Ice-binding site of snow mold fungus antifreeze protein deviates from structural regularity and high conservation

Variations on a theme: non-canonical DUF3494 ice-binding proteins

Among the many ice-binding proteins (IBPs) found in microorganisms (bacteria, archaea, fungi and algae), the canonical DUF3494 beta-barrel type is the most common. Until now, little variation has been found in this structure: an initial coil leads into an alpha helix that directs the following coils into a reverse stack, with the final coil ending up next to the initial coil. Here, I show that there exist many bacterial proteins whose AlphaFold-predicted structures deviate from the DUF3494 structure so that they are not recognized as belonging to an existing DUF or Pfam family. In these non-canonical DUF3494 (ncDUF3494) proteins, the number of coils in the alpha helix is highly variable, often being as high as 14. The putative ice-binding sides of each of 13 proteins modeled have a well-aligned row of hydrophilic residues, with spacings that are close to the repeat distance on the ice a-axis. A recombinant protein made for one of the proteins showed that it had ice-binding activity, even in the µg/ml range. The ncDUF3494 proteins appear to be found only in bacteria, the great majority of which live in icy habitats. C-terminal PEP-Cterm motifs, which are rare in DUF3494s, are present in most of the ncDUF3494s, possibly indicating a secretory function. The relatively narrow distribution of ncDUF3494 proteins suggests that they are a later development in DUF3494 evolution.

Solvation of molecules from the family of "domain of unknown function" 3494 and their ability to bind to ice

In 2012, the molecular structure of a new, broad class of ice-binding proteins, classified as "domain of unknown function" (DUF) 3494, was described for the first time. These proteins have a common tertiary structure and are characterized by a very wide spectrum of antifreeze activity (from weakly active to hyperactive). The ice-binding surface (IBS) region of these molecules differs significantly in its structure from the IBS of previously known antifreeze proteins (AFPs), showing a complete lack of regularity and high hydrophilicity. The presence of a regular, repeating structural motif in the IBS region of hitherto known AFP molecules, combined with the hydrophobic nature of this surface, promotes the formation of an ice-like ordering of the solvation water layer and, as a result, facilitates the process of transformation of this water layer into ice. It is, therefore, surprising that the newly discovered DUF3494 class of proteins clearly breaks out of this characteristic. In this paper, using molecular dynamics simulations, we analyze the solvation water structure of the IBS region of both DUF3494 family molecules and AFPs. As we show, although the IBS of DUF3494 molecules does not form an ice-like water structure in the solvation layer, this is compensated by the formation of the equivalent of "anchored clathrate water," in the form of a relatively large number of water molecules bound to the surface of the protein molecule and providing potential binding sites for it to the ice surface.

On the engulfment of antifreeze proteins by ice

Antifreeze proteins (AFPs) are remarkable biomolecules that suppress ice formation at trace concentrations. To inhibit ice growth, AFPs must not only bind to ice crystals, but also resist engulfment by ice. The highest supercooling, [Formula: see text], for which AFPs are able to resist engulfment is widely believed to scale as the inverse of the separation, [Formula: see text], between bound AFPs, whereas its dependence on the molecular characteristics of the AFP remains poorly understood. By using specialized molecular simulations and interfacial thermodynamics, here, we show that in contrast with conventional wisdom, [Formula: see text] scales as [Formula: see text] and not as [Formula: see text]. We further show that [Formula: see text] is proportional to AFP size and that diverse naturally occurring AFPs are optimal at resisting engulfment by ice. By facilitating the development of AFP structure-function relationships, we hope that our findings will pave the way for the rational design of AFPs.

Ice Isn't the Only Crystal in Town: Structure Determination of Ice-Binding Proteins via X-Ray Crystallography

Ice-binding proteins (IBPs) are proteins that have the remarkable ability to bind to ice, and their study has intrigued researchers for decades. This chapter explores the importance of structural biology in understanding IBPs and highlights the significant contributions of IBPs to the field of structural biology. The structures of various IBPs from different organisms have been elucidated, revealing key elements involved in ice binding. Structural biology techniques, including nuclear magnetic resonance (NMR) spectroscopy, transmission electron cryo-microscopy (cryo-EM), and X-ray crystallography, play crucial roles in solving protein structures. This article focuses on X-ray crystallography as a tool for investigating IBP structures, providing insights into its theoretical and practical aspects, experimental workflows, and common pitfalls to avoid.

Characterizing Surface Ice-Philicity Using Molecular Simulations and Enhanced Sampling

The formation of ice, which plays an important role in diverse contexts ranging from cryopreservation to atmospheric science, is often mediated by solid surfaces. Although surfaces that interact favorably with ice (relative to liquid water) can facilitate ice formation by lowering nucleation barriers, the molecular characteristics that confer icephilicity to a surface are complex and incompletely understood. To address this challenge, here we introduce a robust and computationally efficient method for characterizing surface ice-philicity that combines molecular simulations and enhanced sampling techniques to quantify the free energetic cost of increasing surface-ice contact at the expense of surface-water contact. Using this method to characterize the ice-philicity of a family of model surfaces that are lattice matched with ice but vary in their polarity, we find that the nonpolar surfaces are moderately ice-phobic, whereas the polar surfaces are highly ice-philic. In contrast, for surfaces that display no complementarity to the ice lattice, we find that ice-philicity is independent of surface polarity and that both nonpolar and polar surfaces are moderately ice-phobic. Our work thus provides a prescription for quantitatively characterizing surface ice-philicity and sheds light on how ice-philicity is influenced by lattice matching and polarity.

Polyproline type II helical antifreeze proteins are widespread in Collembola and likely originated over 400 million years ago in the Ordovician Period

Antifreeze proteins (AFPs) bind to ice crystals to prevent organisms from freezing. A diversity of AFP folds has been found in fish and insects, including alpha helices, globular proteins, and several different beta solenoids. But the variety of AFPs in flightless arthropods, like Collembola, has not yet been adequately assessed. Here, antifreeze activity was shown to be present in 18 of the 22 species of Collembola from cold or temperate zones. Several methods were used to characterize these AFPs, including isolation by ice affinity purification, MALDI mass spectrometry, amino acid composition analysis, tandem mass spectrometry sequencing, transcriptome sequencing, and bioinformatic investigations of sequence databases. All of these AFPs had a high glycine content and were predicted to have the same polyproline type II helical bundle fold, a fold unique to Collembola. These Hexapods arose in the Ordovician Period with the two orders known to produce AFPs diverging around 400 million years ago during the Andean-Saharan Ice Age. Therefore, it is likely that the AFP arose then and persisted in many lineages through the following two ice ages and intervening warm periods, unlike the AFPs of fish which arose independently during the Cenozoic Ice Age beginning ~ 30 million years ago.

