Structure of a peptide antifreeze and mechanism of adsorption to ice

Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice

Using molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water, which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation and distance relative to the surface of ice, which enables the effective binding (via hydrogen bonds) of the molecule with the nascent ice surface. Our results show that the final adsorption of the AFP III molecule on the surface of ice is not achieved by chaotic diffusion movements, but it is preceded by a remote, water-mediated interaction between the IBS and the surface of ice. The key factor that determines the existence of this interaction is the ability of water molecules to spontaneously form large, high-volume aggregates that can be anchored to both the IBS of the AFP molecule and the surface of ice. The results presented in this work for AFP III are in full agreement with the ones obtained by us previously for hyperactive CfAFP, which indicates that the mechanism of the remote interaction of these molecules with ice remains unchanged despite significant differences in the molecular structure of their ice binding sites. For that reason, we can expect that also other types of AFPs interact with the ice surface according to an analogous mechanism.

Engineered Compounds to Control Ice Nucleation and Recrystallization

One of the greatest concerns in the subzero storage of cells, tissues, and organs is the ability to control the nucleation or recrystallization of ice. In nature, evidence of these processes, which aid in sustaining internal temperatures below the physiologic freezing point for extended periods of time, is apparent in freeze-avoidant and freeze-tolerant organisms. After decades of studying these proteins, we now have easily accessible compounds and materials capable of recapitulating the mechanisms seen in nature for biopreser-vation applications. The output from this burgeoning area of research can interact synergistically with other novel developments in the field of cryobiology, making it an opportune time for a review on this topic.

Janus regulation of ice growth by hyperbranched polyglycerols generating dynamic hydrogen bonding

In this study, a new phenomenon describing the Janus effect on ice growth by hyperbranched polyglycerols, which can align the surrounding water molecules, has been identified. Even with an identical polyglycerol, we not only induced to inhibit ice growth and recrystallization, but also to promote the growth rate of ice that is more than twice that of pure water. By investigating the polymer architecture and population, we found that the stark difference in the generation of quasi-structured H₂O molecules at the ice/water interface played a crucial role in the outcome of these opposite effects. Inhibition activity was induced when polymers at nearly fixed loci formed steady hydrogen bonding with the ice surface. However, the formation-and-dissociation dynamics of the interfacial hydrogen bonds, originating from and maintained by migrating polymers, resulted in an enhanced quasi-liquid layer that facilitated ice growth. Such ice growth activity is a unique property unseen in natural antifreeze proteins or their mimetic materials.

Reflections on antifreeze proteins and their evolution

The discovery of radically different antifreeze proteins (AFPs) in fishes during the 1970s and 1980s suggested that these proteins had recently and independently evolved to protect teleosts from freezing in icy seawater. Early forays into the isolation and characterization of AFP genes in these fish showed they were massively amplified, often in long tandem repeats. The work of many labs in the 1980s onward led to the discovery and characterization of AFPs in other kingdoms, such as insects, plants, and many different microorganisms. The distinct ice-binding property that these ice-binding proteins (IBPs) share has facilitated their purification through adsorption to ice, and the ability to produce recombinant versions of IBPs has enabled their structural characterization and the mapping of their ice-binding sites (IBSs) using site-directed mutagenesis. One hypothesis for their ice affinity is that the IBS organizes surface waters into an ice-like pattern that freezes the protein onto ice. With access now to a rapidly expanding database of genomic sequences, it has been possible to trace the origins of some fish AFPs through the process of gene duplication and divergence, and to even show the horizontal transfer of an AFP gene from one species to another.

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.

Polar gigantism and the oxygen-temperature hypothesis: a test of upper thermal limits to body size in Antarctic pycnogonids

The extreme and constant cold of the Southern Ocean has led to many unusual features of the Antarctic fauna. One of these, polar gigantism, is thought to have arisen from a combination of cold-driven low metabolic rates and high oxygen availability in the polar oceans (the 'oxygen-temperature hypothesis'). If the oxygen-temperature hypothesis indeed underlies polar gigantism, then polar giants may be particularly susceptible to warming temperatures. We tested the effects of temperature on performance using two genera of giant Antarctic sea spiders (Pycnogonida), Colossendeis and Ammothea, across a range of body sizes. We tested performance at four temperatures spanning ambient (-1.8°C) to 9°C. Individuals from both genera were highly sensitive to elevated temperature, but we found no evidence that large-bodied pycnogonids were more affected by elevated temperatures than small individuals; thus, these results do not support the predictions of the oxygen-temperature hypothesis. When we compared two species, Colossendeis megalonyx and Ammothea glacialis, C. megalonyx maintained performance at considerably higher temperatures. Analysis of the cuticle showed that as body size increases, porosity increases as well, especially in C. megalonyx, which may compensate for the increasing metabolic demand and longer diffusion distances of larger animals by facilitating diffusive oxygen supply.

