Table 1.
Data collection and refinement statistics.
Fig 1.
The overall structure of IBPv.
(A) Two protein molecules were observed in the asymmetric unit of the IBPv crystal. Each protein molecule contains two ice binding domains, which are colored green and cyan, respectively. Water molecules are depicted as gray spheres. (B) The overall structure of a single IBPv molecule. More water molecules (gray spheres) were bound with B (cyan) domain than A (green) domain.
Fig 2.
Comparison of two domains of IBPv.
(A) The stereo view of the secondary structure of domain A, colored from blue (N terminal end) to red (C terminal end). (B) Structural alignment of domain A (green) and domain B (cyan).
Fig 3.
Hydrophobic interactions and disulfide bonds.
(A) & (B) The aligned hydrophobic residues inside the β-helix of domain A and B. In each core, four rows of tightly packed side chains were found, those residues were summarized in Table 2. (C) & (D) The hydrophobic interactions between the α-helix and β-helix for domain A and domain B. The amino groups of K170 and K387 and the hydroxyl groups of Y89 and Y304 point outward, allowing the hydrocarbon chains and the phenyl groups to from hydrophobic interactions with other non-polar side chains at the interfaces. (E) & (F) The intra-domain disulfide bond formed in A domain and B domain. N-T stands for N terminal end, C-T stands for C terminal end, and S-S stands for disulfide bond.
Table 2.
Summary of hydrophobic core of each domain.
Fig 4.
(A) The predicted IBS on domain A. The two rows of aligned side chains are in blue, water molecules in gray. (B) Stick diagram of the IBS of domain A and surrounding water. Each water molecule formed at least one hydrogen bond with protein backbone. (C) The predicted IBS on domain B. The two rows of aligned side chains are in blue, water molecules in gray. One row of well packed water molecules was found between the two rows of aligned side chains. The other row of water is located on the other side of the aligned small side chains. (D) Stick diagram of the IBS of domain B and surrounding water. Each water molecule formed at least one hydrogen bond with protein backbone. (E) Water molecules form pentagonal and hexagonal rings at the IBS on domain B. Overall structure of domain B is displayed as cartoon (cyan). Ala row on the IBS of domain B is illustrated as stick diagram (blue).
Fig 5.
Antifreeze activities of the IBPv mutants.
(A) The CD spectra of IBPv and its mutants. (B) TH of IBPv and its mutants. (C) The CD spectra of IBPv_a and its mutants. (D) TH of IBPv_a and its mutants.
Fig 6.
Structural comparison of homologous AFPs.
(A) The structural alignment of IBPv_a, IBPv_b, ColAFP, LeIBP, FfIBP, TisAFP6 and TisAFP8. Residues were colored by Qres, which was related to the distance of Cα after the alignment. Blue-white-red indicated from less deviance to large deviance between the Cα of aligned residues. (B) IBPv_a, IBPv_b, ColAFP, LeIBP, and TisAFP6 were aligned by their structure data, but were colored according to primary sequence similarity using BLOSUM 60. Blue-white-red indicated from high similarity to low similarity. (C) The structural alignment of the hyperactive β helical AFPs. ColAFP, FfIBP, TisAFP8 and IBPv_b. Residues were colored by Qres values. Blue-white-red indicated from less deviance to large deviance between the Cα of aligned residues.