Growth Inhibition Mechanism of an Ice–Water Interface by a Mutant of Winter Flounder Antifreeze Protein: A Molecular Dynamics Study

Probing the interaction between biomolecules under sub-zero temperature conditions by electrophoresis in ice grain boundaries

BACKGROUND

Psychrophiles can survive under cryogenic conditions because of various biomolecules. These molecules interact with cells, ice crystals, and lipid bilayers to enhance their functionality. Previous studies typically measured these interactions by thawing frozen samples and conducting biological assays at room temperature; however, studying these interactions under cryogenic conditions is crucial. This is because these biomolecules can function at lower temperatures. Therefore, a platform for measuring chemical interactions under sub-zero temperature conditions must be established.

RESULTS

The chemical interactions between biomolecules under sub-zero temperature conditions were evaluated within ice grain boundaries with a channel-like structure, which circumvents the need for thawing. An aqueous solution of sucrose was frozen within a microfluidic channel, facilitating the formation of freeze-concentrated solutions (FCSs) that functioned as size-tunable electrophoretic fields. Avidin proteins or single-stranded DNA (ssDNA) were introduced into the FCS in advance. Probe micro/nanospheres whose surfaces were modified with molecules complementary to the target analytes were introduced into the FCS. If the targets have functionalities under sub-zero temperature conditions, they interact with complementary molecules. The chemical interactions between the target molecules and nanospheres led to the aggregation of the particles. The size tunability of the diameter of the FCS channels enabled the recognition of aggregation levels, which is indicative of interaction reactivity. The avidin-biotin interaction and ssDNA hybridization served as models for chemical interactions, demonstrating interactivity under sub-zero temperature conditions. The results presented herein suggest the potential for in situ measurement of biochemical assays in the frozen state, elucidating the functionality of bio-related macromolecules at or slightly below 0 °C.

SIGNIFICANCE

This is the first methodology to evaluate chemical interactions under sub-zero temperature conditions without employing the freeze-and-thaw process. This method has the advantage of revealing the chemical interactions only at low temperatures. Therefore, it can be used to screen and evaluate the functionality of cryo-related biomolecules, including cold-shock and antifreeze proteins.

Bridging polymer chemistry and cryobiology

Polymers, especially charged polymers, are the key to a sustainable future, as they have the capability to act as alternatives to plastics, reduce the impact of global warming, and offer solutions to global environmental pollution problems. Biomaterial polymers have proven to be incredibly effective in a multitude of applications, including clinical applications. In the fields of cryobiology and cryopreservation, polymers have emerged as credible alternatives to small molecules and other compounds, yielding excellent results. This review outlines the results of research in the areas of polymer chemistry and cryobiology, which have not been discussed together previously. Herein, we explain how recent polymer research has enabled the development of polymeric cryoprotectants with novel mechanisms and the development of novel methods for the intracellular delivery of substances, such as drugs, using a cryobiological technique called the freeze-concentration effect. Our findings indicate that interdisciplinary collaboration between cryobiologists and polymer chemists has led to exciting developments that will further cell biology and medical research.

Ice Recrystallization Inhibition by Amino Acids: The Curious Case of Alpha- and Beta-Alanine

Extremophiles produce macromolecules which inhibit ice recrystallization, but there is increasing interest in discovering and developing small molecules that can modulate ice growth. Realizing their potential requires an understanding of how these molecules function at the atomistic level. Here, we report the discovery that the amino acid l-α-alanine demonstrates ice recrystallization inhibition (IRI) activity, functioning at 100 mM (∼10 mg/mL). We combined experimental assays with molecular simulations to investigate this IRI agent, drawing comparison to β-alanine, an isomer of l-α-alanine which displays no IRI activity. We found that the difference in the IRI activity of these molecules does not originate from their ice binding affinity, but from their capacity to (not) become overgrown, dictated by the degree of structural (in)compatibility within the growing ice lattice. These findings shed new light on the microscopic mechanisms of small molecule cryoprotectants, particularly in terms of their molecular structure and overgrowth by ice.

