3QF6

Neutron structure of type-III Antifreeze Protein allows the reconstruction of AFP-ice interface

Summary for 3QF6

• Entry DOI: 10.2210/pdb3qf6/pdb
• Related: 1HG7
• Descriptor: Type-3 ice-structuring protein HPLC 12 (2 entities in total)
• Functional Keywords: ice binding protein, antifreeze protein
• Biological source: Macrozoarces americanus (ocean pout)
• Cellular location: Secreted : P19614
• Total number of polymer chains: 1
• Total formula weight: 7017.28

Authors

Howard, E.I.,Blakeley, M.P.,Haertlein, M.,Petit-Haertlein, I.,Mitschler, A.,Fisher, S.J.,Cousido-Siah, A.,Salvay, A.G.,Popov, A.,Muller-Dieckmann, C.,Petrova, T.,Podjarny, A. (deposition date: 2011-01-21, release date: 2011-06-22, Last modification date: 2024-03-20)

Primary citation

Howard, E.I.,Blakeley, M.P.,Haertlein, M.,Petit-Haertlein, I.,Mitschler, A.,Fisher, S.J.,Cousido-Siah, A.,Salvay, A.G.,Popov, A.,Muller-Dieckmann, C.,Petrova, T.,Podjarny, A.
Neutron structure of type-III antifreeze protein allows the reconstruction of AFP-ice interface.
J.Mol.Recognit., 24:724-732, 2011

PubMed Abstract: Antifreeze proteins (AFPs) inhibit ice growth at sub-zero temperatures. The prototypical type-III AFPs have been extensively studied, notably by X-ray crystallography, solid-state and solution NMR, and mutagenesis, leading to the identification of a compound ice-binding surface (IBS) composed of two adjacent ice-binding sections, each which binds to particular lattice planes of ice crystals, poisoning their growth. This surface, including many hydrophobic and some hydrophilic residues, has been extensively used to model the interaction of AFP with ice. Experimentally observed water molecules facing the IBS have been used in an attempt to validate these models. However, these trials have been hindered by the limited capability of X-ray crystallography to reliably identify all water molecules of the hydration layer. Due to the strong diffraction signal from both the oxygen and deuterium atoms, neutron diffraction provides a more effective way to determine the water molecule positions (as D(2) O). Here we report the successful structure determination at 293 K of fully perdeuterated type-III AFP by joint X-ray and neutron diffraction providing a very detailed description of the protein and its solvent structure. X-ray data were collected to a resolution of 1.05 Å, and neutron Laue data to a resolution of 1.85 Å with a "radically small" crystal volume of 0.13 mm(3). The identification of a tetrahedral water cluster in nuclear scattering density maps has allowed the reconstruction of the IBS-bound ice crystal primary prismatic face. Analysis of the interactions between the IBS and the bound ice crystal primary prismatic face indicates the role of the hydrophobic residues, which are found to bind inside the holes of the ice surface, thus explaining the specificity of AFPs for ice versus water.

PubMed: 21472814
DOI: 10.1002/jmr.1130

Experimental method

NEUTRON DIFFRACTION (1.85 Å)