title: Quantitative and qualitative analysis of type III antifreeze protein structure and function.
abstract: Some cold water marine fishes avoid cellular damage because of freezing by expressing antifreeze proteins (AFPs) that bind to ice and inhibit its growth; one such protein is the globular type III AFP from eel pout. Despite several studies, the mechanism of ice binding remains unclear because of the difficulty in modeling the AFP-ice interaction. To further explore the mechanism, we have determined the x-ray crystallographic structure of 10 type III AFP mutants and combined that information with 7 previously determined structures to mainly analyze specific AFP-ice interactions such as hydrogen bonds. Quantitative assessment of binding was performed using a neural network with properties of the structure as input and predicted antifreeze activity as output. Using the cross-validation method, a correlation coefficient of 0.60 was obtained between measured and predicted activity, indicating successful learning and good predictive power. A large loss in the predictive power of the neural network occurred after properties related to the hydrophobic surface were left out, suggesting that van der Waal's interactions make a significant contribution to ice binding. By combining the analysis of the neural network with antifreeze activity and x-ray crystallographic structures of the mutants, we extend the existing ice-binding model to a two-step process: 1) probing of the surface for the correct ice-binding plane by hydrogen-bonding side chains and 2) attractive van der Waal's interactions between the other residues of the ice-binding surface and the ice, which increases the strength of the protein-ice interaction.
authors: Department of Biochemistry, Queen's University, Kingston, Ontario, K7L 3N6 Canada.
authors: S P
authors: SP
authors: Graether
authors: C I
authors: CI
authors: DeLuca
authors: J
authors: J
authors: Baardsnes
authors: G A
authors: GA
authors: Hill
authors: P L
authors: PL
authors: Davies
authors: Z
authors: Z
authors: Jia
mesh_terms: D021301:Antifreeze Proteins; D006023:Glycoproteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D016571:Neural Networks, Computer; D011487:Protein Conformation; D013329:Structure-Activity Relationship
chemical_list: D021301:Antifreeze Proteins; D006023:Glycoproteins