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

Mahatabuddin, Sheikh; Fukami, Daichi; Arai, Tatsuya; Nishimiya, Yoshiyuki; Shimizu, R; Shibazaki, C.; Kondo, Hidemasa; Adachi, Motoyasu; Tsuda, Sakae

doi:10.1073/pnas.1800635115

Cited by 32 publications

(44 citation statements)

References 43 publications

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“…Such IBSs are similarly constructed on each AFP structure, which are chartacterized by a planar hydrophobic surface that incorporates several polar groups 14 . Two IBSs bound to the () prism and () pyramidal planes are uniquely located side by side in AFPIII 20 . With using the informaton of putative ice-binding residues and structural coordinates, we evaluated approximate size of IBS (Å 2 ) for each AFP sample (Supplementary Table S1).…”

Section: Resultsmentioning

confidence: 99%

“…Fungal AFP was also identified from a mid-latitude snow-mold Typhula ishikariensis , whose 8 th isoform (Tis8) exhibited a strong ability of ice binding, and constructs a 7-ladder β-helical structure with a triangular cross-section (Mw = 22 kDa) 18,19 . In contrast, a defective isoform of AFPIII, whose A20 is replaced with Leu (A20L), was suggested to bind only weakly to ice crystal surface 20 . Figure 1 compares the three-dimensional structures and ice-binding sites determined for these five AFP molecules (AFPI-III, Tis8, and A20L).…”

Section: Introductionmentioning

confidence: 99%

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Ice recrystallization is strongly inhibited when antifreeze proteins bind to multiple ice planes

Rahman¹,

Arai²,

Yamauchi³

et al. 2019

Sci Rep

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Ice recrystallization is a phenomenon observed as the increase in ice crystal size within an already frozen material. Antifreeze proteins (AFPs), a class of proteins capable of arresting ice crystal growth, are known to inhibit this phenomenon even at sub milli-molar concentrations. A tremendous range in the possible applications of AFPs is hence expected in both medical and industrial fields, while a key determinant of the ice recrystallization inhibition (IRI) is hardly understood. Here, IRI efficiency and ice plane affinity were examined for the wild-type AFPI–III, a defective AFPIII isoform, and a fungal AFP isoform. To simplify the IRI analysis using the formal representation of Ostwald-ripening (r3 = r03 + kt), we monitored specific ice grains exhibiting only uniform growth, for which maximum Feret diameter was measured. The cube of an ice grain’s radius (r3) increased proportionately with time (t), and its slope gave the recrystallization rate (k). There was a significant difference in the IRI efficiency between the samples, and the fungal AFP possessing the activity with the smallest amount (0.27 μM) exhibited an affinity to multiple ice planes. These results suggest that the IRI efficiency is maximized when AFPs bind to a whole set of ice planes.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Ice recrystallization is strongly inhibited when antifreeze proteins bind to multiple ice planes

Rahman¹,

Arai²,

Yamauchi³

et al. 2019

Sci Rep

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“…AFP I was hence thought to possess an ability to expand its target area from the local to the entire surface of an ice crystal. No such concentration dependence was observed for AFP III ( Figure 3A, right) [7], which is bound to a dumbbell-like area composed of first prism and pyramidal planes [24].…”

Section: Analysis Of Fluorescence-based Ice Plane Affinity (Fipa) Formentioning

confidence: 93%

“…The list below shows AFPs and their target ice planes: Each target plane was determined according to the illumination area called "FIPA pattern" on the spherical ice crystal, to which fluorescent AFPs adsorbs. A wider FIPA pattern implies an extensive AFP adsorption, which leads to an effective ice growth inhibition and a high TH activity [24]. Figure 3A,B illustrate the known FIPA patterns observed for the fluorescent AFP I and III, respectively [7].…”

Section: Analysis Of Fluorescence-based Ice Plane Affinity (Fipa) Formentioning

confidence: 96%

“…An IBS of an AFP species generally accompanies the hydration waters in an ice-like arrangement, for which an anchoring role to bring the host protein to a specific ice plane has been speculated [22][23][24]. An interfacial region between bulk waters and bulk ice consists of a 10 to 15 Å-thick, intrinsically disordered "quasi-liquid layer," which is more ordered than bulk waters, but less ordered compared with the hexagonal ice lattice [54,55].…”

Section: Oligomerization Hypothesis For Type II Antifreeze Proteinmentioning

confidence: 99%

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Fish-Derived Antifreeze Proteins and Antifreeze Glycoprotein Exhibit a Different Ice-Binding Property with Increasing Concentration

et al. 2020

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The concentration of a protein is highly related to its biochemical properties, and is a key determinant for its biotechnological applications. Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) are structurally diverse macromolecules that are capable of binding to embryonic ice crystals below 0 °C, making them useful as protectants of ice-block formation. In this study, we examined the maximal solubility of native AFP I–III and AFGP with distilled water, and evaluated concentration dependence of their ice-binding property. Approximately 400 mg/mL (AFP I), 200 mg/mL (AFP II), 100 mg/mL (AFP III), and >1800 mg/mL (AFGP) of the maximal solubility were estimated, and among them AFGP’s solubility is much higher compared with that of ordinary proteins, such as serum albumin (~500 mg/mL). The samples also exhibited unexpectedly high thermal hysteresis values (2–3 °C) at 50–200 mg/mL. Furthermore, the analysis of fluorescence-based ice plane affinity showed that AFP II binds to multiple ice planes in a concentration-dependent manner, for which an oligomerization mechanism was hypothesized. The difference of concentration dependence between AFPs and AFGPs may provide a new clue to help us understand the ice-binding function of these proteins.

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Hydrogen‐Bond Free Energy of Local Biological Water

Park

Lee

et al. 2020

Angewandte Chemie

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Here,w ep ropose an experimental methodology based on femtosecond-resolved fluorescence spectroscopyt o measure the hydrogen (H)-bond free energy of water at protein surfaces under isothermal conditions.Ademonstration was conducted by installing anon-canonical isostere of tryptophan (7-azatryptophan) at the surface of ac oiled-coil protein to exploit the photoinduced proton transfer of its chromophoric moiety,7-azaindole.The H-bond free energy of this biological water was evaluated by comparing the rates of proton transfer, sensitive to the hydration environment, at the protein surface and in bulk water,a nd it was found to be higher than that of bulk water by 0.4 kcal mol À1 .T he free-energy difference is dominated by the entropic cost in the H-bond network among water molecules at the hydrophilic and charged protein surface. Our study opens ad oor to accessing the energetics and dynamics of local biological water to give insight into its roles in protein structure and function.

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

Cited by 32 publications

References 43 publications

Ice recrystallization is strongly inhibited when antifreeze proteins bind to multiple ice planes

Ice recrystallization is strongly inhibited when antifreeze proteins bind to multiple ice planes

Fish-Derived Antifreeze Proteins and Antifreeze Glycoprotein Exhibit a Different Ice-Binding Property with Increasing Concentration

Hydrogen‐Bond Free Energy of Local Biological Water

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