Amino acid insertion reveals a necessary three-helical intermediate in the folding pathway of the colicin E7 immunity protein Im7

J Mol Biol. 2009 Oct 2;392(4):1074-86. doi: 10.1016/j.jmb.2009.07.085. Epub 2009 Aug 3.

Abstract

The small (87-residue) alpha-helical protein Im7 (an inhibitor protein for colicin E7 that provides immunity to cells producing colicin E7) folds via a three-state mechanism involving an on-pathway intermediate. This kinetic intermediate contains three of four native helices that are oriented in a non-native manner so as to minimise exposed hydrophobic surface area at this point in folding. The short (6-residue) helix III has been shown to be unstructured in the intermediate ensemble and does not dock onto the developing hydrophobic core until after the rate-limiting transition state has been traversed. After helix III has docked, it adopts an alpha-helical secondary structure, and the side chains of residues within this region provide contacts that are crucial to native-state stability. In order to probe further the role of helix III in the folding mechanism of Im7, we created a variant that contains an eight-amino-acid polyalanine-like helix stabilised by a Glu-Arg salt bridge and an Asn-Pro-Gly capping motif, juxtaposed C-terminal to the natural 6-residue helix III. The effect of this insertion on the structure of the native protein and its folding mechanism were studied using NMR and varphi-value analysis, respectively. The results reveal a robust native structure that is not perturbed by the presence of the extended helix III. Mutational analysis performed to probe the folding mechanism of the redesigned protein revealed a conserved mechanism involving the canonical three-helical intermediate. The results suggest that folding via a three-helical species stabilised by both native and non-native interactions is an essential feature of Im7 folding, independent of the helical propensity of helix III.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / genetics*
  • Amino Acids / metabolism
  • Carrier Proteins / chemistry*
  • Carrier Proteins / genetics*
  • Carrier Proteins / metabolism
  • Cloning, Molecular
  • Colicins / metabolism
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics*
  • Escherichia coli Proteins / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Mutagenesis, Insertional / physiology*
  • Peptide Fragments / chemistry
  • Peptide Fragments / metabolism
  • Protein Binding
  • Protein Folding*
  • Protein Structure, Secondary / genetics
  • Recombinant Proteins / chemistry

Substances

  • Amino Acids
  • Carrier Proteins
  • Colicins
  • E colicin-binding immunity protein Im7, E coli
  • Escherichia coli Proteins
  • Peptide Fragments
  • Recombinant Proteins

Associated data

  • PDB/2K0D