Depression of Freezing Point by Glycoproteins from an Antarctic Fish

Does freezing induce self-assembly of polymers? A molecular dynamics study

This work investigates the freezing-induced self-assembly (FISA) of polyvinyl alcohol (PVA) and PVA-like polymers using molecular dynamics simulations. In particular, the effect of the degree of supercooling, degree of polymerization, polymer type, and initial local concentration on the FISA was studied. It was found that the preeminent factor responsible for FISA is not the diffusion of the polymers away from the nucleating ice front, but the increase in the polymer's local concentration upon freezing of the solvent (water). At a higher degree of supercooling, the polymers are engulfed by the growing ice front, impeding their diffusion into the supercooled solution and finally inhibiting their self-assembly. Conversely, at a relatively lower degree of supercooling, the rate of diffusion of the polymers into the supercooled solution is higher, which increases their local concentration and results in FISA. FISA was also observed to depend on the polymer-solvent interactions. Strongly favorable solute-solvent interactions hinder the self-assembly, whereas unfavorable solute-solvent interactions promote the self-assembly. The polymer and aggregate morphology were investigated using the radius of gyration, end-to-end distance, and asphericity analysis. This study brings molecular insights into the quintessential factors governing self-assembly via freezing of the solvent, which is a novel self-assembly technique especially suitable for biomedical applications.

Engulfment Avalanches and Thermal Hysteresis for Antifreeze Proteins on Supercooled Ice

Antifreeze proteins (AFPs) bind to the ice-water surface and prevent ice growth at temperatures below 0 °C through a Gibbs-Thomson effect. Each adsorbed AFP creates a metastable depression on the surface that locally resists ice growth, until ice engulfs the AFP. We recently predicted the susceptibility to engulfment as a function of AFP size, distance between AFPs, and supercooling [ J. Chem. Phys. 2023, 158, 094501]. For an ensemble of AFPs adsorbed on the ice surface, the most isolated AFPs are the most susceptible, and when an isolated AFP gets engulfed, its former neighbors become more isolated and more susceptible to engulfment. Thus, an initial engulfment event can trigger an avalanche of subsequent engulfment events, leading to a sudden surge of unrestrained ice growth. This work develops a model to predict the supercooling at which the first engulfment event will occur for an ensemble of randomly distributed AFP pinning sites on an ice surface. Specifically, we formulate an inhomogeneous survival probability that accounts for the AFP coverage, the distribution of AFP neighbor distances, the resulting ensemble of engulfment rates, the ice surface area, and the cooling rate. We use the model to predict thermal hysteresis trends and compare with experimental data.

Free energy barriers for anti-freeze protein engulfment in ice: Effects of supercooling, footprint size, and spatial separation

Anti-freeze proteins (AFPs) protect organisms at freezing conditions by attaching to the ice surface and arresting its growth. Each adsorbed AFP locally pins the ice surface, resulting in a metastable dimple for which the interfacial forces counteract the driving force for growth. As supercooling increases, these metastable dimples become deeper, until metastability is lost in an engulfment event where the ice irreversibly swallows the AFP. Engulfment resembles nucleation in some respects, and this paper develops a model for the "critical profile" and free energy barrier for the engulfment process. Specifically, we variationally optimize the ice-water interface and estimate the free energy barrier as a function of the supercooling, the AFP footprint size, and the distance to neighboring AFPs on the ice surface. Finally, we use symbolic regression to derive a simple closed-form expression for the free energy barrier as a function of two physically interpretable, dimensionless parameters.

Diffusion Attachment Model for Long Helical Antifreeze Proteins to Ice

Some of the most potent antifreeze proteins (AFPs) are approximately rigid helical structures that bind with one side in contact with the ice surface at specific orientations. These AFPs take random orientations in solution; however, most orientations become sterically inaccessible as the AFP approaches the ice surface. The effect of these inaccessible orientations on the rate of adsorption of AFP to ice has never been explored. Here, we present a diffusion-controlled theory of adsorption kinetics that accounts for these orientational restrictions to predict a rate constant for adsorption (k_on, in m/s) as a function of the length and width of the AFP molecules. We find that k_on decreases with length and diameter of the AFP and is almost proportional to the inverse of the area of the binding surface. We demonstrate that the restricted orientations create an entropic barrier to AFP adsorption, which we compute to be approximately 7 k_BT for most AFPs and up to 9 k_BT for Maxi, the largest known AFP. We compare the entropic resistance 1/k_on to resistances for diffusion through boundary layers and across typical distances in the extracellular matrix and find that these entropic and diffusion resistances could become comparable in the small confined spaces of biological environments.