Protein engineering of antifreeze proteins reveals that their activity scales with the area of the ice-binding site

Antifreeze proteins (AFPs) protect organisms from freezing by binding to ice crystals to prevent their growth. Here, we have investigated how the area of an AFP's ice-binding site (IBS) changes its antifreeze activity. The polyproline type II helical bundle fold of the 9.6-kDa springtail (Collembola) AFP from Granisotoma rainieri (a primitive arthropod) facilitates changes to both IBS length and width. A one quarter decrease in area reduced activity to less than 10%. A one quarter increase in IBS width, through the addition of a single helix, tripled antifreeze activity. However, increasing IBS length by a similar amount actually reduced activity. Expanding the IBS area can greatly increase antifreeze activity but needs to be evaluated by experimentation on a case-by-case basis.

Life from a Snowflake: Diversity and Adaptation of Cold-Loving Bacteria among Ice Crystals

Incredible as it is, researchers have now the awareness that even the most extreme environment includes special habitats that host several forms of life. Cold environments cover different compartments of the cryosphere, as sea and freshwater ice, glaciers, snow, and permafrost. Although these are very particular environmental compartments in which various stressors coexist (i.e., freeze–thaw cycles, scarce water availability, irradiance conditions, and poorness of nutrients), diverse specialized microbial communities are harbored. This raises many intriguing questions, many of which are still unresolved. For instance, a challenging focus is to understand if microorganisms survive trapped frozen among ice crystals for long periods of time or if they indeed remain metabolically active. Likewise, a look at their site-specific diversity and at their putative geochemical activity is demanded, as well as at the equally interesting microbial activity at subzero temperatures. The production of special molecules such as strategy of adaptations, cryoprotectants, and ice crystal-controlling molecules is even more intriguing. This paper aims at reviewing all these aspects with the intent of providing a thorough overview of the main contributors in investigating the microbial life in the cryosphere, touching on the themes of diversity, adaptation, and metabolic potential.

Structural diversity of marine anti-freezing proteins, properties and potential applications: a review

Cold-adapted organisms, such as fishes, insects, plants and bacteria produce a group of proteins known as antifreeze proteins (AFPs). The specific functions of AFPs, including thermal hysteresis (TH), ice recrystallization inhibition (IRI), dynamic ice shaping (DIS) and interaction with membranes, attracted significant interest for their incorporation into commercial products. AFPs represent their effects by lowering the water freezing point as well as preventing the growth of ice crystals and recrystallization during frozen storage. The potential of AFPs to modify ice growth results in ice crystal stabilizing over a defined temperature range and inhibiting ice recrystallization, which could minimize drip loss during thawing, improve the quality and increase the shelf-life of frozen products. Most cryopreservation studies using marine-derived AFPs have shown that the addition of AFPs can increase post-thaw viability. Nevertheless, the reduced availability of bulk proteins and the need of biotechnological techniques for industrial production, limit the possible usage in foods. Despite all these drawbacks, relatively small concentrations are enough to show activity, which suggests AFPs as potential food additives in the future. The present work aims to review the results of numerous investigations on marine-derived AFPs and discuss their structure, function, physicochemical properties, purification and potential applications.

Seasonal ice nucleation activity of water samples from alpine rivers and lakes in Obergurgl, Austria

Heterogeneous ice nucleation plays an important role in many environmental processes such as ice cloud formation, freezing of water bodies or biological freeze protection in the cryosphere. New information is needed about the seasonal availability, nature, and activity of ice nucleating particles (INPs) in alpine environments. These INPs trigger the phase transition from liquid water to solid ice at elevated subzero temperatures. We collected water samples from a series of alpine rivers and lakes (two valleys and their rivers, an artificial pond, and a natural lake system) in Obergurgl, Austria in June 2016, July 2016, November 2016, and May 2017. Each alpine river and lake was sampled multiple times across different seasons, depending on site access during different times of the year. Water samples were filtered through a 0.22 μm membrane filter to separate microbial INPs from the water, and both fractions were analyzed for ice nucleation activity (INA) by an emulsion freezing method. Microorganisms were cultured from the filters, and the cultures then analyzed for INA. Portions of the filtered samples were concentrated by lyophilization to observe potential enhancement of INA. Two sediment samples were taken as reference points for inorganic INPs. Sub-micron INPs were observed in all of the alpine water sources studied, and a seasonal shift to a higher fraction of microbial ice nucleators cultured on selective media was observed during the winter collections. Particles larger than 0.22 μm showed INA, and microbes were cultured from this fraction. Results from 60 samples gave evidence of a seasonal change in INA, presence of submicrometer INPs, and show the abundance of culturable microorganisms, with late spring and early summer showing the most active biological INPs. With additional future research on this topic ski resorts could make use of such knowledge of geographical and seasonal trends of microbial INPs in freshwater habitats in order to improve the production of artificial snow.

Antifreeze proteins and their biomimetics for cell cryopreservation: Mechanism, function and application-A review

Cell-based therapy is a promising technology for intractable diseases and health care applications, in which cryopreservation has become an essential procedure to realize the production of therapeutic cells. Ice recrystallization is the major factor that affects the post-thaw viability of cells. As a typical series of biomacromolecules with ice recrystallization inhibition (IRI) activity, antifreeze proteins (AFPs) have been employed in cell cryopreservation. Meanwhile, synthesized materials with IRI activity have emerged in the name of biomimetics of AFPs to expand their availability and practicality. However, fabrication of AFPs mimetics is in a chaotic period. There remains little commonality among different AFPs mimetics, then it is difficult to set guidelines on their design. With no doubt, a comprehensive understanding on the antifreezing mechanism of AFPs in molecular level will enable us to rebuild the function of AFPs, and provide convenience to clarify the relationship between structure and function of these early stage biomimetics. In this review, we would discuss those previously reported biomimetics to summarize their structure characteristics concerning the IRI activity and attempt to develop a roadmap for guiding the design of novel AFPs mimetics.

High Water Density at Non-Ice-Binding Surfaces Contributes to the Hyperactivity of Antifreeze Proteins

Antifreeze proteins (AFPs) can bind to ice nuclei thereby inhibiting their growth and their hydration shell is believed to play a fundamental role. Here, we use molecular dynamics simulations to characterize the hydration shell of four moderately-active and four hyperactive AFPs. The local water density around the ice-binding-surface (IBS) is found to be lower than that around the non-ice-binding surface (NIBS) and this difference correlates with the higher hydrophobicity of the former. While the water-density increase (with respect to bulk) around the IBS is similar between moderately-active and hyperactive AFPs, it differs around the NIBS, being higher for the hyperactive AFPs. We hypothesize that while the lower water density at the IBS can pave the way to protein binding to ice nuclei, irrespective of the antifreeze activity, the higher density at the NIBS of the hyperactive AFPs contribute to their enhanced ability in inhibiting ice growth around the bound AFPs.