Crystal structure of an insect antifreeze protein reveals ordered waters on the ice-binding surface

Antifreeze proteins (AFPs) are characterized by their ability to adsorb to the surface of ice crystals and prevent any further crystal growth. AFPs have independently evolved for this purpose in a variety of organisms that encounter the threat of freezing, including many species of polar fish, insects, plants and microorganisms. Despite their diverse origins and structures, it has been suggested that all AFPs can organize ice-like water patterns on one side of the protein (the ice-binding site) that helps bind the AFP to ice. Here, to test this hypothesis, we have solved the crystal structure at 2.05 Å resolution of an AFP from the longhorn beetle, Rhagium mordax with five molecules in the unit cell. This AFP is hyperactive, and its crystal structure resembles that of the R. inquisitor ortholog in having a β-solenoid fold with a wide, flat ice-binding surface formed by four parallel rows of mainly Thr residues. The key difference between these structures is that the R. inquisitor AFP crystallized with its ice-binding site (IBS) making protein-protein contacts that limited the surface water patterns. Whereas the R. mordax AFP crystallized with the IBSs exposed to solvent enabling two layers of unrestricted ordered surface waters to be seen. These crystal waters make close matches to ice lattice waters on the basal and primary prism planes.

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.

Investigation of the antifreeze mechanism and effect on quality characteristics of largemouth bass (Micropterus salmoides) during F-T cycles by hAFP

The interaction between herring antifreeze protein (hAFP) and ice crystals was studied by molecular dynamics simulation in this paper. On this basis, the effect of hAFP on the quality attributes of largemouth bass after three freezing-thawing (F-T) cycles was studied. Scanning electron microscope was conducted to analyze the microstructure changes of muscle fibers. The content of dityrosine/total sulfhydryl/carbonyl and the Ca2+-ATPase activity were measured to explore the degree of protein oxidation. Raman and intrinsic fluorescence spectra were used to measure the protein secondary structure and tertiary conformation. Results showed that hAFP protected the organisms from freezing by binding to the ice crystals, decreasing the freezing point and inhibiting the recrystallization. Furthermore, hAFP combined with chitosan magnetic (CS@Fe3O4) nanoparticles or vacuum impregnation hAFP was shown to be an effective method to reduce the mechanical damage of ice crystals to samples, and decrease the oxidation degree of samples during F-T cycles.

Effect of surface charge density on the ice recrystallization inhibition activity of nanocelluloses

Recently nanocelluloses have been found to possess ice recrystallization inhibition (IRI) activity, which have several potential applications. The present study focuses on the relationship between the surface charge density (SCD) of nanocelluloses and IRI activity. Cellulose nanocrystals (CNCs) and 2, 2, 6, 6-tetramethylpiperidine-1-oxyl oxidized cellulose nanofibrils (TEMPO-CNFs) with similar degrees of polymerization (DP) or fibril lengths but with different SCDs were prepared and characterized for IRI activity. When the SCD of CNCs was progressively reduced, an initial increase of IRI activity was observed, followed by a decrease due to fibril aggregation. CNCs with a low SCD became IRI active at increased unfrozen water fractions and higher annealing temperatures. TEMPO-CNFs with a low SCD also had higher IRI activity. Additionally, lowering pH to protonate the carboxylate groups of TEMPO-CNFs enhanced the IRI activity. These research findings are important in producing nanocelluloses with enhanced IRI activity and understanding their structure-activity relationship.

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

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

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.

Anisotropy in Stable Conformations of Hydroxylate Ions between the {001} and {110} Planes of TiO2 Rutile Crystals for Glycolate, Lactate, and 2-Hydroxybutyrate Ions Studied by Metadynamics Method

Control over TiO2 rutile crystal growth and morphology using additives is essential for the development of functional materials. Computer simulation studies on the thermodynamically stable conformations of additives at the surfaces of rutile crystals contribute to understanding the mechanisms underlying this control. In this study, a metadynamics method was combined with molecular dynamics simulations to investigate the thermodynamically stable conformations of glycolate, lactate, and 2-hydroxybutyrate ions at the {001} and {110} planes of rutile crystals. Two simple atom-atom distances were selected as collective variables for the metadynamics method. At the {001} plane, a conformation in which the COO- group was oriented toward the surface was found to be the most stable for the lactate and 2-hydroxybutyrate ions, whereas a conformation in which the COO- group was oriented toward water was the most stable for the glycolate ion. At the {110} plane, a conformation in which the COO- group was oriented toward the surface was the most stable for all three hydroxylate ions, and a second most stable conformation was also observed for the lactate ion at positions close to the {110} plane. For all three hydroxylate ions (α-hydroxycarboxylate ions), the stability of the most stable conformation was higher for the {110} plane than for the {001} plane. At both planes, the stability of the most stable conformation was highest for the 2-hydroxybutyrate ion and lowest for the glycolate ion. Supposing that all three hydroxylate ions serve to decrease the surface free energy at the rutile surface and that a more stable conformation at the rutile surface leads to a greater decrease in the surface free energy, the present results partially explain experimentally observed differences in the changes in growth rate and morphology of rutile crystals in the presence of glycolic, lactic, and 2-hydroxybutyric acids.

