Antifreeze Activity Research Articles

Modelling of short synthetic antifreeze peptides: Insights into ice-pinning mechanism

Organisms living in icy environments produce antifreeze proteins to control ice growth and recrystallization. It has been proposed that these molecules pin the surface of ice crystals, thus inducing the formation of a curved surface that arrests crystal growth. Such proteins are very appealing for many potential applications in food industry, material science and cryoconservation of organs and tissues. Unfortunately, their structural complexity has seriously hampered their practical use, while efficient and accessible synthetic analogues are highly desirable. In this paper, we used molecular dynamics based techniques to model the interaction of three short antifreeze synthetic peptides with an ice surface. The employed protocols succeeded in reproducing the ice pinning action of antifreeze peptides and the consequent ice growth arrest, as well as in distinguishing between antifreeze and control peptides, for which no such effect was observed. Principal components analysis of peptides trajectories in different simulation settings permitted to highlight the main structural features associated to antifreeze activity. Modeling results are highly correlated with experimentally measured properties, and insights on ice-peptide interactions and on conformational patterns favoring antifreeze activity will prompt the design of new and improved antifreeze peptides.

Deciphering the Role of the Non-ice-binding Surface in the Antifreeze Activity of Hyperactive Antifreeze Proteins.

Antifreeze proteins (AFPs) show thermal hysteresis through specific interaction with the ice crystal. Hyperactive AFPs interact with the ice surface through a threonine-rich motif present at their ice-binding surface (IBS). Ordering of water around the IBS was extensively investigated. However, the role of non-IBS in ice growth inhibition is yet to be understood completely. The present study explores the nature of hydration and its length-scale evaluation around the non-IBS for hyperactive AFPs. We observed that the hydration layer of non-IBS is liquid-like, even in highly supercooled conditions, and the nature of hydration is drastically different from the hydration pattern of non-AFP surfaces. In similar conditions, the hydration layer around the IBS is ice-like ordered. Non-IBS of the hyperactive AFP exposes toward the bulk and is able to maintain the liquid-like character of its hydration water up to 15 Å. We also find that the amino acid compositions and their spatial distribution on the non-IBS are markedly different from those of the IBS and non-AFP surfaces. These results elucidate the combined role of IBS and non-IBS in ice-growth inhibition. While IBS is required to adsorb on ice efficiently, the exposed non-IBS may prevent ice nucleation/growth on top of the bound AFPs.

Antifreeze protein complements cryoprotective dehydration in the freeze-avoiding springtail Megaphorura arctica

The springtail, Megaphorura arctica, is freeze-avoiding and survives sub-zero temperatures by cryoprotective dehydration. At the onset of dehydration there is some supercooling of body fluids, and the danger of inoculative freezing, which would be lethal. To see if the springtails are protected by antifreeze proteins in this pre-equilibrium phase, we examined extracts from cold-acclimated M. arctica and recorded over 3 °C of freezing point depression. Proteins responsible for this antifreeze activity were isolated by ice affinity. They comprise isoforms ranging from 6.5 to 16.9 kDa, with an amino acid composition dominated by glycine (>35 mol%). Tryptic peptide sequences were used to identify the mRNA sequence coding for the smallest isoform. This antifreeze protein sequence has high similarity to one characterized in Hypogastrura harveyi, from a different springtail order. If these two antifreeze proteins are true homologs, we suggest their origin dates back to the Permian glaciations some 300 million years ago.

Computational Study of Differences between Antifreeze Activity of Type-III Antifreeze Protein from Ocean Pout and Its Mutant.

The antifreeze activity of a type-III antifreeze protein (AFP) expressed in ocean pout (Zoarces americanus) is compared with that of a specific mutant (T18N) using all-atom molecular dynamics simulations. The antifreeze activity of the mutant is only 10% of the wild-type AFP. The results from this simulation study revealed the following insights into the mechanism of antifreeze action by type-III AFPs. The AFP gets adsorbed to the advancing ice front due to its hydrophobic nature. A part of the hydrophobicity is caused by the presence of clathrate structure of water molecules near the ice-binding surface (IBS). The mutation in the AFP disrupts this structure and thereby reduces the ability of the mutant to adsorb to the ice-water interface leading to the loss of antifreeze activity. The mutation, however, has no effect on the ability of the adsorbed protein to bind to the growing ice phase. Simulations also revealed that all surfaces of the protein can bind to the ice phase, although the IBS is the preferred surface.

