Experimental and Computational Analyses of the Energetic Basis for Dual Recognition of Immunity Proteins by Colicin Endonucleases

Anthony H. Keeble, Lukasz A. Joachimiak, María Jesus Maté, Nicola Meenan, Nadine Kirkpatrick, David Baker, Colin Kleanthous

Research output: Contribution to journalArticlepeer-review

35 Scopus citations


Colicin endonucleases (DNases) are bound and inactivated by immunity (Im) proteins. Im proteins are broadly cross-reactive yet specific inhibitors binding cognate and non-cognate DNases with Kd values that vary between 10- 4 and 10- 14 M, characteristics that are explained by a 'dual-recognition' mechanism. In this work, we addressed for the first time the energetics of Im protein recognition by colicin DNases through a combination of E9 DNase alanine scanning and double-mutant cycles (DMCs) coupled with kinetic and calorimetric analyses of cognate Im9 and non-cognate Im2 binding, as well as computational analysis of alanine scanning and DMC data. We show that differential ΔΔGs observed for four E9 DNase residues cumulatively distinguish cognate Im9 association from non-cognate Im2 association. E9 DNase Phe86 is the primary specificity hotspot residue in the centre of the interface, which is coordinated by conserved and variable hotspot residues of the cognate Im protein. Experimental DMC analysis reveals that only modest coupling energies to Im9 residues are observed, in agreement with calculated DMCs using the program ROSETTA and consistent with the largely hydrophobic nature of E9 DNase-Im9 specificity contacts. Computed values for the 12 E9 DNase alanine mutants showed reasonable agreement with experimental ΔΔG data, particularly for interactions not mediated by interfacial water molecules. ΔΔG predictions for residues that contact buried water molecules calculated using solvated rotamer models met with mixed success; however, we were able to predict with a high degree of accuracy the location and energetic contribution of one such contact. Our study highlights how colicin DNases are able to utilise both conserved and variable amino acids to distinguish cognate from non-cognate Im proteins, with the energetic contributions of the conserved residues modulated by neighbouring specificity sites.

Original languageEnglish (US)
Pages (from-to)745-759
Number of pages15
JournalJournal of Molecular Biology
Issue number4
StatePublished - Jun 13 2008
Externally publishedYes


  • alanine scanning
  • crystallography
  • double-mutant cycles
  • protein-protein interactions
  • specificity

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology


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