Crystal-plane-dependent effects of antifreeze glycoprotein impurity for ice growth dynamics

An impurity effect on ice crystal growth in supercooled water is an important subject in relation to ice crystal formation in various conditions in the Earth's cryosphere regions. In this review, we consider antifreeze glycoprotein molecules as an impurity. These molecules are well known as functional molecules for controlling ice crystal growth by their adsorption on growing ice/water interfaces. Experiments on free growth of ice crystals in supercooled water containing an antifreeze protein were conducted on the ground and in the International Space Station, and the normal growth rates for the main crystallographic faces of ice, namely, basal and prismatic faces, were precisely measured as functions of growth conditions and time. The crystal-plane-dependent functions of AFGP molecules for ice crystal growth were clearly shown. Based on the magnitude relationship for normal growth rates among basal, prismatic and pyramidal faces, we explain the formation of a dodecahedral external shape of an ice crystal in relation to the key principle governing the growth of polyhedral crystals. Finally, we emphasize that the crystal-plane dependence of the function of antifreeze proteins on ice crystal growth relates to the freezing prevention of living organisms in sub-zero temperature conditions. This article is part of the theme issue 'The physics and chemistry of ice: scaffolding across scales, from the viability of life to the formation of planets'.

Collective Transformation of Water between Hyperactive Antifreeze Proteins: RiAFPs

We demonstrate, by molecular dynamics simulations, that water confined between a pair of insect hyperactive antifreeze proteins from the longhorn beetle Rhagium inquisitor is discontinuously expelled as the two proteins approach each other at a certain distance. The extensive striped hydrophobic–hydrophilic pattern on the surface, comprising arrays of threonine residues, enables water to form three independent ice channels through the assistance of hydroxyl groups, even at 300 K. The transformation is reminiscent of a freezing–melting transition rather than a drying transition and governs the stable protein–protein separation in the evaluation of the potential of mean force. The collectivity of water penetration or expulsion and the hysteresis in the time scale of ten nanoseconds predict a potential first-order phase transition at the limit of infinite size and provide a new framework for the water-mediated interaction between solutes.

Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation

Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.

Effects of hydrophobic and hydrogen-bond interactions on the binding affinity of antifreeze proteins to specific ice planes

Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice surfaces such as primary prism, secondary prism, basal, and pyramidal planes. The ice-binding site of TmAFP, which is full of threonine (Thr), binds to the primary-prism plane but does not bind to other ice planes, in agreement with experiments showing the fast adsorption of TmAFP to the primary-prism plane. To mimic the ice-binding site of shorthorn sculpin AFP (ssAFP; type I) that predominantly consists of alanine (Ala) and has the binding affinity to the secondary-prism plane, the ice-binding site of TmAFP was mutated by replacing a few Thr residues with Ala residues, showing that mutated TmAFP binds to the secondary-prism plane, similar to the ice-binding affinity of ssAFP. Ala residues are located at the cavity of ice, while Thr residues form hydrogen bonds with water molecules. When the mutated TmAFP is further modified by removing Thr, it does not bind to the secondary-prism plane. These findings indicate that simulations can successfully capture the experimentally observed binding affinity of AFP to specific ice planes, to an extent dependent on hydrophobicity of the ice-binding site. In particular, the addition of hydrophobic residues influences the ice-binding affinity of TmAFP, while a certain amount of hydrophilic residue is still required for hydrogen-bond interactions, which supports experimental observations regarding the key roles of hydrophobic and hydrophilic interactions on the AFP-ice binding.

