Theoretical study of interaction of winter flounder antifreeze protein with ice

From freezing to functioning: cellular strategies of cold-adapted bacteria for surviving in extreme environments

The ability of cold-adapted bacteria to survive in extreme cold and diverse temperatures is due to their unique attributes like cell membrane stability, up-regulation of peptidoglycan biosynthesis, increased production of extracellular polymeric substances, and expansion of membrane pigment. Various cold-adapted proteins, including ice-nucleating proteins (INPs), antifreeze proteins (AFPs), cold shock proteins (Csps), and cold-acclimated proteins (CAPs), help the bacteria to survive in these environments. To sustain cells from extreme cold conditions and maintain stability in temperature fluctuations, survival strategies at the molecular level and their mechanism play significant roles in adaptations in cryospheric conditions. Furthermore, cold shock domains present in the multifunctional cold shock proteins play crucial roles in their adaptation strategies. The considerable contribution of lipopeptides, osmolytes, and membrane pigments plays an integral part in their survival in extreme environments. This review summarizes the evolutionary history of cold-adapted bacteria and their molecular and cellular adaptation strategies to thrive in harsh cold environments. It also discusses the importance of carotenoids produced, lipid composition, cryoprotectants, proteins, and chaperones related to this adaptation. Furthermore, the functions and mechanisms of adaptations within the cell are discussed briefly. One can utilize and explore their potential in various biotechnology applications and their evolutionary journey by knowing the inherent mechanism of their molecular and cellular adaptation to cold climatic conditions. This review will help all branches of the life science community understand the basic microbiology of psychrophiles and their hidden prospect in life science research.

Anti-freezing hydrogel regulated by ice-structuring proteins/cellulose nanofibers system as flexible sensor for winter sports

Conductive hydrogels are widely used as sensors in wearable devices. However, hydrogels cannot endure harsh low-temperature environments. Herein, a new regulatory system based on natural ice-structuring proteins (ISPs) and cellulose nanofibers (CNFs) is introduced into hydrogel network consisting of chemically crosslinked network of copolymerized acrylamide and 2-acrylamide-2-methylpropanesulfonic acid, and physically crosslinked polyvinyl alcohol chains, affording an anti-freezing hydrogel with high conductivity (2.63 S/m). These hydrogels show excellent adhesion behavior to various matrices (including aluminum, glass, pigskin, and plastic). Their mechanical properties are significantly improved with the increase in CNF content (tensile strength of 106.4 kPa, elastic modulus of 133.8 kPa). In addition, ISPs inhibit the growth of ice. This endows the hydrogels with anti-freezing property and allows them to maintain satisfactory mechanical properties, conductivity and sensing properties below zero degrees. Moreover, this hydrogel shows high sensitivity to tensile and compressive deformation (GF = 5.07 at 600-800 % strain). Therefore, it can be utilized to develop strain-type pressure sensors that can be attached directly to human skin for detecting various body motions accurately, reliably, and stably. This study proposes a simple strategy to improve the anti-freezing property of hydrogels, which provides new insights for developing flexible hydrogel electronic devices for application in winter sports.

How Can Ice Emerge at 0 °C?

The classical nucleation theory shows that bulk water freezing does not occur at temperatures above ≈ -30 °C, and that at higher temperatures ice nucleation requires the presence of some ice-binding surfaces. The temperature and rate of ice nucleation depend on the size and level of complementarity between the atomic structure of these surfaces and various H-bond-rich/depleted crystal planes. In our experiments, the ice nucleation temperature was within a range from -8 °C to -15 °C for buffer and water in plastic test tubes. Upon the addition of ice-initiating substances (i.e., conventional AgI or CuO investigated here), ice appeared in a range from -3 °C to -7 °C, and in the presence of the ice-nucleating bacterium Pseudomonas syringae from -1 °C to -2 °C. The addition of an antifreeze protein inhibited the action of the tested ice-initiating agents.