Anti freeze proteins (Afp): Properties, sources and applications - A review

Extreme cold marine and freshwater temperatures (below 4 °C) induce massive deterioration to the cell membranes of organisms resulting in the formation of ice crystals, consequently causing organelle damage or cell death. One of the adaptive mechanisms organisms have evolved to thrive in cold environments is the production of antifreeze proteins with the functional capabilities to withstand frigid temperatures. Antifreeze proteins are extensively identified in different cold-tolerant species and they facilitate the persistence of cold-adapted organisms by decreasing the freezing point of their body fluids. Various structurally diverse types of antifreeze proteins detected possess the ability to modify ice crystal growth by thermal hysteresis and ice recrystallization inhibition. The unique properties of antifreeze proteins have made them a promising resource in industry, biomedicine, food storage and cryobiology. This review collates the findings of the various studies carried out in the past and the recent developments observed in the properties, functional mechanisms, classification, distinct sources and the ever-increasing applications of antifreeze proteins. This review also summarizes the possibilities of the way forward to identify new avenues of research on anti-freeze proteins.

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.

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.

Characterization of a novel β-helix antifreeze protein from the desert beetle Anatolica polita

Many ectotherms organisms produce antifreeze proteins (AFPs) which inhibit the growth of ice by binding to the surface of ice crystals. In this study, a novel antifreeze protein gene from the desert beetle Anatolica polita (named as Apafp752) was expressed in a high level in Escherichia coli strain BL21 (DE3). An approximately 30kDa fusion protein thioredoxin (Trx)-ApAFP752 was purified through Ni-NTA affinity chromatography and gel filtration chromatography. The activity of the purified fusion protein Trx-ApAFP752 was analyzed by thermal hysteresis activity (THA) and cryoprotection assay. The results suggested that Trx-ApAFP752 conferred freeze resistance on bacterium in a concentration- and time-dependent manner and the cryoprotective effect increased under alkaline conditions. Circular Dichroism (CD) spectrum analysis showed that the recombinant protein of ApAFP752 possessing β-sheet as the main structure was stable under a wide range of pH from 2.0 to 11.0 and thermal stability below 50°C. The predicted 3D structure showed that Trx-ApAFP752 could form a β-helix structure on the antifreeze protein part, which placed most of the Thr in a regular array on one side of the protein to form a putative ice-binding surface.

Ice-structuring peptides derived from bovine collagen

Antifreeze proteins belonging to structurally diverse families of genetically coded proteins from several living organisms have been isolated and characterized in the past. This paper reports that collagen peptides of a certain molecular size range derived from Alcalase hydrolysis of bovine gelatin are able to inhibit recrystallization of ice in frozen ice cream mix as well as in frozen sucrose solutions in a manner similar to natural antifreeze proteins. The optimum conditions for producing such ice-structuring peptides (ISP) were hydrolysis at pH 9.0 for 30 min at 45 degrees C and an Alcalase-to-gelatin ratio of 0.176 unit per gram of gelatin. The collagen peptides were fractionated on size exclusion (Sephadex G-50) and ion exchange (sulfopropyl-Sephadex C-25) columns, and the molecular mass distribution of the ice-structuring peptide fractions was determined by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry. The collagen peptide fractions in the molecular mass range of 600-2700 Da inhibited ice recrystallization in a supercooled ice cream mix and in concentrated sucrose solutions. The cationic collagen peptides within this fraction with molecular mass in the range of 1600-2400 Da were more effective than the anionic peptides in inhibiting ice crystal growth.

Antifreeze proteins at the ice/water interface: three calculated discriminating properties for orientation of type I proteins

Antifreeze proteins (AFPs) protect many plants and organisms from freezing in low temperatures. Of the different AFPs, the most studied AFP Type I from winter flounder is used in the current computational studies to gain molecular insight into its adsorption at the ice/water interface. Employing molecular dynamics simulations, we calculate the free energy difference between the hydrophilic and hydrophobic faces of the protein interacting with ice. Furthermore, we identify three properties of Type I "antifreeze" proteins that discriminate among these two orientations of the protein at the ice/water interface. The three properties are: the "surface area" of the protein; a measure of the interaction of the protein with neighboring water molecules as determined by the number of hydrogen bond count, for example; and the side-chain orientation angles of the threonine residues. All three discriminants are consistent with our free energy results, which clearly show that the hydrophilic protein face orientations toward the ice/water interface, as hypothesized from experimental and ice/vacuum simulations, are incorrect and support the hypothesis that the hydrophobic face is oriented toward the ice/water interface. The adsorption free energy is calculated to be 2-3 kJ/mol.

Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state

The physical nature underlying intermolecular interactions between two rod-like winter flounder antifreeze protein (AFP) molecules and their implication for the mechanism of antifreeze function are examined in this work using molecular dynamics simulations, augmented with free energy calculations employing a continuum solvation model. The energetics for different modes of interactions of two AFP molecules is examined in both vacuum and aqueous phases along with the water distribution in the region encapsulated by two antiparallel AFP backbones. The results show that in a vacuum two AFP molecules intrinsically attract each other in the antiparallel fashion, where their complementary charge side chains face each other directly. In the aqueous environment, this attraction is counteracted by both screening and entropic effects. Therefore, two nearly energetically degenerate states, an aggregated state and a dissociated state, result as a new aspect of intermolecular interaction in the paradigm for the mechanism of action of AFP. The relevance of these findings to the mechanism of function of freezing inhibition in the context of our work on Antarctic cod antifreeze glycoprotein (Nguyen et al., Biophysical Journal, 2002, Vol. 82, pp. 2892-2905) is discussed.