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 study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface

Using computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein relative to the ice crystal before the final attachment to the ice surface takes place, accompanied by the solidification of the interfacial water. It is possible because the solvation water of the ice-binding plane of CfAFP is susceptible to the overlapping with the solvation water of ice and is mostly changeable into ice itself. These remote interactions significantly increase efficacy of the adsorption process by facilitating the geometric adjustment of the active region of the CfAFP molecule to the ice surface. Because of the ordered nature of the water molecules at the ice-binding plane, the energy of their interactions with the ice-binding surface of the protein does not change upon the ongoing solidification of solvation water. However, the structure of the solvation water is not strictly ice-like and the growth of ice in the interfacial water is not initiated at the side of the protein. On the contrary, we find that solvation water of CfAFP solidifies slower than solvation water of ice - the solidification of interfacial water starts at the surface of ice. Moreover, in the presence of the CfAFP molecule, also solvation water of ice solidifies slower compared to the situation when the protein is not present next to the ice surface. Additionally, the presence of the protein molecule shifts the ratio of cubic to hexagonal ice that spontaneously forms at the ice surface, by introducing another layer of ordered water molecules - opposite to the ice lattice, at the other side of the crystallizing layer of water.

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.

Molecular Dynamics Analysis of Synergistic Effects of Ions and Winter Flounder Antifreeze Protein Adjacent to Ice-Solution Surfaces

The control of freezing saline water at the micrometer level has become very important in cryosurgery and cryopreservation of stem cells and foods. Adding antifreeze protein to saline water is a promising method for controlling the freezing because the protein produces a gap between the melting point and the freezing point. Furthermore, a synergistic effect of the solutes occurs in which the freezing point depression of a mixed solution is more noticeable than the sum of two freezing point depressions of single-solute solutions. However, the mechanism of this effect has not yet been clarified. Thus, we have carried out a molecular dynamics simulation on aqueous solutions of winter flounder antifreeze protein and sodium chloride or calcium chloride with an ice layer. The results show that the cations inhibit the hydrogen bond among water molecules not only in the salt solutions but also in the mixed solutions. This inhibition depends on the local number of ions and the valence of cations. The space for water molecules to form the hydrogen bonds becomes small in the case of the mixed solution of the protein and calcium chloride. These findings are consistent with the synergistic effect. In addition, it is found that the diffusion of ions near positively-charged residues is attenuated. This attenuation causes an increase in the possibility of water molecules staying near or inside the hydration shells of the ions. Furthermore, the first hydration shells of the cations become weak in the vicinity of the arginine, lysine and glutamic-acid residues. These factors can be considered to be possible mechanisms of the synergistic effect.

Structures, dynamics, and hydrogen-bond interactions of antifreeze proteins in TIP4P/Ice water and their dependence on force fields

Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice-water interfaces at a realistic melting temperature using TIP4P/Ice water model. To test compatibility of protein force fields (FFs) with TIP4P/Ice water, CHARMM, AMBER, and OPLS FFs were applied. CHARMM and AMBER FFs predict more β-sheet structure and lower diffusivity of TmAFP at the ice-water interface than does OPLS FF, indicating that β-sheet structure is important for the TmAFP-interface binding and antifreeze activity. In particular, CHARMM FF more clearly distinguishes the strengths of hydrogen bonds in the ice-binding and non-ice-binding sites of TmAFP than do other FFs, in agreement with experiments, implying that CHARMM FF can be a reasonable choice to simulate proteins with TIP4P/Ice water. Simulations of mutated TmAFPs show that for the same density of Thr residues, continuous arrangement of Thr with the distance of 0.4~0.6 nm induces the higher extent of antifreeze activity than does intermittent arrangement of Thr with larger distances. These findings suggest the choice of CHARMM FF for AFP-TIP4P/Ice simulations and help explain the relationship between Thr-residue arrangement and antifreeze activity.

Molecular Dynamics at the Interface between Ice and Poly(vinyl alcohol) and Ice Recrystallization Inhibition

Ice formation is a ubiquitous process that poses serious challenges for many areas. Nature has evolved a variety of different mechanisms to regulate ice formation. For example, many cold-adapted species produce antifreeze proteins (AFPs) and/or antifreeze glycoproteins (AFGPs) to inhibit ice recrystallization. Although several synthetic substitutes for AF(G)Ps have been developed, the fundamental principles of designing AF(G)P mimics are still missing. In this study, we explored the molecular dynamics of ice recrystallization inhibition (IRI) by poly(vinyl alcohol) (PVA), a well-recognized ice recrystallization inhibitor, to shed light on the otherwise hidden ice-binding mechanisms of chain polymers. Our molecular dynamics simulations revealed a stereoscopic, geometrical match between the hydroxyl groups of PVA and the water molecules of ice, and provided microscopic evidence of the adsorption of PVA to both the basal and prism faces of ice and the incorporation of short-chain PVA into the ice lattice. The length of PVA, i.e., the number of hydroxyl groups, seems to be a key factor dictating the performance of IRI, as the PVA molecule must be large enough to prevent the joining together of adjacent curvatures in the ice front. The findings in this study will help pave the path for addressing a pressing challenge in designing synthetic ice recrystallization inhibitors rationally, by enriching our mechanistic understanding of IRI process by macromolecules.

