Computational Predictions of the Mutant Behavior of AraC

Monica Berrondo, Jeffrey J. Gray, Robert Schleif

Research output: Contribution to journalArticlepeer-review

Abstract

An algorithm implemented in Rosetta correctly predicts the folding capabilities of the 17-residue N-terminal arm of the AraC gene regulatory protein when arabinose is bound to the protein and the dramatically different structure of this arm when arabinose is absent. The transcriptional activity of 43 mutant AraC proteins with alterations in the arm sequences was measured in vivo and compared with their predicted folding properties. Seventeen of the mutants possessed regulatory properties that could be directly compared with folding predictions. Sixteen of the 17 mutants were correctly predicted. The algorithm predicts that the N-terminal arm sequences of AraC homologs fold to the Escherichia coli AraC arm structure. In contrast, it predicts that random sequences of the same length and many partially randomized E. coli arm sequences do not fold to the E. coli arm structure. The high level of success shows that relatively "simple" computational methods can in some cases predict the behavior of mutant proteins with good reliability.

Original languageEnglish (US)
Pages (from-to)462-470
Number of pages9
JournalJournal of molecular biology
Volume398
Issue number3
DOIs
StatePublished - May 2010

Keywords

  • Mutant activity prediction
  • Protein folding
  • Protein structure prediction

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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