Ordered hydration layer mediated ice adsorption of a globular antifreeze protein: mechanistic insight

The ice binding surface of a type III AFP induces water ordering at lower temperature, which mediates its adsorption on the ice surface.

Calcium ion implicitly modulates the adsorption ability of ion-dependent type II antifreeze proteins on an ice/water interface: a structural insight

Ca²⁺modulates the dynamics of ion-dependent type II AFP to efficiently adsorb on ice surface with high degree of specificity.

Protein evolution revisited

Antifreeze proteins (AFPs) protect marine fishes from freezing in icy seawater. They evolved relatively recently, most likely in response to the formation of sea ice and Cenozoic glaciations that occurred less than 50 million years ago, following a greenhouse Earth event. Based on their diversity, AFPs have independently evolved on many occasions to serve the same function, with some remarkable examples of convergent evolution at the structural level, and even instances of lateral gene transfer. For some AFPs, the progenitor gene is recognizable. The intense selection pressure exerted by icy seawater, which can rapidly kill unprotected fish, has led to massive AFP gene amplification, as well as some partial gene duplications that have increased the size and activity of the antifreeze. The many protein evolutionary processes described in Gordon H. Dixon's Essays in Biochemistry article will be illustrated here by examples from studies on AFPs. Abbreviations: AFGP: antifreeze glycoproteins; AFP: antifreeze proteins; GHD: Gordon H. Dixon; SAS: sialic acid synthase; TH: thermal hysteresis.

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.

Balance between hydration enthalpy and entropy is important for ice binding surfaces in Antifreeze Proteins

Antifreeze Proteins (AFPs) inhibit the growth of an ice crystal by binding to it. The detailed binding mechanism is, however, still not fully understood. We investigated three AFPs using Molecular Dynamics simulations in combination with Grid Inhomogeneous Solvation Theory, exploring their hydration thermodynamics. The observed enthalpic and entropic differences between the ice-binding sites and the inactive surface reveal key properties essential for proteins in order to bind ice: While entropic contributions are similar for all sites, the enthalpic gain for all ice-binding sites is lower than for the rest of the protein surface. In contrast to most of the recently published studies, our analyses show that enthalpic interactions are as important as an ice-like pre-ordering. Based on these observations, we propose a new, thermodynamically more refined mechanism of the ice recognition process showing that the appropriate balance between entropy and enthalpy facilitates ice-binding of proteins. Especially, high enthalpic interactions between the protein surface and water can hinder the ice-binding activity.

Investigation of changes in structure and thermodynamic of spruce budworm antifreeze protein under subfreezing temperature

The aim of this theoretical work is to investigate of the changes in structure and thermodynamics of spruce budworm antifreeze protein (sbAFP) at low temperatures by using molecular dynamics simulation. The aqueous solution will form ice crystal network under the vaguely hexagonal shape at low temperature and fully represented the characteristics of hydrophobic interaction. Like ice crystal network, the cyclohexane region (including cyclohexane molecules) have enough of the characteristics of hydrophobic interaction. Therefore, in this research the cyclohexane region will be used as a representation of ice crystal network to investigate the interactions of sbAFP and ice crystal network at low temperature. The activity of sbAFP in subfreezing environment, therefore, can be clearly observed via the changes of the hydrophobic (cyclohexane region) and hydrophilic (water region) interactions. The obtained results from total energies, hydrogen bond lifetime correlation C(t), radial distribution function, mean square deviation and snapshots of sbAFP complexes indicated that sbAFP has some special changes in structure and interaction with water and cyclohexane regions at 278 K, as being transition temperature point of water molecules in sbAFP complex at low temperatures, which is more structured and support the experimental observation that the sbAFP complex becomes more rigid as the temperature is lowered.

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights

BACKGROUND

Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis.

RESULTS

Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds.

CONCLUSIONS

This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.

Conformational and hydration properties modulate ice recognition by type I antifreeze protein and its mutants

Mutation of wfAFP changes the intrinsic dynamics in such a way that it significantly influences water mediated AFP adsorption on ice.

Exploring the Effects of Subfreezing Temperature and Salt Concentration on Ice Growth Inhibition of Antarctic Gram-Negative Bacterium Marinomonas Primoryensis Using Coarse-Grained Simulation

The aim of this work is to study the freezing process of water molecules surrounding Antarctic Gram-negative bacterium Marinomonas primoryensis antifreeze protein (MpAFP) and the MpAFP interactions to the surface of ice crystals under various marine environments (at different NaCl concentrations of 0.3, 0.6, and 0.8 mol/l). Our result indicates that activating temperature region of MpAFPs reduced as NaCl concentration increased. Specifically, MpAFP was activated and functioned at 0.6 mol/l with temperatures equal or larger 278 K, and at 0.8 mol/l with temperatures equal or larger 270 K. Additionally, MpAFP was inhibited by ice crystal network from 268 to 274 K and solid-liquid hybrid from 276 to 282 K at 0.3 mol/l concentration. Our results shed lights on structural dynamics of MpAFP among different marine environments.

Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin

The hydration layer surrounding a protein plays an essential role in its biochemical function and consists of a heterogeneous ensemble of water molecules with different local environments and different dynamics. What determines the degree of dynamical heterogeneity within the hydration shell and how this changes with temperature remains unclear. Here, we combine molecular dynamics simulations and analytic modeling to study the hydration shell structure and dynamics of a typical globular protein, ubiquitin, and of the spruce budworm hyperactive antifreeze protein over the 230-300 K temperature range. Our results show that the average perturbation induced by both proteins on the reorientation dynamics of water remains moderate and changes weakly with temperature. The dynamical heterogeneity arises mostly from the distribution of protein surface topographies and is little affected by temperature. The ice-binding face of the antifreeze protein induces a short-ranged enhancement of water structure and a greater slowdown of water reorientation dynamics than the non-ice-binding faces whose effect is similar to that of ubiquitin. However, the hydration shell of the ice-binding face remains less tetrahedral than the bulk and is not "ice-like". We finally show that the hydrogen bonds between water and the ice-binding threonine residues are particularly strong due to a steric confinement effect, thereby contributing to the strong binding of the antifreeze protein on ice crystals.

Animal ice-binding (antifreeze) proteins and glycolipids: an overview with emphasis on physiological function

Ice-binding proteins (IBPs) assist in subzero tolerance of multiple cold-tolerant organisms: animals, plants, fungi, bacteria etc. IBPs include: (1) antifreeze proteins (AFPs) with high thermal hysteresis antifreeze activity; (2) low thermal hysteresis IBPs; and (3) ice-nucleating proteins (INPs). Several structurally different IBPs have evolved, even within related taxa. Proteins that produce thermal hysteresis inhibit freezing by a non-colligative mechanism, whereby they adsorb onto ice crystals or ice-nucleating surfaces and prevent further growth. This lowers the so-called hysteretic freezing point below the normal equilibrium freezing/melting point, producing a difference between the two, termed thermal hysteresis. True AFPs with high thermal hysteresis are found in freeze-avoiding animals (those that must prevent freezing, as they die if frozen) especially marine fish, insects and other terrestrial arthropods where they function to prevent freezing at temperatures below those commonly experienced by the organism. Low thermal hysteresis IBPs are found in freeze-tolerant organisms (those able to survive extracellular freezing), and function to inhibit recrystallization – a potentially damaging process whereby larger ice crystals grow at the expense of smaller ones – and in some cases, prevent lethal propagation of extracellular ice into the cytoplasm. Ice-nucleator proteins inhibit supercooling and induce freezing in the extracellular fluid at high subzero temperatures in many freeze-tolerant species, thereby allowing them to control the location and temperature of ice nucleation, and the rate of ice growth. Numerous nuances to these functions have evolved. Antifreeze glycolipids with significant thermal hysteresis activity were recently identified in insects, frogs and plants.

Heterologous expression of antifreeze protein gene AnAFP from Ammopiptanthus nanus enhances cold tolerance in Escherichia coli and tobacco

Antifreeze proteins are a class of polypeptides produced by certain animals, plants, fungi and bacteria that permit their survival under the subzero environments. Ammopiptanthus nanus is the unique evergreen broadleaf bush endemic to the Mid-Asia deserts. It survives at the west edge of the Tarim Basin from the disappearance of the ancient Mediterranean in the Tertiary Period. Its distribution region is characterized by the arid climate and extreme temperatures, where the extreme temperatures range from -30 °C to 40 °C. In the present study, the antifreeze protein gene AnAFP of A. nanus was used to transform Escherichia coli and tobacco, after bioinformatics analysis for its possible function. The transformed E. coli strain expressed the heterologous AnAFP gene under the induction of isopropyl β-D-thiogalactopyranoside, and demonstrated significant enhancement of cold tolerance. The transformed tobacco lines expressed the heterologous AnAFP gene in response to cold stress, and showed a less change of relative electrical conductivity under cold stress, and a less wilting phenotype after 16 h of -3 °C cold stress and thawing for 1h than the untransformed wild-type plants. All these results imply the potential value of the AnAFP gene to be used in genetic modification of commercially important crops for improvement of cold tolerance.

Designing ice recrystallization inhibitors: from antifreeze (glyco)proteins to small molecules

Ice recrystallization occurs during cryopreservation and is correlated with reduced cell viability after thawing.