Mechanistic elucidation of freezing-induced surface decomposition of aluminum oxyhydroxide adjuvant

The freezing-induced aggregation of aluminum-based (Alum) adjuvants has been considered as the most important cause of reduced vaccine potency. However, the intrinsic properties that determine the functionality of Alum after freezing have not been elucidated. In this study, we used engineered aluminum oxyhydroxide nanoparticles (AlOOH NPs) and demonstrated that cryogenic freezing led to the mechanical pressure-mediated reduction of surface hydroxyl. The sugar-based surfactant, octyl glucoside (OG), was demonstrated to shield AlOOH NPs from the freezing-induced loss of hydroxyl content and the aggregation through the reduction of recrystallization-induced mechanical stress. As a result, the antigenic adsorption property of frozen AlOOH NPs could be effectively protected. When hepatitis B surface antigen (HBsAg) was adjuvanted with OG-protected frozen AlOOH NPs in mice, the loss of immunogenicity was inhibited. These findings provide insights into the freezing-induced surface decomposition of Alum and can be translated to design of protectants to improve the stability of vaccines.

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The freezing stress led to the destruction of surface hydroxyl group on AlOOH NPs

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Octyl glucoside protected AlOOH NPs from freezing-induced surface decomposition

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Octyl glucoside protected vaccines from freezing-induced loss of immunogenicity

Physical Basis of Functioning of Antifreeze Protein

Abstract

Antifreeze proteins, expressed in cold-blooded organisms, prevent ice formation in their bodies, and thus help them to survive in extremely cold winter temperatures. However, the mechanism of action of these proteins is still not clear. In any case, it is not simply a decrease in the temperature of normal ice formation. In this work, investigating the ice-binding protein (a mutant form of the antifreeze protein cfAFP from the spruce budworm Choristoneura fumiferana, which overwinters in needles), we showed that this antifreeze protein does not at all lower the freezing point of water and, paradoxically, increases the melting point of ice. On the other hand, calculations based on the theory of crystallization show that at temperatures of 0 ° to –30°C ice can only appear on surfaces that contact water, but not in the body of water. These facts suggest a new perspective on the role of antifreeze proteins: their task is not (as it is commonly believed) to bind with nascent ice crystals already formed in the organism and stop their growth, but to bind to those surfaces, on which ice nuclei can appear, and thus completely inhibit the ice formation in supercooled water or biological fluid.

Low-temperature adaptive conductive hydrogel based on ice structuring proteins/CaCl2 anti-freeze system as wearable strain and temperature sensor

Conductive hydrogels as wearable devices meet the basic demands of mechanical flexibility and smart sensing. However, achieving anti-freeze property in conductive hydrogels is still challengeable. Here, a novel anti-freezing system based on ice structuring proteins and CaCl₂ was introduced to enable a conductive hydrogel with low-temperature adaptability. Both formation of ice nuclei and ice growth of the hydrogel at sub-zero temperature could be inhibited. Supported by the anti-freeze system, the hydrogel revealed good flexibility (890% at -20 °C), recovery and conductivity (0.50 S/m at -20 °C) at both room temperature and sub-zero temperature. The low-temperature adaptability enabled the hydrogel to be used as strain and temperature sensors at both room temperature and sub-zero temperature. The anti-freeze system in this work is expected to open up a new avenue to promote the conductive hydrogel with low-temperature adaptability.

Ice Growth Suppression in the Solution Flows of Antifreeze Protein and Sodium Chloride in a Mini-Channel

The control of ice growth inside channels of aqueous solution flows is important in numerous fields, including (a) cold-energy transportation plants and (b) the preservation of supercooled human organs for transplantation. A promising method for this control is to add a substance that influences ice growth in the flows. However, limited results have been reported on the effects of such additives. Using a microscope, we measured the growth of ice from one sidewall toward the opposite sidewall of a mini-channel, where aqueous solutions of sodium chloride and antifreeze protein flowed. Our aim was to considerably suppress ice growth by mixing the two solutes. Inclined interfaces, the overlapping of serrated interfaces, and interfaces with sharp and flat tips were observed in the cases of the protein-solution, salt-solution, and mixed-solution flows, respectively. In addition, it was found that the average interface velocity in the case of the mixed-solution flow was the lowest and decreased by 64% compared with that of pure water. This significant suppression of the ice-layer growth can be attributed to the synergistic effects of the ions and antifreeze protein on the diffusion of protein.