Effect of in vitro cold acclimation of Deschampsia antarctica on the accumulation of proteins with antifreeze activity.

Deschampsia antarctica has managed to colonize the maritime Antarctic. One of the main factors associated with its tolerance to low temperatures is the presence of apoplastic proteins with antifreeze activity. This work focuses on the effect of cold acclimation of D. antarctica on the accumulation of apoplastic proteins with antifreeze activity. Antifreeze proteins present in apoplastic extracts were purified by ice affinity purification, and their identity was determined by protein sequencing. D. antarctica plants were subjected to 22 days of cold acclimation at 4 °C. The highest content of apoplastic proteins with antifreeze activity was obtained at between 12 and 16 days of acclimation. Protein sequencing allowed their identification with >95% probability. Percentage coverage was 74% with D. antarctica ice recrystallization inhibition protein 1 (DaIRIP1) and 55% with DaIRIP3. Cold acclimation of D. antarctica improved the yield of apoplastic proteins, and resulted in an increase in the antifreeze activity of apoplastic extracts. An in silico analysis suggested that the fluctuations presented by the three-dimensional structures of DaIRIPs help to explain the presence of certain DaIRIPs in apoplastic extracts under the cold acclimation conditions evaluated.

Antifreeze Water-Rich Dormant Cysts of the Terrestrial Ciliate Colpoda cucullus Nag-1 at −65 ℃: Possible Involvement of Ultra-Antifreeze Polysaccharides

We found that the water-rich (osmolality below 0.052 Osm/l) wet resting cysts of the soil ciliate Colpoda cucullus Nag-1 were tolerant to extremely low temperature (−65℃). When cell fluid obtained from the resting cysts was cooled at −65℃, small particles of ice crystals did not grow into large ice crystals. At −65℃, the cysts shrank due to an outflow of water, because a vapor pressure difference was produced between the cell interior and freezing surrounding medium. The osmolality of these shrunk cells was estimated 0.55 Osm/l, and the freezing point depression of the shrunk cell fluid was estimated to be 1.02℃. Hence, the antifreeze ability of wet cysts at −65℃can not be explained by freezing point depression due to elevation of cytoplasmic osmolality. The cytoplasm of resting cysts was vividly stained red with periodic acid-Schiff (PAS) and stained purple with toluidine blue. On the other hand, the excystment-induced cysts were not stained with PAS, and exhibited a loss of the antifreeze activity. PAS staining of SDSPAGE gel obtained from encysting Colpoda cells showed that a large amount of PAS-positive macromolecules accumulated as the encystment stage progressed. These results suggest that antifreeze polysaccharides may be involved in the antifreeze activity of C. cucullus Nag-1 dormant forms.

Synthesis of Anthracene Conjugates of Truncated Antifreeze Protein Sequences: Effect of the End Group and Photocontrolled Dimerization on Ice Recrystallization Inhibition Activity.

Biomacromolecular antifreezes distinguish ice from water, function by binding to specific planes of ice, and could have many applications from cryobiology to aerospace where ice is a problem. In biology, antifreeze protein (AFP) activity is regulated by protein expression levels via temperature and light-regulated expression systems, but in the laboratory (or applications), the antifreeze activity is "always on" without any spatial or temporal control, and hence methods to enable this switching represent an exciting synthetic challenge. Introduction of an abiotic functionality into short peptides (e.g., from solid-phase synthesis) to enable switching is also desirable rather than on full-length recombinant proteins. Here, truncated peptide sequences based on the consensus repeat sequence from type-I AFPs (TAANAAAAAAA) were conjugated to an anthracene unit to explore their photocontrolled dimerization. Optimization of the synthesis to ensure solubility of the hydrophobic peptide included the addition of a dilysine solubilizing linker. It was shown that UV-light exposure triggered reversible dimerization of the AFP sequence, leading to an increase in molecular weight. Assessment of the ice recrystallization inhibition activity of the peptides before and after dimerization revealed only small effects on activity. However, it is reported here for the first time that addition of the anthracene unit to a 22-amino-acid truncated peptide significantly enhanced ice recrystallization inhibition compared to the free peptide, suggesting an accessible synthetic route to allow AFP activity using shorter, synthetically accessible peptides with a photoreactive functionality.