Basidiomycetous Yeast, Glaciozyma antarctica, Forming Frost-Columnar Colonies on Frozen Medium

The basidiomycetous yeast, Glaciozyma antarctica, was isolated from various terrestrial materials collected from the Sôya coast, East Antarctica, and formed frost-columnar colonies on agar plates frozen at −1 °C. Thawed colonies were highly viscous, indicating that the yeast produced a large number of extracellular polysaccharides (EPS). G. antarctica was then cultured on frozen media containing red food coloring to observe the dynamics of solutes in unfrozen water; pigments accumulated in frozen yeast colonies, indicating that solutes were concentrated in unfrozen water of yeast colonies. Moreover, the yeast produced a small quantity of ice-binding proteins (IBPs) which inhibited ice crystal growth. Solutes in unfrozen water were considered to accumulate in the pore of frozen colonies. The extracellular IBPs may have held an unfrozen state of medium water after accumulation in the frost-columnar colony.

Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity

Antifreeze proteins (AFPs) inhibit ice growth by adsorbing onto specific ice planes. Microbial AFPs show diverse antifreeze activity and ice plane specificity, while sharing a common molecular scaffold. To probe the molecular mechanisms responsible for AFP activity, we here characterized the antifreeze activity and crystal structure of TisAFP7 from the snow mold fungus Typhula ishikariensis. TisAFP7 exhibited intermediate activity, with the ability to bind the basal plane, compared with a hyperactive isoform TisAFP8 and a moderately active isoform TisAFP6. Analysis of the TisAFP7 crystal structure revealed a bound-water network arranged in a zigzag pattern on the surface of the protein's ice-binding site (IBS). While the three AFP isoforms shared the water network pattern, the network on TisAFP7 IBS was not extensive, which was likely related to its intermediate activity. Analysis of the TisAFP7 crystal structure also revealed the presence of additional water molecules that form a ring-like network surrounding the hydrophobic side chain of a crucial IBS phenylalanine, which might be responsible for the increased adsorption of AFP molecule onto the basal plane. Based on these observations, we propose that the extended water network and hydrophobic hydration at IBS together determine the TisAFP activity.

Snow mold of winter cereals: a complex disease and a challenge for resistance breeding

Snow mold resistance is a complex quantitative trait highly affected by environmental conditions during winter that must be addressed by resistance breeding. Snow mold resistance in winter cereals is an important trait for many countries in the Northern Hemisphere. The disease is caused by at least four complexes of soilborne fungi and oomycetes of which Microdochium nivale and M. majus are among the most common pathogens. They have a broad host range covering all winter and spring cereals and can basically affect all plant growth stages and organs. Their attack leads to a low germination rate, and/or pre- and post-emergence death of seedlings after winter and, depending on largely unknown environmental conditions, also to foot rot, leaf blight, and head blight. Resistance in winter wheat and triticale is governed by a multitude of quantitative trait loci (QTL) with mainly additive effects highly affected by genotype × environment interaction. Snow mold resistance interacts with winter hardiness in a complex way leading to a co-localization of resistance QTLs with QTLs/genes for freezing tolerance. In practical breeding, a multistep procedure is necessary with (1) freezing tolerance tests, (2) climate chamber tests for snow mold resistance, and (3) field tests in locations with and without regularly occurring snow cover. In the future, resistance sources should be genetically characterized also in rye by QTL mapping or genome-wide association studies. The development of genomic selection procedures should be prioritized in breeding research.

Crystal waters on the nine polyproline type II helical bundle springtail antifreeze protein from Granisotoma rainieri match the ice lattice

A springtail (Collembola) identified as Granisotoma rainieri was collected from snow in Hokkaido, Japan, in late winter when nighttime temperatures were below zero. Extracts of these arthropods showed antifreeze activity by shaping ice crystals and stopping their growth. The glycine-rich proteins responsible for this freezing point depression were isolated by ice-affinity purification and had principal masses of ~ 6.9 and 9.6 kDa. We identified a transcript for a 9.6-kDa component and produced it as a His-tagged recombinant protein for structural analysis. Its crystal structure was solved to a resolution of 1.21 Å and revealed a polyproline type II helical bundle, similar to the six-helix Hypogastrura harveyi AFP, but with nine helices organized into two layers held together by an extensive network of hydrogen bonds. One of the layers is flat, regular, and hydrophobic and likely serves as the ice-binding side. Although this surface makes close protein-protein contacts with its symmetry mate in the crystal, it has bound chains of waters present that resemble those on the basal and primary prism planes of ice. Molecular dynamic simulations indicate most of these crystal waters would preferentially occupy these sites if exposed to bulk solvent in the absence of the symmetry mate. These prepositioned waters lend further support to the ice-binding mechanism in which AFPs organize ice-like waters on one surface to adsorb to ice. DATABASES: Structural data are available in the Protein Data Bank under the accession number 7JJV. Transcript data are available in GenBank under accession numbers MT780727, MT780728, MT780729, MT780730, MT780731 and MT985982.

Ice-Binding Proteins Associated with an Antarctic Cyanobacterium, Nostoc sp. HG1

Ice-binding proteins (IBPs) have been identified in numerous polar algae and bacteria, but so far not in any cyanobacteria, despite the abundance of cyanobacteria in polar regions. We previously reported strong IBP activity associated with an Antarctic Nostoc species. In this study, to identify the proteins responsible, as well as elucidate their origin, we sequenced the DNA of an environmental sample of this species, designated Nostoc sp. HG1, and its bacterial community and attempted to identify IBPs by looking for known IBPs in the metagenome and by looking for novel IBPs by tandem mass spectrometry (MS/MS) proteomics analyses of ice affinity-purified proteins. The metagenome contained over 116 DUF3494-type IBP genes, the most common type of IBP identified so far. One of the IBPs could be confidently assigned to Nostoc, while the others could be attributed to diverse bacteria, which, surprisingly, accounted for the great majority of the metagenome. Recombinant Nostoc IBPs (nIBPs) had strong ice-structuring activities, and their circular dichroism spectra were consistent with the secondary structure of a DUF3494-type IBP. nIBP is unusual in that it is the only IBP identified so far to have a PEP (amino acid motif) C-terminal signal, a signal that has been associated with anchoring to the outer cell membrane. These results suggest that the observed IBP activity of Nostoc sp. HG1 was due to a combination of endogenous and exogenous IBPs. Amino acid and nucleotide sequence analyses of nIBP raise the possibility that it was acquired from a planctomycete.IMPORTANCE The horizontal transfer of genes encoding ice-binding proteins (IBPs), proteins that confer freeze-thaw tolerance, has allowed many microorganisms to expand their ranges into polar regions. One group of microorganisms for which nothing is known about its IBPs is cyanobacteria. In this study, we identified a cyanobacterial IBP and showed that it was likely acquired from another bacterium, probably a planctomycete. We also showed that a consortium of IBP-producing bacteria living with the Nostoc contribute to its IBP activity.

