Novel dimeric β-helical model of an ice nucleation protein with bridged active sites

BMC Struct Biol. 2011 Sep 27;11:36. doi: 10.1186/1472-6807-11-36.


Background: Ice nucleation proteins (INPs) allow water to freeze at high subzero temperatures. Due to their large size (>120 kDa), membrane association, and tendency to aggregate, an experimentally-determined tertiary structure of an INP has yet to be reported. How they function at the molecular level therefore remains unknown.

Results: Here we have predicted a novel β-helical fold for the INP produced by the bacterium Pseudomonas borealis. The protein uses internal serine and glutamine ladders for stabilization and is predicted to dimerize via the burying of a solvent-exposed tyrosine ladder to make an intimate hydrophobic contact along the dimerization interface. The manner in which PbINP dimerizes also allows for its multimerization, which could explain the aggregation-dependence of INP activity. Both sides of the PbINP structure have tandem arrays of amino acids that can organize waters into the ice-like clathrate structures seen on antifreeze proteins.

Conclusions: Dimerization dramatically increases the 'ice-active' surface area of the protein by doubling its width, increasing its length, and presenting identical ice-forming surfaces on both sides of the protein. We suggest that this allows sufficient anchored clathrate waters to align on the INP surface to nucleate freezing. As PbINP is highly similar to all known bacterial INPs, we predict its fold and mechanism of action will apply to these other INPs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Bacterial Outer Membrane Proteins / chemistry*
  • Bacterial Outer Membrane Proteins / metabolism
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Catalytic Domain
  • Dimerization
  • Hydrophobic and Hydrophilic Interactions
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Protein Structure, Secondary
  • Pseudomonas / metabolism
  • Solvents / chemistry
  • Surface Properties
  • Water / chemistry


  • Bacterial Outer Membrane Proteins
  • Bacterial Proteins
  • Solvents
  • ice nucleation protein
  • Water