Novel dimeric β-helical model of an ice nucleation protein with bridged active sites
Open Access
- 27 September 2011
- journal article
- Published by Springer Science and Business Media LLC in BMC Structural Biology
- Vol. 11 (1), 36
- https://doi.org/10.1186/1472-6807-11-36
Abstract
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. 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 Pb INP dimerizes also allows for its multimerization, which could explain the aggregation-dependence of INP activity. Both sides of the Pb INP structure have tandem arrays of amino acids that can organize waters into the ice-like clathrate structures seen on antifreeze proteins. 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 Pb INP is highly similar to all known bacterial INPs, we predict its fold and mechanism of action will apply to these other INPs.Keywords
This publication has 39 references indexed in Scilit:
- Anchored clathrate waters bind antifreeze proteins to iceProceedings of the National Academy of Sciences of the United States of America, 2011
- Overview of theCCP4 suite and current developmentsActa crystallographica. Section D, Structural biology, 2011
- Minimalist design of water-soluble cross-β architectureProceedings of the National Academy of Sciences of the United States of America, 2010
- Aromatic Cross-Strand Ladders Control the Structure and Stability of β-Rich Peptide Self-Assembly MimicsJournal of Molecular Biology, 2008
- X-ray Structure of Snow Flea Antifreeze Protein Determined by Racemic Crystallization of Synthetic Protein EnantiomersJournal of the American Chemical Society, 2008
- Crystal Structure and Standardized Geometric Analysis of InlJ, a Listerial Virulence Factor and Leucine-Rich Repeat Protein with a Novel Cysteine LadderJournal of Molecular Biology, 2008
- GROMACS: Fast, flexible, and freeJournal of Computational Chemistry, 2005
- Coot: model-building tools for molecular graphicsActa crystallographica. Section D, Structural biology, 2004
- WebLogo: A Sequence Logo Generator: Figure 1Genome Research, 2004
- AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMRJournal of Biomolecular NMR, 1996