Antifreeze proteins and homogeneous nucleation: On the physical determinants impeding ice crystal growth

Antifreeze proteins (AFPs) are biopolymers capable of interfering with ice growth. Their antifreeze action is commonly understood considering that the AFPs, by pinning the ice surface, force the crystal-liquid interface to bend forming an ice meniscus, causing an increase in the surface free energy and resulting in a decrease in the freezing point ΔT^max. Here, we present an extensive computational study for a model protein adsorbed on a TIP4P/Ice crystal, computing ΔT^max as a function of the average distance d between AFPs, with simulations spanning over 1 µs. First, we show that the lower the d, the larger the ΔT^max. Then, we find that the water-ice-protein contact angle along the line ΔT^max(d) is always larger than 0°, and we provide a theoretical interpretation. We compute the curvature radius of the stable solid-liquid interface at a given supercooling ΔT ≤ ΔT^max, connecting it with the critical ice nucleus at ΔT. Finally, we discuss the antifreeze capability of AFPs in terms of the protein-water and protein-ice interactions. Our findings establish a unified description of the AFPs in the contest of homogeneous ice nucleation, elucidating key aspects of the antifreeze mechanisms and paving the way for the design of novel ice-controlling materials.

Self-Deicing Electrolyte Hydrogel Surfaces with Pa-level Ice Adhesion and Durable Antifreezing/Antifrost Performance

Despite the remarkable advances in mitigating ice formation and accretion, however, no engineered anti-icing surfaces today can durably prevent frost formation, droplet freezing, and ice accretion in an economical and ecofriendly way. Herein, sustainable and low-cost electrolyte hydrogel (EH) surfaces are developed by infusing salted water into a hydrogel matrix for avoiding icing. The EH surfaces can both prevent ice/frost formation for an extremely long time and reduce ice adhesion strength to ultralow value (Pa-level) at a tunable temperature window down to -48.4 °C. Furthermore, ice can self-remove from the tilted EH surface within 10 s at -10 °C by self-gravity. As demonstrated by both molecular dynamic simulations and experiments, these extreme performances are attributed to the diffusion of ions to the interface between EH and ice. The sustainable anti-icing properties of EH can be maintained by replenishing in real-time with available ion sources, indicating the promising applications in offshore platforms and ships.

Bioactive molecules from protists: Perspectives in biotechnology

For hundreds of years, mankind has benefited from the natural metabolic processes of microorganisms to obtain basic products such as fermented foods and alcoholic beverages. More recently, microorganisms have been exploited for the production of antibiotics, vitamins and enzymes to be used in medicine and chemical industries. Additionally, several modern drugs, including those for cancer therapy, are natural products or their derivatives. Protists are a still underexplored source of natural products potentially of interest for biotechnological and biomedical applications. This paper focuses on some examples of bioactive molecules from protists and associated bacteria and their possible use in biotechnology.

An Ice-Binding Protein from an Antarctic Ascomycete Is Fine-Tuned to Bind to Specific Water Molecules Located in the Ice Prism Planes

Many microbes that survive in cold environments are known to secrete ice-binding proteins (IBPs). The structure–function relationship of these proteins remains unclear. A microbial IBP denoted AnpIBP was recently isolated from a cold-adapted fungus, Antarctomyces psychrotrophicus. The present study identified an orbital illumination (prism ring) on a globular single ice crystal when soaked in a solution of fluorescent AnpIBP, suggesting that AnpIBP binds to specific water molecules located in the ice prism planes. In order to examine this unique ice-binding mechanism, we carried out X-ray structural analysis and mutational experiments. It appeared that AnpIBP is made of 6-ladder β-helices with a triangular cross section that accompanies an “ice-like” water network on the ice-binding site. The network, however, does not exist in a defective mutant. AnpIBP has a row of four unique hollows on the IBS, where the distance between the hollows (14.7 Å) is complementary to the oxygen atom spacing of the prism ring. These results suggest the structure of AnpIBP is fine-tuned to merge with the ice–water interface of an ice crystal through its polygonal water network and is then bound to a specific set of water molecules constructing the prism ring to effectively halt the growth of ice.

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

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.

Ice Binding Proteins: Diverse Biological Roles and Applications in Different Types of Industry

More than 80% of Earth’s surface is exposed periodically or continuously to temperatures below 5 °C. Organisms that can live in these areas are called psychrophilic or psychrotolerant. They have evolved many adaptations that allow them to survive low temperatures. One of the most interesting modifications is production of specific substances that prevent living organisms from freezing. Psychrophiles can synthesize special peptides and proteins that modulate the growth of ice crystals and are generally called ice binding proteins (IBPs). Among them, antifreeze proteins (AFPs) inhibit the formation of large ice grains inside the cells that may damage cellular organelles or cause cell death. AFPs, with their unique properties of thermal hysteresis (TH) and ice recrystallization inhibition (IRI), have become one of the promising tools in industrial applications like cryobiology, food storage, and others. Attention of the industry was also caught by another group of IBPs exhibiting a different activity—ice-nucleating proteins (INPs). This review summarizes the current state of art and possible utilizations of the large group of IBPs.

Ice-Binding Proteins in a Chrysophycean Snow Alga: Acquisition of an Essential Gene by Horizontal Gene Transfer

All ice-associated algae examined so far have genes for ice-binding proteins (IBPs), which suggest that these proteins are essential for survival in icy habitats. The most common type of IBP, type 1 IBPs (also referred to as DUF3494 IBPs), is also found in ice-associated bacteria and fungi. Previous studies have suggested that algal IBP genes were acquired by horizontal transfer from other microorganisms (probably bacteria). However, it remains unclear whether this is also the case for algae distantly related to the ones examined so far and whether microorganisms other than bacteria could be the donors. Furthermore, there is only limited evidence that these proteins are expressed at low temperature. Here, we show that Kremastochrysopsis austriaca (Chrysophyceae), an Austrian snow alga that is not closely related to any of the ice-associated algae examined so far, also produces IBPs, although their activity was weak. Sequencing the algal genome and the transcriptomes of cells grown at 1 and 15°C revealed three isoforms of a type 1 IBP. In agreement with their putative function, the three isoforms were strongly upregulated by one to two orders of magnitude at 1°C compared to 15°C. In a phylogenetic tree, the K. austriaca IBPs were distant from other algal IBPs, with the closest matches being bacterial proteins. These results suggest that the K. austriaca IBPs were derived from a gene that was acquired from a bacterium unrelated to other IBP donor bacteria and confirm by their presence in yet another alga the essential role of algal IBPs.

