Local Ice Melting by an Antifreeze Protein

The influence of a type III antifreeze protein and its mutants on methane hydrate adsorption-inhibition: a molecular dynamics simulation study

Antifreeze proteins (AFPs) inhibit ice growth in various organisms at subzero temperature. Recently, AFPs as a hydrate inhibitor have been a topic of intense discussion, while the detailed mechanism remains obscure. The present work aims to explore molecular insight into the adsorption and inhibition of an AFP III on methane hydrate. Three polar, hydrophilic, and neutral amino acids (Asn14, Thr18, and Gln44) are mutated to elucidate the molecular mechanism of AFP III antifreeze activity. Another triple mutation is also designed to investigate the effect of the side chain. Atomistic molecular dynamics simulations provide detailed structural and dynamical aspects of protein residues and water molecules at the hydrate/water interface. Initially, it was proposed that the AFP III operates by the adsorption-inhibition mechanism on hydrates, almost similar to that of ice. The exchange of amide and hydroxyl groups by mutagenesis alters the shape of the side chain and the capability of hydrogen bonding and demonstrates that hydrogen bonds are not directly responsible for the AFP III antifreeze activity. Moreover, we deciphered that the length of the pendant group is an important factor in the entrapment of the AFP III on the hydrate cages, which is compatible with van der Waals interactions between the side chains and hydrate surface. The results suggest that this interaction is sensitive to the geometry and shape of the hydrate-binding surface (HBS) of the AFP, which implies that the interface between hydrates and the AFP is relatively rigid.

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.

Mechanisms of antifreeze proteins investigated via the site-directed spin labeling technique

The site-directed spin labeling (SDSL) technique was used to examine the antifreeze mechanisms of type-I antifreeze proteins (AFPs). The effects on the growth of seed ice crystals by the spin-label groups attached to different side chains of the AFPs were observed, and the states of water molecules surrounding the spin-label groups were probed via analyses of variable-temperature (VT) dependent electron paramagnetic resonance (EPR) spectra. The first set of experiments revealed the antifreeze activities of the spin-labeled AFPs at the microscopic level, while the second set of experiments displayed those at the molecular level. The experimental results confirmed the putative ice-binding surface (IBS) of type-I AFPs. The VT EPR spectra indicate that type-I AFPs can inhibit the nucleation of seed ice crystals down to ~ - 20 °C in their aqueous solutions. Thus, the present authors believe that AFPs protect organisms from freezing damage in two ways: (1) inhibiting the nucleation of seed ice crystals, and (2) hindering the growth of seed ice crystals once they have formed. The first mechanism should play a more significant role in protecting against freezing damage among organisms living in cold environments. The VT EPR spectra also revealed that liquid-like water molecules existed around the spin-labeled non-ice-binding side chains of the AFPs frozen within the ice matrices, and ice surrounding the spin-label groups melted at subzero temperatures during the heating process. This manuscript concludes with the proposed model of antifreeze mechanisms of AFPs based on the experimental results.

Molecular dynamics studies show solvation structure of type III antifreeze protein is disrupted at low pH

Antifreeze proteins are a class of biological molecules of interest in many research and industrial applications due to their highly specialized function, but there is little information of their stability and properties under varied pH derived from computational studies. To gain novel insights in this area, we conducted molecular dynamics (MD) simulations with the antifreeze protein 1KDF at varied temperatures and pH. Water solvation and H-bond formation around specific residues - ASN14, THR18 and GLN44 - involved in its antifreeze activity were extensively studied. We found that at pH1 there was a disruption in water solvation around the basal and the ice binding surfaces of the molecule. This was induced by a small change in the secondary structure propensities of some titrable residues, particularly GLU35. This change explains the experimentally observed reduction in antifreeze activity previously reported for this protein at pH1. We also found that THR18 showed extremely low H-bond formation, and that the three antifreeze residues all had very low average H-bond lifetimes. Our results confirm long-standing assumptions that these small, compact molecules can maintain their antifreeze activity in a wide range of pH, while demonstrating the mechanism that may reduce antifreeze activity at low pH. This aspect is useful when considering industrial and commercial use of antifreeze proteins subject to extreme pH environments, in particular in food industrial applications.

