Ice-binding surface of fish type III antifreeze.
We employed computational techniques, including molecular docking, energy minimization, and molecular dynamics simulation, to investigate the ice-binding surface of fish type III antifreeze protein (AFP). The putative ice-binding site was previously identified by mutagenesis, structural analysis, and flatness evaluation. Using a high-resolution x-ray structure of fish type III AFP as a model, we calculated the ice-binding interaction energy of 11 surface patches chosen to cover the entire surface of the protein. These various surface patches exhibit small but significantly different ice-binding interaction energies. For both the prism ice plane and an "ice" plane in which water O atoms are randomly positioned, our calculations show that a surface patch containing 14 residues (L19, V20, T18, S42, V41, Q9, P12, A16, M21, T15, Q44, I13, N14, K61) has the most favorable interaction energy and corresponds to the previously identified ice-binding site of type III AFP. Although in general agreement with the earlier studies, our results also suggest that the ice-binding site may be larger than the previously identified "core" cluster that includes mostly hydrophilic residues. The enlargement mainly results from the inclusion of peripheral hydrophobic residues and K61.
Chen
G
G
Department of Chemistry, Beijing Normal University, Beijing 100875, China.
Jia
Z
Z
D000595:Amino Acid Sequence; D000818:Animals; D021301:Antifreeze Proteins; D001665:Binding Sites; D002151:Calorimetry; D003198:Computer Simulation; D005399:Fishes; D006023:Glycoproteins / Q000737:chemistry* / Q000378:metabolism; D007053:Ice; D008958:Models, Molecular; D011487:Protein Conformation; D013499:Surface Properties; D013816:Thermodynamics
D021301:Antifreeze Proteins; D006023:Glycoproteins; D007053:Ice