Functional importance of short-range binding and long-range solvent interactions in helical antifreeze peptides

Short-range ice binding and long-range solvent perturbation both have been implicated in the activity of antifreeze proteins and antifreeze glycoproteins. We study these two mechanisms for activity of winter flounder antifreeze peptide. Four mutants are characterized by freezing point hysteresis (activity), circular dichroism (secondary structure), Förster resonance energy transfer (end-to-end rigidity), molecular dynamics simulation (structure), and terahertz spectroscopy (long-range solvent perturbation). Our results show that the short-range model is sufficient to explain the activity of our mutants, but the long-range model provides a necessary condition for activity: the most active peptides in our data set all have an extended dynamical hydration shell. It appears that antifreeze proteins and antifreeze glycoproteins have reached different evolutionary solutions to the antifreeze problem, utilizing either a few precisely positioned OH groups or a large quantity of OH groups for ice binding, assisted by long-range solvent perturbation.

Thermolabile antifreeze protein produced in Escherichia coli for structural analysis

The only hyperactive antifreeze protein (AFP) found to date in fishes is an extreme variant of the 3-kDa, alpha-helical, alanine-rich type I AFP, which is referred to here as type Ih. Purification of the 33-kDa homodimeric AFP Ih from a natural source was hampered by its low levels in fish plasma; by the need to remove the more abundant smaller isoforms; and by its extreme thermolability. Moreover, ice affinity as a purification tool was spoiled by the tendency of fish IgM antibodies to bind to ice in the presence of AFPs. In order to produce enough protein for crystallography we expressed AFP Ih as a recombinant protein in the Arctic Express® strain of Escherichia coli at 12 °C, just below the thermal denaturation temperature of 16-18 °C. His-tags were not useful because they compromised the activity and yield of AFP Ih. But in the absence of fish antibodies we were able to recover 10-mg quantities of the antifreeze protein using two cycles of ice affinity purification followed by anion-exchange chromatography to remove contaminating chaperones. The purified recombinant AFP Ih yielded diffraction-quality crystals with an extremely asymmetrical unit cell. By transferring the genes of the chaperones into a methionine auxotroph we were able to grow this host at low temperatures and produce sufficient selenomethionine-labeled AFP Ih for crystallography.

The Thr- and Ala-rich hyperactive antifreeze protein from inchworm folds as a flat silk-like β-helix

Inchworm larvae of the pale beauty geometer moth, Campaea perlata, exhibit strong (6.4 °C) freezing point depression activity, indicating the presence of hyperactive antifreeze proteins (AFPs). We have purified two novel Thr- and Ala-rich AFPs from the larvae as small (∼3.5 kDa) and large (∼8.3 kDa) variants and have cloned the cDNA sequences encoding both. They have no homology to known sequences in current BLAST databases. However, these proteins and the newly characterized AFP from the Rhagium inquisitor beetle both contain stretches rich in alternating Thr and Ala residues. On the basis of these repeats, as well as the discontinuities between them, a detailed structural model is proposed for the 8.3 kDa variant. This 88-residue protein is organized into an extended parallel-stranded β-helix with seven strands connected by classic β-turns. The alternating β-strands form two β-sheets with a thin core composed of interdigitating Ala and Ser residues, similar to the thin hydrophobic core proposed for some silks. The putative ice-binding face of the protein has a 4 × 5 regular array of Thr residues and is remarkably flat. In this regard, it resembles the nonhomologous Thr-rich AFPs from other moths and some beetles, which contain two longer rows of Thr in contrast to the five shorter rows in the inchworm protein. Like that of some other hyperactive AFPs, the spacing between these ice-binding Thr residues is a close match to the spacing of oxygen atoms on several planes of ice.

Anchored clathrate waters bind antifreeze proteins to ice

The mechanism by which antifreeze proteins (AFPs) irreversibly bind to ice has not yet been resolved. The ice-binding site of an AFP is relatively hydrophobic, but also contains many potential hydrogen bond donors/acceptors. The extent to which hydrogen bonding and the hydrophobic effect contribute to ice binding has been debated for over 30 years. Here we have elucidated the ice-binding mechanism through solving the first crystal structure of an Antarctic bacterial AFP. This 34-kDa domain, the largest AFP structure determined to date, folds as a Ca(2+)-bound parallel beta-helix with an extensive array of ice-like surface waters that are anchored via hydrogen bonds directly to the polypeptide backbone and adjacent side chains. These bound waters make an excellent three-dimensional match to both the primary prism and basal planes of ice and in effect provide an extensive X-ray crystallographic picture of the AFPice interaction. This unobstructed view, free from crystal-packing artefacts, shows the contributions of both the hydrophobic effect and hydrogen bonding during AFP adsorption to ice. We term this mode of binding the "anchored clathrate" mechanism of AFP action.