Adsorption of Kinetic Hydrate Inhibitors on Growing Surfaces: A Molecular Dynamics Study

We investigate the mechanism of a typical kinetic hydrate inhibitor (KHI), polyvinylcaprolactam (PVCap), which has been applied to prevent hydrate plugs from forming in gas pipe lines, using molecular dynamics simulations of crystal growth of ethylene oxide hydrate. Water-soluble ethylene oxide is chosen as a guest species to avoid problems associated with the presence of the gas phase in the simulation cell such as slow crystal growth. A PVCap dodecamer adsorbs irreversibly on the hydrate surface which grows at supercooling of 3 K when the hydrophobic part of two pendent groups are trapped in open cages at the surface. The amide hydrogen bonds make no contribution to the adsorption. PVCap can adsorb on various crystallographic planes of sI hydrate. This is in contrast to antifreeze proteins, each of which prefers a specific plane of ice. The trapped PVCap gives rise to necessarily the concave surface of the hydrate. The crystal growth rate decreases with increasing surface curvature, indicating that the inhibition by PVCap is explained by the Gibbs-Thomson effect.

Operation of Kelvin Effect in the Activities of an Antifreeze Protein: A Molecular Dynamics Simulation Study

Ice growth and melting inhibition activities of antifreeze proteins (AFPs) are better explained by the adsorption-inhibition mechanism. Inhibition occurs as a result of the Kelvin effect induced by adsorbed protein molecules onto the surface of seed ice crystal. However, the Kelvin effect has not been explored by the state-of-the-art experimental techniques. In this work, atomistic molecular dynamics simulations have been carried out with Tenebrio molitor antifreeze protein ( TmAFP) placed at ice-water interface to probe the Kelvin effect in the mechanism of AFPs. Simulations show that, below equilibrium melting temperature, ice growth is inhibited through the convex ice-water interface formation toward the water phase and, above equilibrium melting temperature, ice melting is inhibited through the concave ice-water interface formation inward to ice phase. Simulations further reveal that the radius of curvature of the interface formed to stop the ice growth increases with decrease in the degree of supercooling. Our results are in qualitative agreement with the theoretical prediction of the Kelvin effect and thus reveal its operation in the activities of AFPs.

Antifreeze Glycoproteins Bind Reversibly to Ice via Hydrophobic Groups

Antifreeze molecules allow organisms to survive in subzero environments. Antifreeze glycoproteins (AFGPs), produced by polar fish, are the most potent inhibitors of ice recrystallization. To date, the molecular mechanism by which AFGPs bind to ice has not yet been elucidated. Mutation experiments cannot resolve whether the binding occurs through the peptide, the saccharides, or both. Here, we use molecular simulations to determine the mechanism and driving forces for binding of AFGP8 to ice, its selectivity for the primary prismatic plane, and the molecular origin of its exceptional ice recrystallization activity. Consistent with experiments, AFGP8 in simulations preferentially adopts the PPII helix secondary structure in solution. We show that the segregation of hydrophilic and hydrophobic groups in the PPII helix is vital for ice binding. Binding occurs through adsorption of methyl groups of the peptide and disaccharides to ice, driven by the entropy of dehydration of the hydrophobic groups as they nest in the cavities at the ice surface. The selectivity to the primary prismatic plane originates in the deeper cavities it has compared to the basal plane. We estimate the free energy of binding of AFGP8 and the longer AFGPs4-6, and find them to be consistent with the reversible binding demonstrated in experiments. The simulations reveal that AFGP8 binds to ice through a myriad of conformations that it uses to diffuse through the ice surface and find ice steps, to which it strongly adsorbs. We interpret that the existence of multiple, weak binding sites is the key for the exceptional ice recrystallization inhibition activity of AFGPs.

