Polypentagonal ice-like water networks emerge solely in an activity-improved variant of ice-binding protein

• Published in: Proceedings of the National Academy of Sciences - PNAS 2018-05, Vol.115 (21), p.5456-5461
• Main Authors: Mahatabuddin, Sheikh, Fukami, Daichi, Arai, Tatsuya, Nishimiya, Yoshiyuki, Shimizu, Rumi, Shibazaki, Chie, Kondo, Hidemasa, Adachi, Motoyasu, Tsuda, Sakae
• Format: Article
• Language: English
• Subjects: Animals; Antifreeze Proteins - chemistry; Antifreeze Proteins - genetics; Antifreeze Proteins - metabolism; Bifurcations; Binding Sites; Biological Sciences; Biophysical Phenomena; Carrier Proteins - chemistry; Carrier Proteins - genetics; Carrier Proteins - metabolism; Clusters; Complementarity; Crystal defects; Crystal structure; Crystallography, X-Ray; Crystals; Fish Proteins - chemistry; Fish Proteins - genetics; Fish Proteins - metabolism; Fishes - metabolism; Freezing; Hydration; Ice; Ice - analysis; Ice crystals; Molecules; Mutants; Mutation; Networks; Protein Binding; Protein Conformation; Protein Isoforms; Proteins; Water - chemistry; Water - metabolism; Zoarcidae
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1800635115

Polypentagonal water networks were recently observed in a protein capable of binding to ice crystals, or ice-binding protein (IBP). To examine such water networks and clarify their role in ice-binding, we determined X-ray crystal structures of a 65-residue defective isoform of a Zoarcidae-derived IBP (wild type, WT) and its five single mutants (A20L, A20G, A20T, A20V, and A20I). Polypentagonal water networks composed of ∼50 semiclathrate waters were observed solely on the strongest A20I mutant, which appeared to include a tetrahedral water cluster exhibiting a perfect position match to the (1010) first prism plane of a single ice crystal. Inclusion of another symmetrical water cluster in the polypentagonal network showed a perfect complementarity to the waters constructing the (2021) pyramidal ice plane. The order of ice-binding strength was A20L < A20G < WT < A20T < A20V < A20I, where the top three mutants capable of binding to the first prism and the pyramidal ice planes commonly contained a bifurcated γ-CH₃ group. These results suggest that a fine-tuning of the surface of Zoarcidae-derived IBP assisted by a side-chain group regulates the holding property of its polypentagonal water network, the function of which is to freeze the host protein to specific ice planes.