Increased Productivity and Antifreeze Activity of Ice-binding Protein from Flavobacterium frigoris PS1 Produced using Escherichia coli as Bioreactor

Ice-binding proteins (IBPs) inhibit the growth and recrystallization of intracellular ice, enabling polar organisms to survive at subzero temperatures. IBPs are promising materials in biomedical applications such as cryopreservation and the hypothermic storage of cells, tissues, and organs. In this study, recombinant IBP from the antarctic bacterium Flavobacterium frigoris PS1 (FfIBP) was produced by Escherichia coli used as bioreactor, to examine the feasibility of scale-up. Oxygen transfer was the most important factor influencing cell growth and FfIBP production during pilot-scale fermentation. The final yield of recombinant FfIBP produced by E. coli harboring the pET28a-FfIBP vector system was 1.6 g/L, 3.8-fold higher than that from the previously published report using pCold I-FfIBP vector system, and its thermal hysteresis activity was 2.5°C at 9.7 µM. This study demonstrates the successful pilot-scale production of FfIBP.

Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP).

Antifreeze glycoproteins are a class of biological agents which enable living at temperatures below the freezing point of the body fluids. Antifreeze glycopeptides usually consist of repeating tripeptide unit (-Ala-Ala-Thr*-), glycosylated at the threonine side chain. However, on the microscopic level, the mechanism of action of these compounds remains unclear. As previous research has shown, antifreeze activity of antifreeze glycopeptides strongly relies on the overall conformation of the molecule as well an on the stereochemistry of amino acid residues. The desired monoglycosylated analogues with acetylated amino termini and the carboxy termini in form of N-methylamide have been synthesized. Conformational nuclear magnetic resonance (NMR) studies of the designed analogues have shown a strong influence of the stereochemistry of amino acid residues on the peptide chain stability, which could be connected to the antifreeze activity of these compounds. A better understanding of the mechanism of action of antifreeze glycopeptides would allow applying these materials, e.g., in food industry and biomedicine.

Presence of a basic secretory protein in xylem sap and shoots of poplar in winter and its physicochemical activities against winter environmental conditions.

XSP25, previously shown to be the most abundant hydrophilic protein in xylem sap of Populus nigra in winter, belongs to a secretory protein family in which the arrangement of basic and acidic amino acids is conserved between dicotyledonous and monocotyledonous species. Its gene expression was observed at the same level in roots and shoots under long-day conditions, but highly induced under short-day conditions and at low temperatures in roots, especially in endodermis and xylem parenchyma in the root hair region of Populus trichocarpa, and its protein level was high in dormant buds, but not in roots or branches. Addition of recombinant PtXSP25 protein mitigated the denaturation of lactate dehydrogenase by drying, but showed only a slight effect on that caused by freeze-thaw cycling. Recombinant PtXSP25 protein also showed ice recrystallization inhibition activity to reduce the size of ice crystals, but had no antifreezing activity. We suggest that PtXSP25 protein produced in shoots and/or in roots under short-day conditions and at non-freezing low temperatures followed by translocation via xylem sap to shoot apoplast may protect the integrity of the plasma membrane and cell wall functions from freezing and drying damage in winter environmental conditions.

