Inhibition of Ice Nucleus Growth in Water by Alanine Dipeptide

A molecular dynamics simulation has been carried out for the mixture of an ice nucleus, supercooled water and a molecule of alanine dipeptide (AD). The dipeptide molecule has been allocated near the nucleus surface which corresponds to the prism plane of ice crystal. The molecule is found to approach the ice surface so that the two hydrophilic sites on one side of the molecule (Oc2 and Hn1) are closest to the surface. The hydrogen bond between Hn1 site and the oxygen atom on the prism plane of the ice nucleus is expected. The perturbations of two hydrophilic sites (Oc1 and Hn2), which are surrounded by hydrophobic sites and are pointing away from the surface, attenuate the approach of water molecules to these sites. Thus, these water molecules diffuse. The hydrogen bond between the oxygen atoms on the prism plane and the hydrogen atoms of water molecules is attenuated by the diffusion.     

Interaction among the twelve-residue segment of antifreeze protein type I,or its mutants,water and a hexagonal ice crystal

We have carried out a molecular dynamics analysis on a mixture of supercooled water, a hexagonal ice crystal and segments of winter flounder antifreeze protein. The segment consists of nine alanine residues, two threonine residues and one asparagine residue. Mutant segments, in which the threonine residues are replaced with valine residues, or serine residues, are also used. It is found that the threonine residue near the asparagine residue of the original segment is located in the vicinity of the prism face of the ice crystal. This is due to the hydrogen bond between the hydrophilic sites of these residues and water molecules, and the hydrogen bond between these water molecules and the water molecules on the ice surface. The valine and serine residues in the mutant segments do not approach the prism face of the ice crystal compared with the threonine residue near the asparagine residue. The motion of five segments, closely located side by side, is not remarkable. This is because of the gathering of water molecules caused by hydrophobic hydration, not only around alanine residues but also around the methyl sites of threonine residues.     

The mechanism of the type III antifreeze protein action: a computational study

The random network model of water quantitatively describes the different hydration heat capacities of polar and apolar solutes in terms of differential distortions of the water-water hydrogen bonding angle in the first hydration shell. This method of hydration analysis is applied here to study the hydration of the wild type III thermal hysteresis protein from eel pout and three mutations at residue 16. Wild type and one mutant have full activity, the other two mutants have little or no anti-freeze (thermal hysteresis) activity. The analysis reveals significant differences in the hydration structure of the ice-binding site (centered on residue 16) among four proteins. For the A16T and A16Y mutants with reduced activity, polar groups have a typical polar-like hydration. For the wild type and mutant A16C with 100% of the wild type activity, polar groups have unusual, very apolar-like hydration. In the latter case, hydrating water molecules form a more ice-like pattern of hydrogen bonding on the ice-binding face, while in the former case water-water H-bonds are more distorted and more heterogenous. Overall, the binding surface of active protein strongly enhances the water tetrahedral structure, i.e. promotes ice-like hydration. It is concluded that the specific shape, residue size and clustering of both polar/apolar groups are essential for the binding surface to recognize, and preferentially interact with nascent ice crystals forming in liquid water.     

Ice-like encapsulated water by two cholic acid moieties

Starting from the structure of ice (in which each water molecule is surrounded by other four water molecules forming a tetrahedron with a value of 4.51 Å for the edge O–O distance), and the knowledge that this value also corresponds to the O7–O12 distance of the skeleton of cholic acid, it is hypothesized that two steroid cholic acid moieties, with an appropriate steroid–steroid distance and a belly-to-belly orientation, could encapsulate a single water molecule between them. To check this hypothesis two succinyl derivatives of cholic acid (a monomer and the related head–head dimer in which the succinyl group is the linking bridge) were designed. The expected “ice-like” structure is found in the crystal of the dimer. There is a hydrogen bond synergy between those participating in the “ice-like” structure, and those in which the bridge is involved with the O7–H hydroxy group and the side chain of the steroid.     