Effects of Winter Flounder Antifreeze Protein on the Growth of Ice Particles in an Ice Slurry Flow in Mini-Channels

The control of ice growth in ice slurry is important for many fields, including (a) the cooling of the brain during cardiac arrest, (b) the storage and transportation of fresh fish and fruits, and (c) the development of distributed air-conditioning systems. One of the promising methods for the control is to use a substance such as antifreeze protein. We have observed and report here growth states of ice particles in both quiescent and flowing aqueous solutions of winter flounder antifreeze proteins in mini-channels with a microscope. We also measured ice growth rates. Our aim was to improve the levels of ice growth inhibition by subjecting the antifreeze protein solution both to preheating and to concentrating by ultrafiltration. We have found that the ice growth inhibition by the antifreeze protein decreased in flowing solutions compared with that in quiescent solutions. In addition, unlike unidirectional freezing experiments, the preheating of the antifreeze protein solution reduced the ice growth inhibition properties. This is because the direction of flow, containing HPLC6 and its aggregates, to the ice particle surfaces can change as the ice particle grows, and thus the probability of interaction between HPLC6 and ice surfaces does not increase. In contrast to this, ultrafiltration after preheating the solution improved the ice growth inhibition. This may be due to the interaction between ice surfaces and many aggregates in the concentrates.

Proteomic analysis and microtubule dynamicity of human sperm in electromagnetic cryopreservation

The proteomic changes, microtubule dynamicity, and quality parameters of human sperm were investigated during cryopreservation in an extremely low electromagnetic field (ELEF) condition. Semen samples were obtained from 210 healthy individuals with normospermia and then were divided into three experimental groups: fresh control, frozen control, and frozen ELEF group. Shotgun proteomics was performed to assess the identification of microtubule proteins of the sperm in experimental groups. Microtubule dynamicity, secondary, and tertiary structure modifications of tubulins, characteristics of transmission electron microscopy of sperm as well as sperm quality parameters were evaluated. The expression ratios of α- and β-tubulins were significantly increased after cryopreservation compared with fresh control while this ratio was not significantly different in frozen ELEF group. The expression ratio of tubulin polymerization-promoting protein was significantly decreased after cryopreservation compared with fresh control. The length, width, and the activity of microtubule, secondary, and tertiary structures of tubulins, motility, and the viability of the sperm were decreased in frozen control as compared with fresh control. The microtubule activity, secondary, and tertiary structures of sperm tubulin in frozen ELEF group were higher than frozen control. Transmission electron microscopy of microtubules showed that the size of the width and length of the microtubules in frozen ELEF group were greater than frozen control. Motility, viability, and reactive oxygen species levels were improved in frozen ELEF group when compared with frozen control. While the microtubule dynamicity of the sperm was affected by the cryopreservation, this trait was improved during the electromagnetic cryopreservation resulted in better motility and viability.

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.

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.

Influence of Adsorption Orientation on the Statistical Mechanics Model of Type I Antifreeze Protein: The Thermal Hysteresis Temperature

The antifreeze activity of type I antifreeze proteins (AFPIs) is studied on the basis of the statistical mechanics theory, by taking the AFP's adsorption orientation into account. The thermal hysteresis temperatures are calculated by determining the system Gibbs function as well as the AFP molecule coverage rate on the ice-crystal surface. The numerical results for the thermal hysteresis temperatures of AFP9, HPLC-6, and AAAA2kE are obtained for both of the cases with and without inclusion of the adsorption orientation. The results show that the influence of the adsorption orientation on the thermal hysteresis temperature cannot be neglected. The theoretical results are coincidental preferably with the experimental data.

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.

PicW orthologs from spruce with differential freezing tolerance expressed in Escherichia coli

Spruce can grow at an extra low temperature (LT), and is inferred with important antifreezing gene resources. The research here identified 4 different spruce varieties, named as PicW1, PicW2, PicM and PicK. Sequence alignment showed base-substitution and deficiency mutations among them with sequence identity between 97.61% and 99.25%. Each gene was transferred into E. coli, where protein was induced by IPTG (isopropyl-β-d-thiogalactoside). Strains cultured at -5°C showed the lethal dose 50% (LD-50) between 53h and 57h for the transgenic strains, but 35h for the control. Strains cultivated at -20°C showed the LD-50 between 38h and 44h for the transgenic strains, but 25h for the control. Further, the soluble gene proteins were extracted and purified for Differential Scanning Calorimeter (DSC) test, which showed characteristic thermal hysteresis (TH) value of 0.77°C (PicW1), 0.78°C (PicW2), 0.72°C (PicM), and 0.86°C (PicK) respectively, significantly higher than the value of 0.05°C of the control (BSA). Summarily, four homologous proteins showed good antifreeze property with the range from high to low as PicK>PicW2>PicW1>PicM. It suggested that they can be used as resources for genetic engineering of plant cold tolerance.

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.

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

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

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.