Evaluation of the antifreeze effects and its related mechanism of sericin peptides on the frozen dough of steamed potato bread

This study investigated the effects of sericin peptides (SPs) on frozen potato dough with trehalose as a reference. The results found that SPs decreased freezable water content in frozen dough and increased yeast survival ratio significantly after 4-week frozen storage. Additionally, compared with control group and frozen dough containing 5% of trehalose, frozen dough with 5% of SPs showed less starch granule separation and more complete gluten membrane during 8-week storage. Specific volume of the frozen dough with 5% of SPs decreased by 6.3%, significantly lower than the control and reference groups. Furthermore, compared with trehalose, SPs effectively decreased the hardness and gumminess of steamed potato breads, as well as enhanced their resilience. The quality improvement of frozen potato dough with SPs could be attributed to ideal structural matching, hydrogen bonds, and non-bond interactions between sericin peptides and ice surface, as well as the inhibition of the formation and recrystallization of ice crystals. Practical applications Frozen dough method is widely used in baked flour products, providing fresh, safe, consistent quality products and simplifies the manufacturing process. However, the overall quality of frozen dough decreased gradually during frozen storage. Traditional antifreezes (trehalose and sorbitol) have high calories, which are not conducive to diabetics and obese patients. Therefore, it is essentially important to find a new and efficient antifreeze to replace traditional antifreezes. SPs, the hydrolysate of sericin, exhibited a strong cryoprotection and antifreeze activity according to this study. We can expect a potential application of SPs in cell protection and food preservation.

Hydrolysates from rainbow trout (Oncorhynchus mykiss) processing by-products: Properties when added to fish mince with different freeze-thaw cycles

Rainbow trout (Oncorhynchus mykiss) mixed processing by-product homogenates were subjected to 8 mM CaCl2-5 mM citric acid (1:5 w/v) pretreatments followed by hydrolysis with Alcalase (W-CaCi-RTBH). These hydrolysates decreased the loss of total sulfhydryl groups, protein solubility and protein carbonyl formation in a fish mince after 6 freeze-thaw cycles (P ≤ 0.05). The thermal properties of myosin heavy chains and actin were maintained as shown using differential scanning calorimetry (DSC) (P ≤ 0.05). Based on low field NMR T2 relaxation, the fastest relaxation component (T21) showed no changes with addition of W-CaCi-RTBH into a fish mince after 6 freeze-thaw cycles, indicating no changes for the major pool of water molecules within the myofibrillar protein structure (P ≥ 0.05). After 6 freeze-thaw cycles, W-CaCi-RTBH had better antifreeze activity when combined with sucrose – sorbitol (4%) (P ≤ 0.05). Therefore, W-CaCi-RTBH could potentially be an additive in frozen fish mince.

Hydrogen-Bonding and Hydrophobic Groups Contribute Equally to the Binding of Hyperactive Antifreeze and Ice-Nucleating Proteins to Ice.

Hyperactive insect antifreeze proteins and bacterial ice-nucleating proteins are arguably the most potent ice-binding molecules in nature. These highly effective proteins bind ice through amphiphilic ice-binding sites based on arrays of threonine residues. It remains poorly understood how hydrophilic and hydrophobic groups of the binding site contribute to the ice affinity of proteins. Here, we use molecular simulations to demonstrate that the hydrogen-bonding and hydrophobic groups at the ice-binding site of the antifreeze protein TmAFP of Tenebrio molitor and extended ice-nucleating protein surfaces contribute distinctively yet almost equally in magnitude to their binding free energy to ice. The methyl groups rigidize the ice-binding site, slow the water dynamics at the ice-binding surface, and stabilize the clathrate-like water in the anchored clathrate motif that binds these proteins to ice. We find that hydrophobic dehydration of the methyl group does not contribute to the binding free energy of the protein to ice. The role of the hydroxyl groups is to anchor the clathrate-like water through direct hydrogen-bonding, positioning and slowing the dynamics of water at the trough of the binding site. We uncover a correlation between slower dynamics of water at the binding site for the protein in solution and stronger free energy of binding of the protein to ice. The synergy between hydrophobic and hydrophilic groups unveiled by this study provides guidance for the design of synthetic ice-binding molecules with enhanced ice nucleation and antifreeze activity.