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed.

Type I 'antifreeze' proteins. Structure-activity studies and mechanisms of ice growth inhibition

The type I 'antifreeze' proteins, found in the body fluids of fish inhabiting polar oceans, are alanine-rich alpha-helical proteins that are able to inhibit the growth of ice. Within this class there are two distinct subclasses of proteins: those related to the winter flounder sequence HPLC6 and which contain 11-residue repeat units commencing with threonine; and those from the sculpins that are unique in the N-terminal region that contains established helix breakers and lacks the 11-residue repeat structure present in the rest of the protein. Although 14 type I proteins have been isolated, almost all research has focused on HPLC6, the 37-residue protein from the winter flounder Pseudopleuronectes americanus. This protein modifies both the rate and shape (or 'habit') of ice crystal growth, displays hysteresis and accumulates specifically at the {2 0 2; 1} ice plane. Until very recently, all models to explain the mechanism for this specific interaction have relied on the interaction of the four threonine hydroxyls, which are spaced equally apart on one face of the helix, with the ice lattice. In contrast, proteins belonging to the sculpin family accumulate specifically at the {2 1; 1; 0} plane. The molecular origin of this difference in specificity between the flounder and sculpin proteins is not understood. This review will summarize the structure-activity and molecular modelling and dynamics studies on HPLC6, with an emphasis on recent studies in which the threonine residues have been mutated. These studies have identified important hydrophobic contributions to the ice growth inhibition mechanism. Some 50 mutants of HPLC6 have been reported and the data is consistent with the following requirements for ice growth inhibition: (a) a minimum length of approx. 25 residues; (b) an alanine-rich sequence in order to induce a highly helical conformation; (c) a hydrophobic face; (d) a number of charged/polar residues which are involved in solubility and/or interaction with the ice surface. The emerging picture, that requires further dynamics studies including accurate modelling of the ice/water interface, suggests that a hydrophobic interaction between the surface of the protein and ice is the key to explaining accumulation at specific ice planes, and thus the molecular level mechanism for ice growth inhibition.

Role of glycopeptides and pepddes in inhibition of crystallization of water in polar fishes

In the ice-laden polar oceans, water temperatures of — 2 °C are common. This temperature is 1.1 °C below the equilibrium freezing point ( — 0.9 °C) of the fishes’ body fluids. Avoidance of freezing in these environments has been linked to the presence of unusual blood peptides and glycopeptides. These molecules have molecular masses ranging from 2.5 to 20 kDa and are viewed as having antifreeze properties because they lower the freezing point of water by a non-colligative process. A 2% solution of antifreeze has a freezing point of — 1.2 °C and ice formed in their presence melts at — 0.02 °C. Measurements of antifreeze concentrations in ice indicate that these molecules, unlike other proteins of similar size and conformation, are incorporated into the solid phase during freezing and adsorb to it. Adsorption of the antifreezes to ice appears to inhibit growth along the preferred axes ( a -axes) by raising the curvature of the growth steps on the basal plane. At temperatures below — 1.2 °C, crystal growth occurs in the form of long spicules whose axes are parallel to the c -axis, the non-preferred axis of growth.

Penguin egg-white and polar fish blood-serum proteins

The development of, and findings in, a long-term research program on penguin proteins and polar fish blood proteins are described. Two of the egg-white proteins from the Adelie penguin (Pygoscelis adeliae) have unique properties: a glycoprotein named penalbumin that is a major constituent with some characteristics similar to ovalbumin, and an ovomucoid with strong inhibitory capacity for subtilisin as well as for bovine trypsin and alpha-chymotrypsin. The antifreeze glycoproteins from Antarctic fish (Trematomus borchgrevinki and Dissostichus mawsoni) and an Arctic fish (Boreogadus saida) appear to function noncolligatively by lowering the freezing temperature without affecting the melting point. Current evidence indicates that the antifreeze glycoprotein functions at the ice-solution interface, either on the ice surface or in a transition layer between the solution and the ice.

Amino acid composition of proteins: Selection against the genetic code

Distribution of amino acids in 68 representative proteins is compared with their distribution among 61 codons of the genetic code. Average amounts of lysine, aspartic acid, glutamic acid, and alanine are above the levels anticipated from the genetic code, and arginine, serine, leucine, cysteine, proline, and histidine are below such levels. Arginine plus lysine account for 11.0 percent of codons and aspartic acid plus glutamic acid account for 11.3 percent; thus the average charge is roughly neutral.