Effect of a mutation on the structure and dynamics of an α-helical antifreeze protein in water and ice

One strategy of psychrophilic organisms to survive subzero temperature is to produce antifreeze protein (AFPs), which inhibit the growth of macromolecular ice. To better understand the binding mechanism, the structure and dynamics of several AFPs have been studied by nuclear magnetic resonance (NMR) and X-ray crystallography. The results have shown that different organisms can use diverse structures (alpha-helix, beta-helix, or different globular folds) to achieve the same function. A number of studies have focused on understanding the relationship between the alpha-helical structure of fish type I AFP and its function as an inhibitor of ice growth. The results have not explained whether the 90% activity loss caused by the conservative mutation of two threonines to serines (Thr13Ser/Thr24Ser) is attributable to a change in protein structure in solution or in ice. We examine here the structure and dynamics of the winter flounder type I AFP and the mutant Thr13Ser/Thr24Ser in both solution and solid states using a wide range of NMR approaches. Both proteins remain fully alpha-helical at all temperatures and in ice, demonstrating that the activity change must therefore not be attributable to changes in the protein fold or dynamics but differences in surface properties.

Heterologous expression of type I antifreeze peptide GS-5 in baker's yeast increases freeze tolerance and provides enhanced gas production in frozen dough

The demand for frozen-dough products has increased notably in the baking industry. Nowadays, no appropriate industrial baker's yeast with optimal gassing capacity in frozen dough is, however, available, and it is unlikely that classical breeding programs could provide significant improvements of this trait. Antifreeze proteins, found in diverse organisms, display the ability to inhibit the growth of ice, allowing them to survive at temperatures below 0 degrees C. In this study a recombinant antifreeze peptide GS-5 was expressed from the polar fish grubby sculpin (Myoxocephalus aenaeus) in laboratory and industrial baker's yeast strains of Saccharomyces cerevisiae. Production of the recombinant protein increased freezing tolerance in both strains tested. Furthermore, expression of the GS-5 encoding gene enhanced notably the gassing rate and total gas production in frozen and frozen sweet doughs. These effects are unlikely to be due to reduced osmotic damage during freezing/thawing, because recombinant cells showed growth behavior similar to that of the parent under hypermosmotic stress conditions.

Hyperactive Antifreeze Protein from Winter Flounder Is a Very Long Rod-like Dimer of α-Helices

The winter flounder (Pseudopleuronectes americanus) produces short, monomeric alpha-helical antifreeze proteins (type I AFP), which adsorb to and inhibit the growth of ice crystals. These proteins alone are not sufficiently active to protect this fish against freezing at -1.9 degrees C, the freezing point of seawater. We have recently isolated a hyperactive antifreeze protein from the plasma of the flounder with activity 10-100-fold higher than type I AFP. It is comparable in activity to the AFPs produced by insects, and is capable of conferring freeze resistance to the flounder. This novel AFP has a molecular mass of 16,683 Da and a remarkable amino acid composition that is >60% alanine. CD spectra indicate that the protein is almost entirely alpha-helical at 4 degrees C but partially denatures at 20 degrees C, resulting in a species with a moderately reduced helix content that is stable at up to 50 degrees C. This transformation correlates with irreversible loss of activity. Analytical ultracentrifugation (sedimentation velocity and equilibrium) indicates that the predominant species in solution is dimeric (molecular weight, 32,275). Size-exclusion chromatography reveals a 2-fold higher apparent molecular weight suggesting that this molecule has an unusually large Stokes radius. The axial ratio of the dimer calculated from the sedimentation velocity data is 18:1, confirming that this protein has an extraordinarily long, rod-like structure, consistent with a novel dimeric alpha-helical arrangement. The structural model that best fits these data is one in which the approximately 195 amino acids of each monomer form one approximately 290-A long alpha-helix and associate via a unique dimerization motif that is distinct from that of the leucine zipper and any other coiled-coil.

Theoretical study of interaction of winter flounder antifreeze protein with ice

Antifreeze proteins (AFPs) are synthesized by various organisms to enable their cells to survive subzero environment. These proteins bind to small ice crystals and inhibit their growth, which if left uncontrolled would be fatal to cells. The crystal structures of a number of AFPs have been determined; however, crystallographic analysis of AFP-ice complex is nearly impossible. Molecular modeling studies of AFPs' interaction with ice surface is therefore invaluable. Early models of AFP-ice interaction suggested H-bond as the primary driving force behind such interaction. Recent experimental evidence, however, suggested that hydrophobic interactions could be the main contributor to AFP-ice association. All computational studies published to date were carried out to verify the H-bond model, and no works attempting to verify the hydrophobic interaction model have been published. In this work, we Monte Carlo-minimized complexes of several AFPs with ice taking into account nonbonded interactions, H-bonds, and the hydration potential for proteins. Parameters of the hydration potential for ice were developed with the assumption that the free energy of the water-ice association should be close to zero at equilibrium melting temperature. Our calculations demonstrate that desolvation of hydrophobic groups in the AFPs upon their binding to the grooves at the ice surface is indeed the major stabilizing contributor to the free energy of AFP-ice binding. This study is consistent with available structural and mutation data on AFPs. In particular, it explains the paradoxical finding that substitution of Thr residues with Val does not affect the potency of winter flounder AFP whereas substitution with Ser abolished its antifreeze activity.