Correction to: Purification of dual-functioning chitinases with hydrolytic and antifreeze activities from Hippophae rhamnoides seedlings

Correction to: Purification of dual-functioning chitinases with hydrolytic and antifreeze activities from Hippophae rhamnoides seedlings

Freeze Tolerance in Sculpins (Pisces; Cottoidea) Inhabiting North Pacific and Arctic Oceans: Antifreeze Activity and Gene Sequences of the Antifreeze Protein.

Many marine species inhabiting icy seawater produce antifreeze proteins (AFPs) to prevent their body fluids from freezing. The sculpin species of the superfamily Cottoidea are widely found from the Arctic to southern hemisphere, some of which are known to express AFP. Here we clarified DNA sequence encoding type I AFP for 3 species of 2 families (Cottidae and Agonidae) belonging to Cottoidea. We also examined antifreeze activity for 3 families and 32 species of Cottoidea (Cottidae, Agonidae, and Rhamphocottidae). These fishes were collected in 2013–2015 from the Arctic Ocean, Alaska, Japan. We could identify 8 distinct DNA sequences exhibiting a high similarity to those reported for Myoxocephalus species, suggesting that Cottidae and Agonidae share the same DNA sequence encoding type I AFP. Among the 3 families, Rhamphocottidae that experience a warm current did not show antifreeze activity. The species inhabiting the Arctic Ocean and Northern Japan that often covered with ice floe showed high activity, while those inhabiting Alaska, Southern Japan with a warm current showed low/no activity. These results suggest that Cottoidea acquires type I AFP gene before dividing into Cottidae and Agonidae, and have adapted to each location with optimal antifreeze activity level.

Purification of dual-functioning chitinases with hydrolytic and antifreeze activities from Hippophae rhamnoides seedlings

Chitinases are glycosyl hydrolases which hydrolyse β-1,4-glycosidic bonds between N-acetylglucosamine residues of chitin. Seabuckthorn (Hippophae rhamnoides), a cold desert plant, is a storehouse of many cold-tolerant proteins including dual-functioning antifreeze proteins (AFPs) possessing both hydrolytic and antifreeze activities. Herein, we report the purification and characterization of antifreeze chitinases from seedlings grown in laboratory conditions. Chitin-affinity chromatography led to homogenous purification of two acidic chitinases HrS CHT1a (33 kDa) and HrS CHT1b (38 kDa) from seedlings. Antifreeze activity of purified AFPs was confirmed by the formation of hexagon-shaped ice crystals using nanolitre osmometer. Similarly, sucrose sandwich splat assay also confirmed their ice recrystallization inhibition activity (1.6-fold decrease in mean ice crystals). The chitinase activity of AFPs was confirmed by chitin hydrolytic assay where higher activity (1.8-fold) was observed in HrS CHT1b (500 U/mg) than HrS CHT1a (222 U/mg). MS identification showed homology of HrS CHT1b with provicilin while HrS CHT1a was identified as uncharacterized protein. In silico analysis showed that purified AFPs differ significantly in biochemical properties which suggests their different physiological roles. Protein association network analysis using string showed interaction of HrS CHT1b with enzymes involved majorly in pathogenic protection (pectinesterase, glycosyl hydrolase protein with chitinase domain). However, HrSCHT1a showed interaction with proteins associated with growth and energy regulation (glycine and purine synthesis, vitamin B metabolism) thereby indicating differential functional roles of both the chitinases. Conserved domain analysis also supported that these AFPs are multifunctional and exhibit differential regulatory roles in enabling the plant growth and defense responses. Further validation of these targets may open gates for commercial utilization of this plant growing abundantly in the Himalayan regions of India for protection of freeze-susceptible crops or biomedical applications.

Determination of the Solution Structure of Antifreeze Glycoproteins Using Two-Dimensional Infrared Spectroscopy.

