Structural conversion of the transformer protein RfaH: New insights derived from protein structure prediction and molecular dynamics simulations

Nicole Balasco, Daniela Barone, Luigi Vitagliano

Research output: Contribution to journalArticle

Abstract

Recent structural investigations have shown that the C-terminal domain (CTD) of the transcription factor RfaH undergoes unique structural modifications that have a profound impact into its functional properties. These modifications cause a complete change in RfaHCTD topology that converts from an α-hairpin to a β-barrel fold. To gain insights into the determinants of this major structural conversion, we here performed computational studies (protein structure prediction and molecular dynamics simulations) on RfaHCTD. Although these analyses, in line with literature data, suggest that the isolated RfaHCTD has a strong preference for the β-barrel fold, they also highlight that a specific region of the protein is endowed with a chameleon conformational behavior. In particular, the Leu-rich region (residues 141-145) has a good propensity to adopt both α-helical and β-structured states. Intriguingly, in the RfaH homolog NusG, whose CTD uniquely adopts the β-barrel fold, the corresponding region is rich in residues as Val or Ile that present a strong preference for the β-structure. On this basis, we suggest that the presence of this Leu-rich element in RfaHCTD may be responsible for the peculiar structural behavior of the domain. The analysis of the sequences of RfaH family (PfamA code PF02357) unraveled that other members potentially share the structural properties of RfaHCTD. These observations suggest that the unusual conformational behavior of RfaHCTD may be rare but not unique.

Original languageEnglish
Pages (from-to)2173-2179
Number of pages7
JournalJournal of Biomolecular Structure and Dynamics
Volume33
Issue number10
DOIs
Publication statusPublished - Oct 3 2015

Keywords

  • amino acid propensities
  • conformational conversion
  • molecular dynamics
  • secondary structure prediction
  • transformer proteins

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

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