Cold survival in freeze-intolerant insects

Antifreeze proteins (AFPs) designate a class of proteins that are able to bind to and inhibit the growth of macromolecular ice. These proteins have been characterized from a variety of organisms. Recently, the structures of AFPs from the spruce budworm (Choristoneura fumiferana) and the yellow mealworm (Tenebrio molitor) have been determined by NMR and X-ray crystallography. Despite nonhomologous sequences, both proteins were shown to consist of beta-helices. We review the structures and dynamics data of these two insect AFPs to bring insight into the structure-function relationship and explore their beta-helical architecture. For the spruce budworm protein, the fold is a left-handed beta-helix with 15 residues per coil. The Tenebrio molitor protein consists of a right-handed beta-helix with 12 residues per coil. Mutagenesis and structural studies show that the insect AFPs present a highly rigid array of threonine residues and bound water molecules that can effectively mimic the ice lattice. Comparisons of the newly determined ryegrass and carrot AFP sequences have led to models suggesting that they might also consist of beta-helices, and indicate that the beta-helix might be used as an AFP structural motif in nonfish organisms.

The role of N and C termini in the antifreeze activity of winter flounder (Pleuronectes americanus) antifreeze proteins

Antifreeze proteins (AFPs) are found in many marine fish and have been classified into five biochemical classes: AFP types I-IV and the antifreeze glycoproteins. Type I AFPs are alpha-helical, partially amphipathic, Ala-rich polypeptides. The winter flounder (Pleuronectes americanus) produces two type I AFP subclasses, the liver-type AFPs (wflAFPs) and the skin-type AFPs (wfsAFPs), that are encoded by distinct gene families with different tissue-specific expression. wfsAFPs and wflAFPs share a high level of identity even though the wfsAFPs have approximately half the activity of the wflAFPs. Synthetic polypeptides based on two representative wflAFPs and wfsAFPs were generated to examine the role of the termini in antifreeze activity. Through systematic exchange of N and C termini between wflAFP-6 and wfsAFP-2, the termini were determined to be the major causative agents for the variation in activity levels between the two AFPs. Furthermore, the termini of wflAFP-6 possessed greater helix-stabilizing ability compared with their wfsAFP-2 counterparts. The observed 50% difference in activity between wflAFP-6 and wfsAFP-2 can be divided into approximately 20% for differences at each termini and approximately 10% for differences in the core. Furthermore, the N terminus was determined to be the most critical component for antifreeze activity.

Reversible binding of the HPLC6 isoform of type I antifreeze proteins to ice surfaces and the antifreeze mechanism studied by multiple quantum filtering-spin exchange NMR experiment

Antifreeze proteins (AFPs) protect organisms from freezing damage by inhibiting the growth of seed-ice crystals. It has long been hypothesized that irreversible binding of AFPs to ice surfaces is responsible for inhibiting the growth of seed-ice crystals as such a mechanism supports the popularly accepted Kelvin effect for the explanation of local freezing-point depression. However, whether the binding is reversible or irreversible is still under debate due to the lack of direct experimental evidence. Here, we report the first direct experimental result, by using the newly developed multiple quantum (MQ) filtering-spin exchange NMR experiment, that shows that the binding of HPLC6 peptides to ice surfaces is reversible. It was found that the reversible process can be explained by the model of monolayer adsorption. These results suggest that the Kelvin effect is not suitable for explaining the antifreeze mechanism, and direct interactions between the peptides and the ice-surface binding sites are the driving forces for the binding of AFPs to ice surfaces. We propose that there exists a concentration gradient of AFP from an ice-binding surface to the solution due to the affinity of ice surfaces to AFPs. This concentration gradient creates a dense layer of AFP in contact with the ice-binding surface, which depresses the local freezing point because of the colligative property, but not the Kelvin effect.