We study the solution structure of antifreeze glycoproteins (AFGPs) with linear and two-dimensional infrared spectroscopy (2D-IR). With 2D-IR, we study the coupling between the amide I and amide II vibrations of AFGPs. The measured nonlinear spectral response constitutes a much more clearly resolved amide I spectrum than the linear absorption spectrum of the amide I vibrations and allows us to identify the different structural elements of AFGPs in solution. We find clear evidence for the presence of polyproline II (PPII) helical structures already at room temperature, and we find that the fraction of PPII structures increases when the temperature is decreased to the biological working temperature of AFGP. We observe that inhibition of the antifreeze activity of AFGP using borate buffer or enhancing the antifreeze activity using sulfate buffer does not lead to significant changes in the protein conformation. This finding indicates that AFGPs bind to ice with their sugar side chains.

The influence of a type III antifreeze protein and its mutants on methane hydrate adsorption-inhibition: a molecular dynamics simulation study.

Antifreeze proteins (AFPs) inhibit ice growth in various organisms at subzero temperature. Recently, AFPs as a hydrate inhibitor have been a topic of intense discussion, while the detailed mechanism remains obscure. The present work aims to explore molecular insight into the adsorption and inhibition of an AFP III on methane hydrate. Three polar, hydrophilic, and neutral amino acids (Asn14, Thr18, and Gln44) are mutated to elucidate the molecular mechanism of AFP III antifreeze activity. Another triple mutation is also designed to investigate the effect of the side chain. Atomistic molecular dynamics simulations provide detailed structural and dynamical aspects of protein residues and water molecules at the hydrate/water interface. Initially, it was proposed that the AFP III operates by the adsorption-inhibition mechanism on hydrates, almost similar to that of ice. The exchange of amide and hydroxyl groups by mutagenesis alters the shape of the side chain and the capability of hydrogen bonding and demonstrates that hydrogen bonds are not directly responsible for the AFP III antifreeze activity. Moreover, we deciphered that the length of the pendant group is an important factor in the entrapment of the AFP III on the hydrate cages, which is compatible with van der Waals interactions between the side chains and hydrate surface. The results suggest that this interaction is sensitive to the geometry and shape of the hydrate-binding surface (HBS) of the AFP, which implies that the interface between hydrates and the AFP is relatively rigid.

Combined molecular dynamics and neural network method for predicting protein antifreeze activity

Antifreeze proteins (AFPs) are a diverse class of proteins that depress the kinetically observable freezing point of water. AFPs have been of scientific interest for decades, but the lack of an accurate model for predicting AFP activity has hindered the logical design of novel antifreeze systems. To address this, we perform molecular dynamics simulation for a collection of well-studied AFPs. By analyzing both the dynamic behavior of water near the protein surface and the geometric structure of the protein, we introduce a method that automatically detects the ice binding face of AFPs. From these data, we construct a simple neural network that is capable of quantitatively predicting experimentally observed thermal hysteresis from a trio of relevant physical variables. The model's accuracy is tested against data for 17 known AFPs and 5 non-AFP controls.

Preparation, primary structure and antifreeze activity of antifreeze peptides from Scomberomorus niphonius skin

In order to evaluate antifreeze activity of antifreeze peptides (AFPs) from Scomberomorus niphonius skin and study the relationship between antifreeze activity and primary structure, peptides were prepared and thermal hysteresis activity (THA), recrystallisation inhibition, molecular weight, and amino acid composition were investigated. Based on the results, alkaline protease was selected to prepare AFPs, and optimal hydrolysis conditions consisted of an enzyme-to-substrate (E/S) ratio of 1/50, pH 8.5, a temperature of 37 °C, and a time of 2 h. Under these conditions, the peptide content reached 39 mg/mL. At the optimal hold temperature of −0.1 °C, the THA of AFPs was 1.7 °C. AFPs significantly reduced the volume of ice crystals. The molecular weight of AFPs ranged from 1426 to 1810 Da. Glycine, alanine, and proline were the most abundant amino acids, and the primary structure was closely correlated with antifreeze activity. The findings suggested these antifreeze peptides have potential as additives in the food industry.