Structure,dynamics and thermodynamic stability of high-pressure ices and clathrate hydrates

We present the recent development of simulation studies on structure and dynamics of high-pressure ices and filled ices. After surveying the representative structures of ices, focus is placed on some properties of one of the ice polymorphs, plastic ice, which has been theoretically predicted but not yet been found experimentally. Its intervention between ice VII and liquid water enables to account for large discrepancies among various experimental melting curves of ice VII. We also examine the dynamical properties of the filled ice in which hydrogen molecules are contained in void space of the low-pressure cubic ice. In contrast to the plastic ice, which has a bearing on ice VII, it exhibits a gradual change to each rotator phase of guest hydrogen and/or host water molecules.     

Supercooling in overwintering azalea flower buds: additional freezing parameters

Results of calorimetric, nuclear magnetic resonance, and low temperature light microscopic studies on supercooled azalea (Rhododendron kosterianum, Schneid.) floral primordia are reported. Heat release during freezing of the supercooled floral primordia is in the range predicted for supercooled pure water. Spin-lattice and spin-spin relaxation times measured by pulsed nuclear magnetic resonance spectroscopy decreased after freezing, suggesting that a redistribution of tissue water is associated with injury to the floral primordium. The calorimetric and low temperature microscopy studies showed no detectable ice formation in floral primordia until the major freezing event at low temperature. No resistance to ice growth is found to exist in the primordium tissues, indicating that a freezing barrier or thermodynamic equilibrium exists between the unfrozen primordium and other flower bud parts which contain ice at subfreezing temperatures.     

Heat capacity of protein folding.

We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal dipoles that are ordered around the unfolded surfaces, where the influence of these surfaces, covered with an "ice-like" shell of water, is represented by an effective field that directs the water dipoles. An intermolecular pair interaction between water molecules is also introduced. The heat capacity of the model exhibits, the common feature of small globular proteins, two peaks corresponding to cold and warm unfolding, respectively. By introducing ad hoc vibrational modes, we obtain quantitatively good accordance with experiments on myoglobin.     

Analysis of thermal hysteresis protein hydration using the random network model

The hydration of polar and apolar groups can be explained quantitatively, via the random network model of water, in terms of differential distortions in first hydration shell water-water hydrogen bonding angle. This method of analyzing solute induced structural distortions of water is applied to study the ice-binding type III thermal hysteresis protein. The analysis reveals subtle but significant differences in solvent structuring of the ice-binding surface, compared to non-ice binding protein surface. The major differences in hydration in the ice-binding region are (i). polar groups have a very apolar-like hydration. (ii). there is more uniform hydration structure. Overall, this surface strongly enhances the tetrahedral, or ice-like, hydration within the primary hydration shell. It is concluded that these two specific features of the hydration structure are important for this surface to recognize, and preferentially interact with nascent ice crystals forming in liquid water.     

Hydrophilicity of cavities in proteins

Water molecules inside cavities in proteins constitute integral parts of the structure. We have sought a quantitative measure of the hydrophilicity of the cavities by calculating energies and free energies of introducing a water molecule into these cavities. A threshold value of the water-protein interaction energy at −12 kcal/mol was found to be able to distinguish hydrated from empty cavities. It follows that buried waters have entropy comparable to that of liquid water or ice. A simple consistent picture of the energetics of the buried waters provided by this study enabled us to address the reliability of buried waters assigned in experiments.     

Crystallization of water in multilamellar vesicles

The two-step crystallization of water in multilamellar vesicles (MLVs) of phosphatidylcholines has been investigated. The main crystallization occurs near -15 degrees C and involves bulk water. Contrary to unilamellar vesicles, a sub-zero phase transition is observed for MLVs at -40 degrees C that corresponds to the crystallization of interstitial water, as proved by Fourier transform infrared absorption and differential scanning calorimetry (DSC) experiments. Furthermore, by means of the DSC method and, more specifically, using the enthalpy change values Delta H(sub) at the sub-zero transition, the number of water molecules per 1,2-dipalmitoylphosphatidylcholine (DPPC) molecule giving rise to this transition has been estimated for different H(2)O/DPPC molar ratios. The curve of the molecular fraction of water molecules involved in the sub-zero transition versus the H(2)O/DPPC molar ratio exhibits a maximum for H(2)O/DPPC equal to 27 (40% in mass of water) and tends towards zero for H(2)O/DPPC ratio values approaching that of the swelling limit of the membrane. A smaller enthalpy value of the sub-zero transition is found for 1-oleoyl-2-palmitoyl-3-phosphatidylcholine (OPPC) than for DPPC. This may be explained by the decrease of interstitial water's quantity when the lipid contains an unsaturated chain. When troxerutin, a hydrophilic drug, is added to the DPPC multilayers, the decrease of Delta H(sub) and melting enthalpy of bulk water is attributed to a decrease of the entropy of the liquid phase owing to the network of water molecules surrounding troxerutin molecules. In all cases, the experiments revealed that the sub-zero transition occurs only in the presence of excess water with respect to the swelling limit of membranes. This evidence could be, at least qualitatively, related to an increase of membrane pressure on interstitial water subsequent to bulk water crystallization.     

