Retro-MoRFS: Identifying protein binding sites by normal and reverse alignment and intrinsic disorder prediction

Bin Xue, A. Keith Dunker, Vladimir N. Uversky

Research output: Contribution to journalArticlepeer-review

29 Scopus citations

Abstract

Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination of sequence alignment and disorder prediction as a tool to improve the confidence of identifying MoRF-based protein-protein interactions. The method of reverse sequence alignment is also rationalized here as a novel approach for finding additional interaction regions, leading to the concept of a retro-MoRF, which has the reversed sequence of an identified MoRF. The set of retro-MoRF binding partners likely overlap the partner-sets of the originally identified MoRFs. The high abundance of MoRF-containing intrinsically disordered proteins in nature suggests the possibility that the number of retro-MoRFs could likewise be very high. This hypothesis provides new grounds for exploring the mysteries of protein-protein interaction networks at the genome level.

Original languageEnglish (US)
Pages (from-to)3725-3747
Number of pages23
JournalInternational journal of molecular sciences
Volume11
Issue number10
DOIs
StatePublished - Oct 2010

Keywords

  • Alignment
  • Intrinsic Disorder
  • Invert
  • PONDR-RIBS
  • Retro
  • Reverse

ASJC Scopus subject areas

  • Computer Science Applications
  • Molecular Biology
  • Catalysis
  • Inorganic Chemistry
  • Spectroscopy
  • Organic Chemistry
  • Physical and Theoretical Chemistry

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