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

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

Neofunctionalization of zona pellucida proteins enhances freeze-prevention in the eggs of Antarctic notothenioids

The mechanisms by which the eggs of the Antarctic notothenioid fishes avoid freezing are not fully understood. Zona pellucida proteins (ZPs) are constituents of the chorion which forms a protective matrix surrounding the egg. Here we report occurrence of freezing temperature-related gene expansion and acquisition of unusual ice melting-promoting (IMP) activity in a family of Antarctic notothenioid ZPs (AnnotoZPs). Members of AnnotoZPs are shown to bind with ice and non-colligatively depress the melting point of a solution in a range of 0.26 to 0.65 °C at a moderate concentration. Eggs of zebrafishes expressing an AnnotoZP transgene show improved melting point depression and enhanced survival in freezing conditions. Mutational analyses in a representative AnnotoZP indicate the ZP domain and patches of acidic residues are essential structures for the IMP activity. AnnotoZPs, therefore, represent a group of macromolecules that prevent freezing by a unique ZP-ice interaction mechanism distinct from the known antifreeze proteins.

Interaction of ice binding proteins with ice, water and ions

Ice binding proteins (IBPs) are produced by various cold-adapted organisms to protect their body tissues against freeze damage. First discovered in Antarctic fish living in shallow waters, IBPs were later found in insects, microorganisms, and plants. Despite great structural diversity, all IBPs adhere to growing ice crystals, which is essential for their extensive repertoire of biological functions. Some IBPs maintain liquid inclusions within ice or inhibit recrystallization of ice, while other types suppress freezing by blocking further ice growth. In contrast, ice nucleating proteins stimulate ice nucleation just below 0 °C. Despite huge commercial interest and major scientific breakthroughs, the precise working mechanism of IBPs has not yet been unraveled. In this review, the authors outline the state-of-the-art in experimental and theoretical IBP research and discuss future scientific challenges. The interaction of IBPs with ice, water and ions is examined, focusing in particular on ice growth inhibition mechanisms.

Experimental correlation between thermal hysteresis activity and the distance between antifreeze proteins on an ice surface

Temperature-controlled microfluidic devices and fluorescence microscopy illustrate the correlation between freezing-point depression and the distance between antifreeze proteins on an ice surface.

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.

Effects of a type I antifreeze protein (AFP) on the melting of frozen AFP and AFP+solute aqueous solutions studied by NMR microimaging experiment

The effects of a type I AFP on the bulk melting of frozen AFP solutions and frozen AFP+solute solutions were studied through an NMR microimaging experiment. The solutes studied include sodium chloride and glucose and the amino acids alanine, threonine, arginine, and aspartic acid. We found that the AFP is able to induce the bulk melting of the frozen AFP solutions at temperatures lower than 0 °C and can also keep the ice melted at higher temperatures in the AFP+solute solutions than those in the corresponding solute solutions. The latter shows that the ice phases were in super-heated states in the frozen AFP+solute solutions. We have tried to understand the first experimental phenomenon via the recent theoretical prediction that type I AFP can induce the local melting of ice upon adsorption to ice surfaces. The latter experimental phenomenon was explained with the hypothesis that the adsorption of AFP to ice surfaces introduces a less hydrophilic water-AFP-ice interfacial region, which repels the ionic/hydrophilic solutes. Thus, this interfacial region formed an intermediate chemical potential layer between the water phase and the ice phase, which prevented the transfer of water from the ice phase to the water phase. We have also attempted to understand the significance of the observed melting phenomena to the survival of organisms that express AFPs over cold winters.