Bioinspired Ice Growth Inhibitors Based on Self-Assembling Peptides

Antifreeze proteins (AFPs) are widely found in organisms living in subzero environments. Their strong ability to inhibit ice growth and recrystallization have inspired considerable bioinspired efforts to engineer artificial ice growth inhibitors for cryopreservation. However, it remains challenging to engineer biocompatible and cost-effective synthetic ice growth inhibitors to meet the increasing needs of cryoprotectants in biomedical research and industry. Here we report the design of artificial ice growth inhibitors based on self-assembling peptides. We demonstrate the importance of threonine residues as well as their spatial arrangement for effective ice binding. The engineered self-assembling ice growth inhibiting peptides show moderate ice inhibiting activity including suppression of ice growth rates and retardation of recrystallization of ice crystals. The applications of these peptides in cryopreservation of enzymes and cells were also demonstrated.

Saturn-Shaped Ice Burst Pattern and Fast Basal Binding of an Ice-Binding Protein from an Antarctic Bacterial Consortium

Ice-binding proteins (IBPs) bind to ice crystals and control their growth, enabling host organisms to adapt to subzero temperatures. By binding to ice, IBPs can affect the shape and recrystallization of ice crystals. The shapes of ice crystals produced by IBPs vary and are partially due to which ice planes the IBPs are bound to. Previously, we have described a bacterial IBP found in the metagenome of the symbionts of Euplotes focardii ( EfcIBP). EfcIBP shows remarkable ice recrystallization inhibition activity. As recrystallization inhibition of IBPs and other materials are important to the cryopreservation of cells and tissues, we speculate that the EfcIBP can play a future role as an ice recrystallization inhibitor in cryopreservation applications. Here we show that EfcIBP results in a Saturn-shaped ice burst pattern, which may be due to the unique ice-plane affinity of the protein that we elucidated using the fluorescent-based ice-plane affinity analysis. EfcIBP binds to ice at a speed similar to that of other moderate IBPs (5 ± 2 mM^-1 s^-1); however, it is unique in that it binds to the basal and previously unobserved pyramidal near-basal planes, while other moderate IBPs typically bind to the prism and pyramidal planes and not basal or near-basal planes. These insights into EfcIBP allow a better understanding of the recrystallization inhibition for this unique protein.

Expression of Ice-Binding Proteins in Caenorhabditis elegans Improves the Survival Rate upon Cold Shock and during Freezing

Ice-binding proteins (IBPs) are capable of binding ice crystals and inhibiting their growth at freezing temperatures. IBPs are also thought to stabilize the cell membrane at non-freezing temperatures near 0 °C. These two effects have been assumed to reduce cold- and freezing-induced damage to cells and tissues. However, knowledge regarding the effects of IBP on the living animals is limited. Here, we characterized the relationship between the IBP effects and the physiological role by using the nematode Caenorhabditis elegans. The expression of fish (NfeIBPs)- and fungus-derived IBPs (AnpIBPs and TisIBP8) in C. elegans improved its survival rate during exposure to 0 and −2 °C (cold shock) and −5 °C (freezing). The observed cold tolerance of C. elegans after cold shock is attributable to the stabilization of cell-membrane lipids with IBPs, and the freezing tolerance at −5 °C can be attributed to the inhibition of ice-crystal growth by the IBPs. Significantly, the survival rate of C. elegans at −5 °C was improved by expression of wild-type AnpIBP and maximized by that of TisIBP8, whereas it was lowered when a defective AnpIBP mutant was expressed. These results suggest that the ice-binding ability of IBP has a good correlation with the survival rate of C. elegans during freezing.

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

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.

Ice-binding proteins and the 'domain of unknown function' 3494 family

Ice-binding proteins (IBPs) control the growth and shape of ice crystals to cope with subzero temperatures in psychrophilic and freeze-tolerant organisms. Recently, numerous proteins containing the domain of unknown function (DUF) 3494 were found to bind ice crystals and, hence, are classified as IBPs. DUF3494 IBPs constitute today the most widespread of the known IBP families. They can be found in different organisms including bacteria, yeasts and microalgae, supporting the hypothesis of horizontal transfer of its gene. Although the 3D structure is always a discontinuous β-solenoid with a triangular cross-section and an adjacent alpha-helix, DUF3494 IBPs present very diverse activities in terms of the magnitude of their thermal hysteresis and inhibition of ice recrystallization. The proteins are secreted into the environments around the host cells or are anchored on their cell membranes. This review covers several aspects of this new class of IBPs, which promise to leave their mark on several research fields including structural biology, protein biochemistry and cryobiology.

Multiple binding modes of a moderate ice-binding protein from a polar microalga

Ice-binding proteins (IBPs) produced by cold-tolerant organisms interact with ice and strongly control crystal growth. The molecular basis for the different magnitudes of activity displayed by various IBPs (moderate and hyperactive) has not yet been clarified. Previous studies questioned whether the moderate activity of some IBPs relies on their weaker binding modus to the ice surface, compared to hyperactive IBPs, rather than relying on binding only to selected faces of the ice crystal. We present the structure of one moderate IBP from the sea-ice diatom Fragilariopsis cylindrus (fcIBP) as determined by X-ray crystallography and investigate the protein's binding modes to the growing ice-water interface using molecular dynamics simulations. The structure of fcIBP is the IBP-1 fold, defined by a discontinuous β-solenoid delimitated by three faces (A, B and C-faces) and braced by an α-helix. The fcIBP structure shows capping loops on both N- and C-terminal parts of the solenoid. We show that the protein adsorbs on both the prism and the basal faces of ice crystals, confirming experimental results. The fcIBP binds irreversibly to the prism face using the loop between the B and the C-faces, involving also the B-face in water immobilization despite its irregular structure. The α-helix attaches the protein to the basal face with a partly reversible modus. Our results suggest that fcIBP has a looser attachment to ice and that this weaker binding modus is the basis to explain the moderate activity of fcIBP.