A beta-helical antifreeze protein isoform with increased activity. Structural and functional insights

The insect spruce budworm (Choristoneura fumiferana)(Cf) produces a number of isoforms of its highly active antifreeze protein (CfAFP). Although most of the CfAFP isoforms are in the 9-kDa range, isoforms containing a 30- or 31-amino acid insertion have also been identified. Here we describe the functional and structural analysis of a selected long isoform, CfAFP-501. X-ray crystal structure determination reveals that the 31-amino acid insertion found in CfAFP-501 forms two additional loops within its highly regular beta-helical structure. This effectively extends the area of the two-dimensional Thr array and ice-binding surface of the protein. The larger isoform has 3 times the thermal hysteresis activity of the 9-kDa CfAFP-337. As well, a deletion of the 31-amino acid insertion within CfAFP-501 to form CfAFP-501-Delta-2-loop, results in a protein with reduced activity similar to the shorter CfAFP isoforms. Thus, the enhanced antifreeze activity of CfAFP-501 is directly correlated to the length of its beta-helical structure and hence the size of its ice-binding face.

Plants in a cold climate

Plants are able to survive prolonged exposure to sub-zero temperatures; this ability is enhanced by pre-exposure to low, but above-zero temperatures. This process, known as cold acclimation, is briefly reviewed from the perception of cold, through transduction of the low-temperature signal to functional analysis of cold-induced gene products. The stresses that freezing of apoplastic water imposes on plant cells is considered and what is understood about the mechanisms that plants use to combat those stresses discussed, with particular emphasis on the role of the extracellular matrix.

Structure and function of antifreeze proteins

High-resolution three-dimensional structures are now available for four of seven non-homologous fish and insect antifreeze proteins (AFPs). For each of these structures, the ice-binding site of the AFP has been defined by site-directed mutagenesis, and ice etching has indicated that the ice surface is bound by the AFP. A comparison of these extremely diverse ice-binding proteins shows that they have the following attributes in common. The binding sites are relatively flat and engage a substantial proportion of the protein's surface area in ice binding. They are also somewhat hydrophobic -- more so than that portion of the protein exposed to the solvent. Surface-surface complementarity appears to be the key to tight binding in which the contribution of hydrogen bonding seems to be secondary to van der Waals contacts.

Antifreeze proteins: characteristics, occurrence and human exposure

Antifreeze proteins (AFPs), also known as ice structuring proteins, bind to and influence the growth of ice crystals. Proteins with these characteristics have been identified in fish living in areas susceptible to ice formation and in numerous plants and insects. This review considers the occurrence of AFPs and relates it to the likely intake by human populations, with a view to forming a judgment about their safety in foods. Intake of AFPs in the diet is likely to be substantial in most northerly and temperate regions. Much of this intake is likely to be from edible plants, given their importance in the diet, but in some regions intake from fish will be significant. Inadequate data exist to estimate intakes from plants but estimates of intake of AFP from fish are presented for two countries with very different fish consumption, the USA and Iceland. Typical short-term exposure, for instance a portion of cod may contain up to 196 mg AFGP, while the AFP content of the same weight of ocean pout would be up to 420 mg. Average available fish AFP in the diet is calculated to be around 1-10 mg/day in the USA and 50-500 mg/day in Iceland, but these estimates are subject to considerable uncertainty. As far as can be ascertained, AFPs are consumed with no evidence of adverse health effects, either short- or long-term. Given the structural diversity of AFPs, one firm general conclusion that can be drawn from the history of consumption of AFPs is that their functional characteristics do not impart any toxicologically significant effect, in a way that, for instance, a property such as cholinesterase inhibition would. Furthermore, specifically in the case of fish AFPs where some consumption data are available, it is reasonable to infer a lack of allergenicity from the absence of reports of this effect.

Crystal structure of beta-helical antifreeze protein points to a general ice binding model

Reported here is the 2.3 A resolution crystal structure of spruce budworm (Choristoneura fumiferana) antifreeze protein (CfAFP), solved by single anomalous scattering. The structure reveals an extremely regular left-handed beta-helical platform consisting of 15-amino acid loops with a repetitive Thr-X-Thr motif displayed on one of the helix's three faces. This motif results in a two-dimensional array of threonine residues in an identical orientation to those in the nonhomologous, right-handed beta-helical beetle AFP from Tenebrio molitor (TmAFP). The CfAFP structure led us to reevaluate our ice binding model, and the analysis of three possible modes of docking gives rise to a binding mechanism based on surface complementarity. This general mechanism is applicable to both fish and insect AFPs.