Recent results on the connection between thermodynamics and dynamics in supercooled water

We review recent results on the connection between thermodynamics and dynamics in a model for water. We verify the Adam-Gibbs relation between entropy and dynamic properties using computer simulations, which allow direct access to the relevant properties. We combine experimental measurements of entropy with the Adam-Gibbs hypothesis to predict dynamic properties in deeply supercooled states, which are difficult to access experimentally. We find evidence suggesting that the glass transition temperature of water may be significantly higher than previously reported, but is still consistent with recent measurements. Finally, we discuss the hypothesis that the dynamical behavior of deeply supercooled water undergoes a crossover from 'fragile' to 'strong' behavior.     

Deep supercooling enabled by surface impregnation with lipophilic substances explains the survival of overwintering buds at extreme freezing

The frost survival mechanism of vegetative buds of angiosperms was suggested to be extracellular freezing causing dehydration, elevated osmotic potential to prevent freezing. However, extreme dehydration would be needed to avoid freezing at the temperatures down to ?45°C encountered by many trees. Buds of Alnus alnobetula, in common with other frost hardy angiosperms, excrete a lipophilic substance, whose functional role remains unclear. Freezing of buds was studied by infrared thermography, psychrometry, and cryomicroscopy. Buds of A. alnobetula did not survive by extracellular ice tolerance but by deep supercooling, down to ?45°C. An internal ice barrier prevented ice penetration from the frozen stem into the bud. Cryomicroscopy revealed a new freezing mechanism. Until now, supercooled buds lost water towards ice masses that form in the subtending stem and/or bud scales. In A. alnobetula, ice forms harmlessly inside the bud between the supercooled leaves. This would immediately trigger intracellular freezing and kill the supercooled bud in other species. In A. alnobetula, lipophilic substances (triterpenoids and flavonoid aglycones) impregnate the surface of bud leaves. These prevent extrinsic ice nucleation so allowing supercooling. This suggests a means to protect forestry and agricultural crops from extrinsic ice nucleation allowing transient supercooling during night frosts.     

Bacterial ice-nucleation proteins

Certain bacteria possess proteins that enable them to nucleate crystallization in supercooled water. These ice-nucleation proteins are thought to produce templates for the assembly of very small seed crystals of ice. The proteins from different species have related, internally repetitive primary structures, which may be directly responsible for aligning the water molecules of the seed crystal.     

Effect of hydrophobic environments on the hypothesized liquid-liquid critical point of water

The complex behavior of liquid water, along with its anomalies and their crucial role in the existence of life, continue to attract the attention of researchers. The anomalous behavior of water is more pronounced at subfreezing temperatures and numerous theoretical and experimental studies are directed towards developing a coherent thermodynamic and dynamic framework for understanding supercooled water. The existence of a liquid–liquid critical point in the deep supercooled region has been related to the anomalous behavior of water. However, the experimental study of supercooled water at very low temperatures is hampered by the homogeneous nucleation of the crystal. Recently, water confined in nanoscopic structures or in solutions has attracted interest because nucleation can be delayed. These systems have a tremendous relevance also for current biological advances; e.g., supercooled water is often confined in cell membranes and acts as a solvent for biological molecules. In particular, considerable attention has been recently devoted to understanding hydrophobic interactions or the behavior of water in the presence of apolar interfaces due to their fundamental role in self-assembly of micelles, membrane formation and protein folding. This article reviews and compares two very recent computational works aimed at elucidating the changes in the thermodynamic behavior in the supercooled region and the liquid–liquid critical point phenomenon for water in contact with hydrophobic environments. The results are also compared to previous reports for water in hydrophobic environments.     