Molecular Dynamics Simulation of Ice Crystal Growth Inhibition by Hexadecyl-trimethyl-ammonium Bromide

Recent experiments have found hexadecyl-trimethyl-ammonium bromide (CTAB) to have superior ice nucleation inhibition properties [ J. Phys. Chem. B 121, 6580]. The mechanism of how the inhibition takes place remains unclear. Therefore, molecular dynamics was used to simulate ice crystallization of a water/CTAB/ice system. The ice crystallization rate for a pure water system was compared for the basal [0001], first prism [101̅0], and secondary prism plane [112̅0], where the basal plane grew the slowest followed by the first prism plane. When CTAB was added to the ice-liquid water system, crystallization was clearly impeded. Even when ice starts growing away from the CTAB molecule, the hydrophilic head would at some point protrude and get caught in the water/ice interface. Once the head of the CTAB was encapsulated in the advancing interface, the hydrophobic body would wriggle around and disrupt the formation of hydrogen bond networks that are essential for ice growth. When the interface clears the length of the body of the CTAB molecule, ice crystallization resumes at its normal pace. In summary, the inhibition of ice growth is a combination of the hydrophilic head acting as an anchor and the dynamic motion of the hydrophobic tail hindering stable hydrogen bonding for ice growth.

Growth suppression of ice crystal basal face in the presence of a moderate ice-binding protein does not confer hyperactivity

Ice-binding proteins (IBPs) affect ice crystal growth by attaching to crystal faces. We present the effects on the growth of an ice single crystal caused by an ice-binding protein from the sea ice microalga Fragilariopsis cylindrus (fcIBP) that is characterized by the widespread domain of unknown function 3494 (DUF3494) and known to cause a moderate freezing point depression (below 1 °C). By the application of interferometry, bright-field microscopy, and fluorescence microscopy, we observed that the fcIBP attaches to the basal faces of ice crystals, thereby inhibiting their growth in the c direction and resulting in an increase in the effective supercooling with increasing fcIBP concentration. In addition, we observed that the fcIBP attaches to prism faces and inhibits their growth. In the event that the effective supercooling is small and crystals are faceted, this process causes an emergence of prism faces and suppresses crystal growth in the a direction. When the effective supercooling is large and ice crystals have developed into a dendritic shape, the suppression of prism face growth results in thinner dendrite branches, and growth in the a direction is accelerated due to enhanced latent heat dissipation. Our observations clearly indicate that the fcIBP occupies a separate position in the classification of IBPs due to the fact that it suppresses the growth of basal faces, despite its moderate freezing point depression.

Comparing the Folds of Prions and Other Pathogenic Amyloids

Pathogenic amyloids are the main feature of several neurodegenerative disorders, such as Creutzfeldt⁻Jakob disease, Alzheimer’s disease, and Parkinson’s disease. High resolution structures of tau paired helical filaments (PHFs), amyloid-β(1-42) (Aβ(1-42)) fibrils, and α-synuclein fibrils were recently reported using cryo-electron microscopy. A high-resolution structure for the infectious prion protein, PrPSc, is not yet available due to its insolubility and its propensity to aggregate, but cryo-electron microscopy, X-ray fiber diffraction, and other approaches have defined the overall architecture of PrPSc as a 4-rung β-solenoid. Thus, the structure of PrPSc must have a high similarity to that of the fungal prion HET-s, which is part of the fungal heterokaryon incompatibility system and contains a 2-rung β-solenoid. This review compares the structures of tau PHFs, Aβ(1-42), and α-synuclein fibrils, where the β-strands of each molecule stack on top of each other in a parallel in-register arrangement, with the β-solenoid folds of HET-s and PrPSc.

Structure of a bacterial ice binding protein with two faces of interaction with ice

Ice-binding proteins (IBPs) contribute to the survival of many living beings at subzero temperature by controlling the formation and growth of ice crystals. This work investigates the structural basis of the ice-binding properties of EfcIBP, obtained from Antarctic bacteria. EfcIBP is endowed with a unique combination of thermal hysteresis and ice recrystallization inhibition activity. The three-dimensional structure, solved at 0.84 Å resolution, shows that EfcIBP belongs to the IBP-1 fold family, and is organized in a right-handed β-solenoid with a triangular cross-section that forms three protein surfaces, named A, B, and C faces. However, EfcIBP diverges from other IBP-1 fold proteins in relevant structural features including the lack of a 'capping' region on top of the β-solenoid, and in the sequence and organization of the regions exposed to ice that, in EfcIBP, reveal the presence of threonine-rich ice-binding motifs. Docking experiments and site-directed mutagenesis pinpoint that EfcIBP binds ice crystals not only via its B face, as common to other IBPs, but also via ice-binding sites on the C face.

DATABASE

Coordinates and structure factors have been deposited in the Protein Data Bank under accession number 6EIO.

An ice-binding and tandem beta-sandwich domain-containing protein in Shewanella frigidimarina is a potential new type of ice adhesin

Out of the dozen different ice-binding protein (IBP) structures known, the DUF3494 domain is the most widespread, having been passed many times between prokaryotic and eukaryotic microorganisms by horizontal gene transfer. This ~25-kDa β-solenoid domain with an adjacent parallel α-helix is most commonly associated with an N-terminal secretory signal peptide. However, examples of the DUF3494 domain preceded by tandem Bacterial Immunoglobulin-like (BIg) domains are sometimes found, though uncharacterized. Here, we present one such protein (SfIBP_1) from the Antarctic bacterium Shewanella frigidimarina. We have confirmed and characterized the ice-binding activity of its ice-binding domain using thermal hysteresis measurements, fluorescent ice plane affinity analysis, and ice recrystallization inhibition assays. X-ray crystallography was used to solve the structure of the SfIBP_1 ice-binding domain, to further characterize its ice-binding surface and unique method of stabilizing or 'capping' the ends of the solenoid structure. The latter is formed from the interaction of two loops mediated by a combination of tandem prolines and electrostatic interactions. Furthermore, given their domain architecture and membrane association, we propose that these BIg-containing DUF3494 IBPs serve as ice-binding adhesion proteins that are capable of adsorbing their host bacterium onto ice.

DATABASE

Submitted new structure to the Protein Data Bank (PDB: 6BG8).

Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere

Genome analyses are being used to characterize plant growth-promoting (PGP) bacteria living in different plant compartiments. In this context, we have recently isolated bacteria from the phyllosphere of an Antarctic plant (Deschampsia antarctica) showing ice recrystallization inhibition (IRI), an activity related to the presence of antifreeze proteins (AFPs). In this study, the draft genomes of six phyllospheric bacteria showing IRI activity were sequenced and annotated according to their functional gene categories. Genome sizes ranged from 5.6 to 6.3 Mbp, and based on sequence analysis of the 16S rRNA genes, five strains were identified as Pseudomonas and one as Janthinobacterium. Interestingly, most strains showed genes associated with PGP traits, such as nutrient uptake (ammonia assimilation, nitrogen fixing, phosphatases, and organic acid production), bioactive metabolites (indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase), and antimicrobial compounds (hydrogen cyanide and pyoverdine). In relation with IRI activity, a search of putative AFPs using current bioinformatic tools was also carried out. Despite that genes associated with reported AFPs were not found in these genomes, genes connected to ice-nucleation proteins (InaA) were found in all Pseudomonas strains, but not in the Janthinobacterium strain.

Fabrication of Anti-Icing Surfaces by Short α-Helical Peptides

We designed 12-amino acid peptides as antifreeze protein (AFP) mimetics and tuned the antifreeze activity of the peptides by their structures. Moreover, these short peptides were first immobilized to surfaces as an anti-icing coating. We discovered that the peptides with higher antifreeze activity exhibited better anti-icing performance. It is the first time that short peptides were successfully applied to fabricate anti-icing surfaces, which is certainly advantageous in comparison to the AFP anti-icing coatings previously reported.

Applications of Antifreeze Proteins: Practical Use of the Quality Products from Japanese Fishes

Numerous embryonic ice crystals are generated in water at the moment of freezing. These crystals grow and merge together to form an ice block that can be generally observed. Antifreeze protein (AFP) is capable of binding to the embryonic ice crystals, inhibiting such an ice block formation. Fish-derived AFP additionally binds to membrane lipid bilayers to prolong the lifetime of cells. These unique abilities of AFP have been studied extensively for the development of advanced techniques, such as ice recrystallization inhibitors, freeze-tolerant gels, cell preservation fluids, and high-porosity ceramics, for which mass-preparation method of the quality product of AFP utilizing fish muscle homogenates made a significant contribution. In this chapter, we present both fundamental and advanced information of fish AFPs that have been especially discovered from mid-latitude sea area, which will provide a hint to develop more advanced techniques applicable in both medical and industrial fields.

Antifreeze proteins

The antifreeze protein (AFP) activity is explained using two models. The first model is using ice binding and the second is using antiice structuralization of water molecules. The description of AFP function using anti-ice structuralization of water molecules is less explored. Therefore, it is of interest to explain AFP function using this model. Protein folding is often described using models where hydrophobic residues move away from water getting buried and hydrophilic residues are exposed to the surface. Thus, the 3D Gauss function stretched on the protein molecule describes the hydrophobicity distribution in a protein molecule. Small antifreeze proteins (less than 150 residues) are often represented by structures with hydrophobic core. Large antifreeze proteins (above 200 residues) contain solenoid (modular repeats). The hydrophobic field of solenoid show different distribution with linear propagation of the bands of different hydrophobicity level having high and low hydrophobicity that is propagated parallel to the long axis of solenoid. This specific ordering of hydrophobicity implies water molecules ordering different from ice. We illustrate this phenomenon using two antifreeze proteins to describe the hypothesis.

Structural basis of antifreeze activity of a bacterial multi-domain antifreeze protein

Antifreeze proteins (AFPs) enhance the survival of organisms inhabiting cold environments by affecting the formation and/or structure of ice. We report the crystal structure of the first multi-domain AFP that has been characterized. The two ice binding domains are structurally similar. Each consists of an irregular β-helix with a triangular cross-section and a long α-helix that runs parallel on one side of the β-helix. Both domains are stabilized by hydrophobic interactions. A flat plane on the same face of each domain’s β-helix was identified as the ice binding site. Mutating any of the smaller residues on the ice binding site to bulkier ones decreased the antifreeze activity. The bulky side chain of Leu174 in domain A sterically hinders the binding of water molecules to the protein backbone, partially explaining why antifreeze activity by domain A is inferior to that of domain B. Our data provide a molecular basis for understanding differences in antifreeze activity between the two domains of this protein and general insight on how structural differences in the ice-binding sites affect the activity of AFPs.

Identification and Characterization of an Isoform Antifreeze Protein from the Antarctic Marine Diatom, Chaetoceros neogracile and Suggestion of the Core Region

Antifreeze proteins (AFPs) protecting the cells against freezing are produced in response to extremely low temperatures in diverse psychrophilic organisms, and they are encoded by multiple gene families. The AFP of Antarctic marine diatom Chaetoceros neogracile is reported in our previous research, but like other microalgae, was considered to probably have additional genes coding AFPs. In this paper, we reported the cloning and characterization of additional AFP gene from C. neogracile (Cn-isoAFP). Cn-isoAFP protein is 74.6% identical to the previously reported Cn-AFP. The promoter sequence of Cn-isoAFP contains environmental stress responsive elements for cold, thermal, and high light conditions. Cn-isoAFP transcription levels increased dramatically when cells were exposed to freezing (−20 °C), thermal (10 °C), or high light (600 μmol photon m⁻² s⁻¹) stresses. The thermal hysteresis (TH) activity of recombinant Cn-isoAFP was 0.8 °C at a protein concentration of 5 mg/mL. Results from homology modeling and TH activity analysis of site-directed mutant proteins elucidated AFP mechanism to be a result of flatness of B-face maintained via hydrophobic interactions.

Why do antifreeze proteins require a solenoid?

Proteins whose presence prevents water from freezing in living organisms at temperatures below 0 °C are referred to as antifreeze proteins. This group includes molecules of varying size (from 30 to over 300 aa) and variable secondary/supersecondary conformation. Some of these proteins also contain peculiar structural motifs called solenoids. We have applied the fuzzy oil drop model in the analysis of four categories of antifreeze proteins: 1 - very small proteins, i.e. helical peptides (below 40 aa); 2 - small globular proteins (40-100 aa); 3 - large globular proteins (>100 aa) and 4 - proteins containing solenoids. The FOD model suggests a mechanism by which antifreeze proteins prevent freezing. In accordance with this theory, the presence of the protein itself produces an ordering of water molecules which counteracts the formation of ice crystals. This conclusion is supported by analysis of the ordering of hydrophobic and hydrophilic residues in antifreeze proteins, revealing significant variability - from perfect adherence to the fuzzy oil drop model through structures which lack a clearly defined hydrophobic core, all the way to linear arrangement of alternating local minima and maxima propagating along the principal axis of the solenoid (much like in amyloids). The presented model - alternative with respect to the ice docking model - explains the antifreeze properties of compounds such as saccharides and fatty acids. The fuzzy oil drop model also enables differentiation between amyloids and antifreeze proteins.