An Effective Antifreeze Protein Predictor with Ensemble Classifiers and Comprehensive Sequence Descriptors

Antifreeze proteins (AFPs) play a pivotal role in the antifreeze effect of overwintering organisms. They have a wide range of applications in numerous fields, such as improving the production of crops and the quality of frozen foods. Accurate identification of AFPs may provide important clues to decipher the underlying mechanisms of AFPs in ice-binding and to facilitate the selection of the most appropriate AFPs for several applications. Based on an ensemble learning technique, this study proposes an AFP identification system called AFP-Ensemble. In this system, random forest classifiers are trained by different training subsets and then aggregated into a consensus classifier by majority voting. The resulting predictor yields a sensitivity of 0.892, a specificity of 0.940, an accuracy of 0.938 and a balanced accuracy of 0.916 on an independent dataset, which are far better than the results obtained by previous methods. These results reveal that AFP-Ensemble is an effective and promising predictor for large-scale determination of AFPs. The detailed feature analysis in this study may give useful insights into the molecular mechanisms of AFP-ice interactions and provide guidance for the related experimental validation. A web server has been designed to implement the proposed method.

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

Microfluidic experiments reveal that antifreeze proteins bound to ice crystals suffice to prevent their growth

Antifreeze proteins (AFPs) are a subset of ice-binding proteins that control ice crystal growth. They have potential for the cryopreservation of cells, tissues, and organs, as well as for production and storage of food and protection of crops from frost. However, the detailed mechanism of action of AFPs is still unclear. Specifically, there is controversy regarding reversibility of binding of AFPs to crystal surfaces. The experimentally observed dependence of activity of AFPs on their concentration in solution appears to indicate that the binding is reversible. Here, by a series of experiments in temperature-controlled microfluidic devices, where the medium surrounding ice crystals can be exchanged, we show that the binding of hyperactive Tenebrio molitor AFP to ice crystals is practically irreversible and that surface-bound AFPs are sufficient to inhibit ice crystal growth even in solutions depleted of AFPs. These findings rule out theories of AFP activity relying on the presence of unbound protein molecules.

Biomolecular electrostatics and solvation: a computational perspective

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

Thermodynamic Analysis of Thermal Hysteresis: Mechanistic Insights into Biological Antifreezes

Antifreeze proteins (AFPs) bind to ice crystal surfaces and thus inhibit the ice growth. The mechanism for how AFPs suppress freezing is commonly modeled as an adsorption-inhibition process by the Gibbs-Thomson effect. Here we develop an improved adsorption-inhibition model for AFP action based on the thermodynamics of impurity adsorption on the crystal surfaces. We demonstrate the derivation of a realistic relationship between surface protein coverage and the protein concentration. We show that the improved model provides a quantitatively better fit to the experimental antifreeze activities of AFPs from distinct structural classes, including fish and insect AFPs, in a wide range of concentrations. Our theoretical results yielded the adsorption coefficients of the AFPs on ice, suggesting that, despite the distinct difference in their antifreeze activities and structures, the affinities of the AFPs to ice are very close and the mechanism of AFP action is a kinetically controlled, reversible process. The applications of the model to more complex systems along with its potential limitations are also discussed.

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.

Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function

Physics-based force fields for ligand-protein docking usually determine electrostatic energy with distance-dependent dielectric (DDD) functions, which do not fully account for the dielectric permittivity variance between approximately 2 in the protein core and approximately 80 in bulk water. Here we propose an atom-atom solvent exposure- and distance-dependent dielectric (SEDDD) function, which accounts for both electrostatic and dehydration energy components. Docking was performed using the ZMM program, the AMBER force field, and precomputed libraries of ligand conformers. At the seeding stage, hundreds of thousands of positions and orientations of conformers from the libraries were sampled within the rigid protein. At the refinement stage, the ten lowest-energy structures from the seeding stage were Monte Carlo-minimized with the flexible ligand and flexible protein. A search was considered a success if the root mean square deviation (RMSD) of the ligand atoms in the apparent global minimum from the x-ray structure was <2 A. Calculations on an examining set of 60 ligand-protein complexes with different DDD functions and solvent-exclusion energy revealed outliers in most of which the ligand-binding site was located at the protein surface. Using a training set of 16 ligand-protein complexes, which did not overlap with the examining set, we parameterized the SEDDD function to minimize the RMSD of the apparent global minima from the x-ray structures. Recalculation of the examining set with the SEDDD function demonstrated a 20% increase in the success rate versus the best-performing DDD function.