Interfacial Water Arrangement in the Ice-Bound State of an Antifreeze Protein: A Molecular Dynamics Simulation Study

Molecular dynamics (MD) simulations have been carried out to study the heterogeneous ice nucleation on modeled peptide surfaces. Simulations show that large peptide surfaces made by TxT (threonine-x-threonine) motifs with the arrangements of threonine (Thr) residues identical to the periodic arrangements of waters on either the basal or prism plane of ice are capable of ice nucleation. Nucleated ice plane is the (0001) basal plane of hexagonal ice (Ih) or (111) plane of cubic ice (Ic). However, due to predefined simulation cell dimensions, the ice growth is only observed on the surface where the Thr residues are arranged like the water arrangement on the basal plane of ice Ih. The γ-methyl and γ-hydroxyl groups of Thr residue are necessary for such ice formation. From this ice nucleation and growth simulation, the interfacial water arrangement in the ice-bound state of Tenebrio molitor antifreeze protein (TmAFP) has been determined. The interfacial water arrangement in the ice-bound state of TmAFP is characterized by five-membered hydrogen bonded rings, where each of the hydroxyl groups of the Thr residues on the ice-binding surface (IBS) of the protein is a ring member. It is found that the water arrangement at the protein-ice interface is distorted from that in bulk ice. Our analysis further reveals that the hydroxyl groups of Thr residues on the IBS of TmAFP form maximum three hydrogen bonds each with the waters in the bound state and methyl groups of Thr residues occupy wider spaces than the normal grooves on the (111) plane of ice Ic. Methyl groups are also located above and along the 3-fold rotational axes of the chair-formed hexagonal hydrogen bonded water rings on the (111) plane.

Anisotropy in geometrically rough structure of ice prismatic plane interface during growth: Development of a modified six-site model of H2O and a molecular dynamics simulation

This paper presents a modified version of the six-site model of H₂O [H. Nada and J. P. J. M. van der Eerden, J. Chem. Phys. 118, 7401 (2003)]. Although the original six-site model was optimized by assuming the cut-off of the Coulomb interaction at an intermolecular distance of 10 Å, the modified model is optimized by using the Ewald method for estimating the Coulomb interaction. Molecular dynamics (MD) simulations of an ice-water interface suggest that the melting point of ice at 1 atm in the modified model is approximately 274.5 K, in good agreement with the real melting point of 273.15 K. MD simulations of bulk ice and water suggest that the modified model reproduces not only the structures and density curves of ice and water, but also the diffusion coefficient of water molecules in water near the melting point at 1 atm. Using the modified model, a large-scale MD simulation of the growth at an ice-water interface of the prismatic plane is performed to elucidate the anisotropy in the interface structure during growth. Simulation results indicate that the geometrical roughness of the ice growth front at the interface is greater in the c-axis direction than in the direction normal to the c-axis when it is analyzed along the axes parallel to the prismatic plane. In addition, during the growth at the interface, the transient appearance of specific crystallographic planes, such as a {202¯1} pyramidal plane, occurs preferentially at the ice growth front. The effect of different ensembles with different simulation systems on the anisotropy in the interface structure is also investigated.

Oscillations and accelerations of ice crystal growth rates in microgravity in presence of antifreeze glycoprotein impurity in supercooled water

The free growth of ice crystals in supercooled bulk water containing an impurity of glycoprotein, a bio-macromolecule that functions as ‘antifreeze’ in living organisms in a subzero environment, was observed under microgravity conditions on the International Space Station. We observed the acceleration and oscillation of the normal growth rates as a result of the interfacial adsorption of these protein molecules, which is a newly discovered impurity effect for crystal growth. As the convection caused by gravity may mitigate or modify this effect, secure observations of this effect were first made possible by continuous measurements of normal growth rates under long-term microgravity condition realized only in the spacecraft. Our findings will lead to a better understanding of a novel kinetic process for growth oscillation in relation to growth promotion due to the adsorption of protein molecules and will shed light on the role that crystal growth kinetics has in the onset of the mysterious antifreeze effect in living organisms, namely, how this protein may prevent fish freezing.

Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity

Water molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel pout) is investigated. A wild type of the protein is used, along with its three mutants, with antifreeze activities equal to 54% or 10% of the activity of the native form. The solvation water of the ice-binding surface and the rest of the protein are analyzed separately. To characterize the structure of solvation shell, parameters describing radial and angular characteristics of the mutual arrangement of the molecules were employed. They take into account short-distance (first hydration shell) or long-distance (two solvation shells) effects. The obtained results and the comparison with the results obtained previously for a hyperactive antifreeze protein from Choristoneura fumiferana lead to the conclusion that the structure and amino acid composition of the active region of the protein evolved to achieve two goals. The first one is the modification of the properties of the solvation water. The second one is the geometrical adjustment of the protein surface to the specific crystallographic plane of ice. Both of these goals have to be achieved simultaneously in order for the protein to perform its function properly. However, they seem to be independent from one another in a sense that very small antifreeze activity does not imply that properties of water become different from the ones observed for the wild type. The proteins with significantly lower activity still modify the mean properties of solvation water in a right direction, in spite of the fact that the accuracy of the geometrical match with the ice lattice is lost because of the mutations. Therefore, we do not observe any correlation between the antifreeze activity and the extent of modification of the properties of solvation water.

Micro- and Nano-Liquid Phases Coexistent with Ice as Separation and Reaction Media

Ice has a variety of scientifically interesting features, some of which have not been reasonably interpreted despite substantial efforts by researchers. Most chemical studies of ice have focused on the elucidation of its physicochemical nature and its roles in the natural environment. Ice often contains impurities, such as salts, and in such cases, a liquid phase coexists with solid ice over a wide temperature range. This impure ice also acts as a cryoreactor, governing the circulation of chemical species of environmental importance. Reactions and phenomena occurring in this liquid phase show features different from those seen in normal bulk aqueous solutions. In the present account, we discuss the chemical characteristics of the liquid phase that develops in a frozen aqueous phase and show how novel analytical systems can be designed based on he features of the liquid phase which are predictable in some cases but unpredictable in others.

Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering

We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298-220 K). We interpret this change in terms of the dynamic transition previously discussed using other probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.

Accelerated Nucleation of Hydroxyapatite Using an Engineered Hydrophobin Fusion Protein

Calcium phosphate mineralization is of particular interest in dental repair. A biomimetic approach using proteins or peptides is a highly promising way to reconstruct eroded teeth. In this study, the screening of several proteins is described for their binding and nucleating activities toward hydroxyapatite. Out of 27 tested candidates, only two hydrophobin fusion proteins showed binding abilities to hydroxyapatite in a mouthwash formulation and an increased nucleation in artificial saliva. Using a semirational approach, one of the two candidates (DEWA_5), a fusion protein consisting of a truncated section of the Bacillus subtilis synthase YaaD, the Aspergillus nidulans hydrophobin DEWA, and the rationally designed peptide P11-4 described in the literature, could be further engineered toward a faster mineral formation. The variants DEWA_5a (40aaYaaD-SDSDSD-DEWA) and DEWA_5b (40aaYaaD-RDRDRD-DEWA) were able to enhance the nucleation activity without losing the ability to form hydroxyapatite. In the case of variant DEWA_5b, an additional increase in the binding toward hydroxyapatite could be achieved. Especially with the variant DEWA_5a, the protein engineering of the rationally designed peptide sequence resulted in a resemblance of an amino acid motif that is found in nature. The engineered peptide resembles the amino acid motif in dentin phosphoprotein, one of the major proteins involved in dentinogenesis.

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.

Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein

Many hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were analyzed and compared with the properties of solvation water present at the surface of ice. The most striking observations concerned the temperature dependence of changes in water structure. In the case of solvation water of the ice-binding plane, the difference between the overall structural ordering of solvation water and bulk water diminished with increasing temperature; in the case of solvation water of the rest of the protein, the trend was opposite. In this respect, the solvation water of the ice-binding plane roughly resembled the hydration layer of ice. Simultaneously, the whole solvation shell of the protein displayed some features that are typical for solvation shells of many other proteins and are not encountered in the solvation water of ice. In the first place, this is an increase in density of water around the protein. The opposite is true for the solvation water of ice - it is less dense than bulk water. Therefore, even though the structure of solvation water of ice-binding plane and the structure of solvation water of ice seem to share some similarities, densitywise they differ.

