume25
Issue number1
DOIs
StatePublished - Jan 2010

Keywords

  • Domain interactions
  • Domain-based discovery
  • Domain-based orthology
  • Interpro
  • Meme/mast

ASJC Scopus subject areas

  • Software
  • Theoretical Computer Science
  • Hardware and Architecture
  • Computer Science Applications
  • Computational Theory and Mathematics

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