Antifreeze protein from shorthorn sculpin: identification of the ice-binding surface

Shorthorn sculpins, Myoxocephalus scorpius, are protected from freezing in icy seawater by alanine-rich, alpha-helical antifreeze proteins (AFPs). The major serum isoform (SS-8) has been reisolated and analyzed to establish its correct sequence. Over most of its length, this 42 amino acid protein is predicted to be an amphipathic alpha-helix with one face entirely composed of Ala residues. The other side of the helix, which is more heterogeneous and hydrophilic, contains several Lys. Computer simulations had suggested previously that these Lys residues were involved in binding of the peptide to the [11-20] plane of ice in the <-1102> direction. To test this hypothesis, a series of SS-8 variants were generated with single Ala to Lys substitutions at various points around the helix. All of the peptides retained significant alpha-helicity and remained as monomers in solution. Substitutions on the hydrophilic helix face at position 16, 19, or 22 had no obvious effect, but those on the adjacent Ala-rich surface at positions 17, 21, and 25 abolished antifreeze activity. These results, with support from our own modeling and docking studies, show that the helix interacts with the ice surface via the conserved alanine face, and lend support to the emerging idea that the interaction of fish AFPs with ice involves appreciable hydrophobic interactions. Furthermore, our modeling suggests a new N terminus cap structure, which helps to stabilize the helix, whereas the role of the lysines on the hydrophilic face may be to enhance solubility of the protein.

Structure of type I antifreeze protein and mutants in supercooled water

Many organisms are able to survive subzero temperatures at which bodily fluids would normally be expected to freeze. These organisms have adapted to these lower temperatures by synthesizing antifreeze proteins (AFPs), capable of binding to ice, which make further growth of ice energetically unfavorable. To date, the structures of five AFPs have been determined, and they show considerable sequence and structural diversity. The type I AFP reveals a single 37-residue alpha-helical structure. We have studied the behavior of wild-type type I AFP and two "inactive" mutants (Ala17Leu and Thr13Ser/Thr24Ser) in normal and supercooled solutions of H(2)O and deuterium oxide (D(2)O) to see if the structure at temperatures below the equilibrium freezing point is different from the structure observed at above freezing temperatures. Analysis of 1D (1)H- and (13)C-NMR spectra illustrate that all three proteins remain folded as the temperature is lowered and even seem to become more alpha-helical as evidenced by (13)C(alpha)-NMR chemical shift changes. Furthermore, (13)C-T(2) NMR relaxation measurements demonstrate that the rotational correlation times of all three proteins behave in a predictable manner under all temperatures and conditions studied. These data have important implications for the structure of the AFP bound to ice as well as the mechanisms for ice-binding and protein oligomerization.

Antifreeze proteins of teleost fishes

Marine teleosts at high latitudes can encounter ice-laden seawater that is approximately 1 degrees C colder than the colligative freezing point of their body fluids. They avoid freezing by producing small antifreeze proteins (AFPs) that adsorb to ice and halt its growth, thereby producing an additional non-colligative lowering of the freezing point. AFPs are typically secreted by the liver into the blood. Recently, however, it has become clear that AFP isoforms are produced in the epidermis (skin, scales, fin, and gills) and may serve as a first line of defense against ice propagation into the fish. The basis for the adsorption of AFPs to ice is something of a mystery and is complicated by the extreme structural diversity of the five antifreeze types. Despite the recent acquisition of several AFP three-dimensional structures and the definition of their ice-binding sites by mutagenesis, no common ice-binding motif or even theme is apparent except that surface-surface complementarity is important for binding. The remarkable diversity of antifreeze types and their seemingly haphazard phylogenetic distribution suggest that these proteins might have evolved recently in response to sea level glaciation occurring just 1-2 million years ago in the northern hemisphere and 10-30 million years ago around Antarctica. Not surprisingly, the expression of AFP genes from different origins can also be quite dissimilar. The most intensively studied system is that of the winter flounder, which has a built-in annual cycle of antifreeze expression controlled by growth hormone (GH) release from the pituitary in tune with seasonal cues. The signal transduction pathway, transcription factors, and promoter elements involved in this process are just beginning to be characterized.

Source of the ice-binding specificity of antifreeze protein type I

Antifreeze proteins (AFPs) are a group of structurally very diverse proteins with the unique capability of binding to the surface of seed ice crystals and inhibiting ice crystal growth. The AFPs bind with high affinity to specific planes of the ice crystal. Previously, this affinity of AFPs has been ascribed to the formation of multiple hydrogen bonds across the protein-ice interface, but more recently van der Waals interactions have been suggested to be the dominant energetic factors for the adsorption. To determine whether van der Waals interactions are also responsible for the binding specificities of AFPs, the protein-ice interaction of the helical AFP Type I from winter flounder (HPLC6) was studied using a Monte Carlo rigid body docking approach. HPLC6 binds in the [1102] direction of the [2021] plane, with the Thr-Ala-Asn surface comprising the protein's binding face. The binding of HPLC6 to this ice plane is highly preferred, but the protein is also found to bind favorably to the [1010] prism plane using a different protein surface comprised of Thr and Ala residues. The results show that van der Waals interactions, despite accounting for most of the intermolecular energy (>80%), are not sufficient to completely explain the AFP binding specificity.