Multiple ice-binding proteins of probable prokaryotic origin in an Antarctic lake alga, Chlamydomonas sp. ICE-MDV (Chlorophyceae)

Ice-associated algae produce ice-binding proteins (IBPs) to prevent freezing damage. The IBPs of the three chlorophytes that have been examined so far share little similarity across species, making it likely that they were acquired by horizontal gene transfer (HGT). To clarify the importance and source of IBPs in chlorophytes, we sequenced the IBP genes of another Antarctic chlorophyte, Chlamydomonas sp. ICE-MDV (Chlamy-ICE). Genomic DNA and total RNA were sequenced and screened for known ice-associated genes. Chlamy-ICE has as many as 50 IBP isoforms, indicating that they have an important role in survival. The IBPs are of the DUF3494 type and have similar exon structures. The DUF3494 sequences are much more closely related to prokaryotic sequences than they are to sequences in other chlorophytes, and the chlorophyte IBP and ribosomal 18S phylogenies are dissimilar. The multiple IBP isoforms found in Chlamy-ICE and other algae may allow the algae to adapt to a greater variety of ice conditions than prokaryotes, which typically have a single IBP gene. The predicted structure of the DUF3494 domain has an ice-binding face with an orderly array of hydrophilic side chains. The results indicate that Chlamy-ICE acquired its IBP genes by HGT in a single event. The acquisitions of IBP genes by this and other species of Antarctic algae by HGT appear to be key evolutionary events that allowed algae to extend their ranges into polar environments.

From ice-binding proteins to bio-inspired antifreeze materials

Ice-binding proteins (IBP) facilitate survival under extreme conditions in diverse life forms. IBPs in polar fishes block further growth of internalized environmental ice and inhibit ice recrystallization of accumulated internal crystals. Algae use IBPs to structure ice, while ice adhesion is critical for the Antarctic bacterium Marinomonas primoryensis. Successful translation of this natural cryoprotective ability into man-made materials holds great promise but is still in its infancy. This review covers recent advances in the field of ice-binding proteins and their synthetic analogues, highlighting fundamental insights into IBP functioning as a foundation for the knowledge-based development of cheap, bio-inspired mimics through scalable production routes. Recent advances in the utilisation of IBPs and their analogues to e.g. improve cryopreservation, ice-templating strategies, gas hydrate inhibition and other technologies are presented.

Concentration-dependent oligomerization of an alpha-helical antifreeze polypeptide makes it hyperactive

A supersoluble 40-residue type I antifreeze protein (AFP) was discovered in a righteye flounder, the barfin plaice (bp). Unlike all other AFPs characterized to date, bpAFP transitions from moderately-active to hyperactive with increasing concentration. At sub-mM concentrations, bpAFP bound to pyramidal planes of ice to shape it into a bi-pyramidal hexagonal trapezohedron, similarly to the other moderately-active AFPs. At mM concentrations, bpAFP uniquely underwent further binding to the whole ice crystal surface including the basal planes. The latter caused a bursting ice crystal growth normal to c-axis, 3 °C of high thermal hysteresis, and alteration of an ice crystal into a smaller lemon-shaped morphology, all of which are well-known properties of hyperactive AFPs. Analytical ultracentrifugation showed this activity transition is associated with oligomerization to form tetramer, which might be the forerunner of a naturally occurring four-helix-bundle AFP in other flounders.

Marine Antifreeze Proteins: Structure, Function, and Application to Cryopreservation as a Potential Cryoprotectant

Antifreeze proteins (AFPs) are biological antifreezes with unique properties, including thermal hysteresis(TH),ice recrystallization inhibition(IRI),and interaction with membranes and/or membrane proteins. These properties have been utilized in the preservation of biological samples at low temperatures. Here, we review the structure and function of marine-derived AFPs, including moderately active fish AFPs and hyperactive polar AFPs. We also survey previous and current reports of cryopreservation using AFPs. Cryopreserved biological samples are relatively diverse ranging from diatoms and reproductive cells to embryos and organs. Cryopreserved biological samples mainly originate from mammals. Most cryopreservation trials using marine-derived AFPs have demonstrated that addition of AFPs can improve post-thaw viability regardless of freezing method (slow-freezing or vitrification), storage temperature, and types of biological sample type.

Hydrophobic ice-binding sites confer hyperactivity of an antifreeze protein from a snow mold fungus

Snow mold fungus, Typhula ishikariensis, secretes seven antifreeze protein isoforms (denoted TisAFPs) that assist in the survival of the mold under snow cover. Here, the X-ray crystal structure of a hyperactive isoform, TisAFP8, at 1.0 Å resolution is presented. TisAFP8 folds into a right-handed β-helix accompanied with a long α-helix insertion. TisAFP8 exhibited significantly high antifreeze activity that is comparable with other hyperactive AFPs, despite its close structural and sequence similarity with the moderately active isoform TisAFP6. A series of mutations introduced into the putative ice-binding sites (IBSs) in the β-sheet and adjacent loop region reduced antifreeze activity. A double-mutant A20T/A212S, which comprises a hydrophobic patch between the β-sheet and loop region, caused the greatest depression of antifreeze activity of 75%, when compared with that of the wild-type protein. This shows that the loop region is involved in ice binding and hydrophobic residues play crucial functional roles. Additionally, bound waters around the β-sheet and loop region IBSs were organized into an ice-like network and can be divided into two groups that appear to mediate separately TisAFP and ice. The docking model of TisAFP8 with the basal plane via its loop region IBS reveals a better shape complementarity than that of TisAFP6. In conclusion, we present new insights into the ice-binding mechanism of TisAFP8 by showing that a higher hydrophobicity and better shape complementarity of its IBSs, especially the loop region, may render TisAFP8 hyperactive to ice binding.

Putting life on ice: bacteria that bind to frozen water

Ice-binding proteins (IBPs) are typically small, soluble proteins produced by cold-adapted organisms to help them avoid ice damage by either resisting or tolerating freezing. By contrast, the IBP of the Antarctic bacterium Marinomonas primoryensis is an extremely long, 1.5 MDa protein consisting of five different regions. The fourth region, a 34 kDa domain, is the only part that confers ice binding. Bioinformatic studies suggest that this IBP serves as an adhesin that attaches the bacteria to ice to keep it near the top of the water column, where oxygen and nutrients are available. Using temperature-controlled cells and a microfluidic apparatus, we show that M. primoryensis adheres to ice and is only released when melting occurs. Binding is dependent on the mobility of the bacterium and the functionality of the IBP domain. A polyclonal antibody raised against the IBP region blocks bacterial ice adhesion. This concept may be the basis for blocking biofilm formation in other bacteria, including pathogens. Currently, this IBP is the only known example of an adhesin that has evolved to bind ice.