The biological function of an insect antifreeze protein simulated by molecular dynamics

Antifreeze proteins (AFPs) protect certain cold-adapted organisms from freezing to death by selectively adsorbing to internal ice crystals and inhibiting ice propagation. The molecular details of AFP adsorption-inhibition is uncertain but is proposed to involve the Gibbs–Thomson effect. Here we show by using unbiased molecular dynamics simulations a protein structure-function mechanism for the spruce budworm Choristoneura fumiferana AFP, including stereo-specific binding and consequential melting and freezing inhibition. The protein binds indirectly to the prism ice face through a linear array of ordered water molecules that are structurally distinct from the ice. Mutation of the ice binding surface disrupts water-ordering and abolishes activity. The adsorption is virtually irreversible, and we confirm the ice growth inhibition is consistent with the Gibbs–Thomson law.

DOI:http://dx.doi.org/10.7554/eLife.05142.001

Water expands as it freezes. If this happens to the water inside plants and animals, the resulting ice crystals can rupture cells. To prevent this, many plants and animals that live in cold climates have evolved ‘antifreeze proteins’. When a small particle of ice first starts to form, the antifreeze proteins bind to it and prevent the water around it freezing, hence preventing the growth of an ice crystal.

There are many different types of antifreeze protein, and some are more active than others. For example, some insects including the spruce budworm are exposed to extremely cold temperatures—sometimes below −30°C—and these insects have antifreeze proteins that are highly active.

It is not fully understood how different antifreeze proteins interact with ice and prevent the growth of ice crystals. This is largely because, as yet, there are no experimental techniques that make it possible to see how antifreeze proteins and water molecules arrange themselves at the surface of a growing particle of ice. Instead, scientists have developed computer simulations to investigate this process. While many of these studies have provided valuable information, the computational methods used have only recently become powerful enough to analyze how the antifreeze proteins approach the surface of the ice particle.

Kuiper et al. carried out simulations involving a highly active antifreeze protein from the spruce budworm. The results of these simulations revealed that this antifreeze protein does not bind directly to ice; instead, water molecules at the surface of the protein act as a bridge between the protein and the ice. These water molecules are highly ordered and though they have similarities with how water is structured in the ice, they are distinct from the ice lattice itself. Furthermore, this arrangement appears to be important for allowing the spruce budworm antifreeze protein to interact with the ice.

This study provides detailed insights as to how a highly active antifreeze protein helps to prevent ice crystals forming. In the future, the computational simulations used here may be extended to study the dynamics of other antifreeze proteins, and also how crystals of other materials form.

DOI:http://dx.doi.org/10.7554/eLife.05142.002

Influence of antifreeze proteins on the ice/water interface

Antifreeze proteins (AFP) are responsible for the survival of several species, ranging from bacteria to fish, that encounter subzero temperatures in their living environment. AFPs have been divided into two main families, moderately and hyperactive, depending on their thermal hysteresis activity. We have studied one protein from both families, the AFP from the snow flea (sfAFP) and from the winter flounder (wfAFP), which belong to the hyperactive and moderately active family, respectively. On the basis of molecular dynamics simulations, we have estimated the thickness of the water/ice interface for systems both with and without the AFPs attached onto the ice surface. The calculation of the diffusion profiles along the simulation box allowed us to measure the interface width for different ice planes. The obtained widths clearly show a different influence of the two AFPs on the ice/water interface. The different impact of the AFPs here studied on the interface thickness can be related to two AFPs properties: the protein hydrophobic surface and the number of hydrogen bonds that the two AFPs faces form with water molecules.

Induced ice melting by the snow flea antifreeze protein from molecular dynamics simulations

Antifreeze proteins (AFP) allow different life forms, insects as well as fish and plants, to survive in subzero environments. AFPs prevent freezing of the physiological fluids. We have studied, through molecular dynamics simulations, the behavior of the small isoform of the AFP found in the snow flea (sfAFP), both in water and at the ice/water interface, of four different ice planes. In water at room temperature, the structure of the sfAFP is found to be slightly unstable. The loop between two polyproline II helices has large fluctuations as well as the C-terminus. Torsional angle analyses show a decrease of the polyproline II helix area in the Ramachandran plots. The protein structure instability, in any case, should not affect its antifreeze activity. At the ice/water interface the sfAFP triggers local melting of the ice surface. Bipyramidal, secondary prism, and prism ice planes melt in the presence of AFP at temperatures below the melting point of ice. Only the basal plane is found to be stable at the same temperatures, indicating an adsorption of the sfAFP on this ice plane as confirmed by experimental evidence.