Stabilization of supercooled fluids by thermal hysteresis proteins.

It has been reported that thermal hysteresis proteins found in many cold-hardy, freeze-avoiding arthropods stabilize their supercooled body fluids. We give evidence that fish antifreeze proteins, which also produce thermal hysteresis, bind to and reduce the efficiency of heterogenous nucleation sites, rather than binding to embryonic ice nuclei. We discuss both possible mechanisms for stabilization of supercooled body fluids and also describe a new method for measuring and defining the supercooling point of small volumes of liquid.     

Ice-binding mechanism of winter flounder antifreeze proteins

We have studied the winter flounder antifreeze protein (AFP) and two of its mutants using molecular dynamics simulation techniques. The simulations were performed under four conditions: in the gas phase, solvated by water, adsorbed on the ice (2021) crystal plane in the gas phase and in aqueous solution. This study provided details of the ice-binding pattern of the winter flounder AFP. Simulation results indicated that the Asp, Asn, and Thr residues in the AFP are important in ice binding and that Asn and Thr as a group bind cooperatively to the ice surface. These ice-binding residues can be collected into four distinct ice-binding regions: Asp-1/Thr-2/Asp-5, Thr-13/Asn-16, Thr-24/Asn-27, and Thr-35/Arg-37. These four regions are 11 residues apart and the repeat distance between them matches the ice lattice constant along the (1102) direction. This match is crucial to ensure that all four groups can interact with the ice surface simultaneously, thereby, enhancing ice binding. These Asx (x = p or n)/Thr regions each form 5-6 hydrogen bonds with the ice surface: Asn forms about three hydrogen bonds with ice molecules located in the step region while Thr forms one to two hydrogen bonds with the ice molecules in the ridge of the (2021) crystal plane. Both the distance between Thr and Asn and the ordering of the two residues are crucial for effective ice binding. The proper sequence is necessary to generate a binding surface that is compatible with the ice surface topology, thus providing a perfect "host/guest" interaction that simultaneously satisfies both hydrogen bonding and van der Waals interactions. The results also show the relation among binding energy, the number of hydrogen bonds, and the activity. The activity is correlated to the binding energy, and in the case of the mutants we have studied the number of hydrogen bonds. The greater the number of the hydrogen bonds the greater the antifreeze activity. The roles van der Waals interactions and the hydrophobic effect play in ice binding are also highlighted. For the latter it is demonstrated that the surface of ice has a clathratelike structure which favors the partitioning of hydrophobic groups to the surface of ice. It is suggested that mutations that involve the deletion of hydrophobic residues (e.g., the Leu residues) will provide insight into the role the hydrophobic effect plays in partitioning these peptides to the surface of ice.     

Computational study of mutarotation in erythrose and threose

For the first time the mutarotation mechanism of furanose rings has been investigated, with and without solvent. The transformations from open-chain furanose to d-erythrose and d-threose have been studied at B3LYP/6-311++G(d,p) and G3MP2B3 levels, in vacuum and in solution through continuum solvation models. We studied the catalytic influence of one, two or three water molecules, as well as simplified models of carbohydrates, that is, methanol and 1,2-ethanediol. Water molecules significantly reduce the energy barrier of the hemiacetal formation occurring between the open-chain and furanose configurations. The energy barrier is optimally reduced by two water molecules. Methanol yields a smaller transition state barrier than the one obtained with a single water molecule. In contrast, 1,2-ethanediol does not provide a lower transition state compared to the barrier in the presence of two water molecules.     

The North East Water polynya (Greenland Sea)

Physical observations of the North East Water (NEW) polynya, located near the north-eastern corner of Greenland, are presented. Data were collected in June 1991 by RV Polarstern. An idea is put forward to explain how the NEW is generated. A northward coastal current interacts with a persistent shelf ice barrier under which water can flow but that retains ice floes and therefore protects the NEW area from ice advection. Since in summer, the combination of currents, barrier and air-sea heat balance gives rise to a polynya. The distribution of upper water column vertical stability in the NEW is also influenced by its generation process. Surface melt water is retained by the shelf ice barrier, causing neutral vertical stability in its lee. Sea ice melting and land runoff then act as two distinct sources of vertical stability enabling the development of plankton blooms, especially in the northern part of the NEW.