Molecular dynamics study of the interactions of ice inhibitors on the ice {001} surface

The interactions of antifreeze protein (AFP) type I, antifreeze glycoproteins, polyvinyl pyrrolidone (PVP), and various amino acids with ice are investigated using Cerius2, a molecular modelling tool. Binding energies of these additives to a major ice crystal face {001} are computed. Binding energy comparison of threonine molecules (by themselves) and as threonine residues within AFP type I demonstrate their role in improving AFP's binding ability to the ice crystal face. The shifts in onset points of ice crystallization with AFP type I, PVP, and amino acids are measured using differential scanning calorimetry. These values when correlated with their respective binding energies reveal a direct proportionality and demonstrate AFP's effectiveness in inhibiting growth and nucleation of ice, over amino acids.     

Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations

Atomistic molecular dynamics simulations are used to investigate the mechanism by which the antifreeze protein from the spruce budworm, Choristoneura fumiferana, binds to ice. Comparison of structural and dynamic properties of the water around the three faces of the triangular prism-shaped protein in aqueous solution reveals that at low temperature the water structure is ordered and the dynamics slowed down around the ice-binding face of the protein, with a disordering effect observed around the other two faces. These results suggest a dual role for the solvation water around the protein. The preconfigured solvation shell around the ice-binding face is involved in the initial recognition and binding of the antifreeze protein to ice by lowering the barrier for binding and consolidation of the protein:ice interaction surface. Thus, the antifreeze protein can bind to the molecularly rough ice surface by becoming actively involved in the formation of its own binding site. Also, the disruption of water structure around the rest of the protein helps prevent the adsorbed protein becoming covered by further ice growth.     

Reversible binding of the HPLC6 isoform of type I antifreeze proteins to ice surfaces and the antifreeze mechanism studied by multiple quantum filtering-spin exchange NMR experiment

Antifreeze proteins (AFPs) protect organisms from freezing damage by inhibiting the growth of seed-ice crystals. It has long been hypothesized that irreversible binding of AFPs to ice surfaces is responsible for inhibiting the growth of seed-ice crystals as such a mechanism supports the popularly accepted Kelvin effect for the explanation of local freezing-point depression. However, whether the binding is reversible or irreversible is still under debate due to the lack of direct experimental evidence. Here, we report the first direct experimental result, by using the newly developed multiple quantum (MQ) filtering-spin exchange NMR experiment, that shows that the binding of HPLC6 peptides to ice surfaces is reversible. It was found that the reversible process can be explained by the model of monolayer adsorption. These results suggest that the Kelvin effect is not suitable for explaining the antifreeze mechanism, and direct interactions between the peptides and the ice-surface binding sites are the driving forces for the binding of AFPs to ice surfaces. We propose that there exists a concentration gradient of AFP from an ice-binding surface to the solution due to the affinity of ice surfaces to AFPs. This concentration gradient creates a dense layer of AFP in contact with the ice-binding surface, which depresses the local freezing point because of the colligative property, but not the Kelvin effect.     

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.     

Formation of ice-like water structure on the surface of an antifreeze protein

Antifreeze proteins (AFPs) are found in different species from polar, alpine, and subarctic regions where they serve to inhibit ice crystal growth by adsorption to ice surfaces. Computational methods have the power to investigate the antifreeze mechanism in atomic detail. Molecular dynamics simulations of water under different conditions have been carried out to test our water model for simulations of biological macromolecules in extreme conditions: very low temperatures (200 K) and at the ice/liquid water interface. We show that the flexible F3C water model reproduces properties of water in the solid phase (ice I(h)), the supercooled liquid phase, and at the ice/liquid water interface. Additionally, the hydration of the type III AFP from ocean pout was studied as a function of temperature. Hydration waters on the ice-binding surface of the AFP were less distorted and more tetrahedral than elsewhere on the surface. More ice-like hydrating water structures formed on the ice-binding surface of the protein such that it created an ice-like structure in water within its first hydration layer but not beyond, suggesting that this portion of the protein has high affinity for ice surfaces.     

A two-dimensional adsorption kinetic model for thermal hysteresis activity in antifreeze proteins

Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs), collectively abbreviated as AF(G)Ps, are synthesized by various organisms to enable their cells to survive in subzero environments. Although the AF(G)Ps are markedly diverse in structure, they all function by adsorbing to the surface of embryonic ice crystals to inhibit their growth. This adsorption results in a freezing temperature depression without an appreciable change in the melting temperature. The difference between the melting and freezing temperatures, termed thermal hysteresis (TH), is used to detect and quantify the antifreeze activity. Insights from crystallographic structures of a number of AFPs have led to a good understanding of the ice-protein interaction features. Computational studies have focused either on verifying a specific model of AFP-ice interaction or on understanding the protein-induced changes in the ice crystal morphology. In order to explain the origin of TH, we propose a novel two-dimensional adsorption kinetic model between AFPs and ice crystal surfaces. The validity of the model has been demonstrated by reproducing the TH curve on two different beta-helical AFPs upon increasing the protein concentration. In particular, this model is able to accommodate the change in the TH behavior observed experimentally when the size of the AFPs is increased systematically. Our results suggest that in addition to the specificity of the AFPs for the ice, the coverage of the AFPs on the ice surface is an equally necessary condition for their TH activity.     

Anisotropy in the crystal growth of hexagonal ice, I(h)

Growth of ice crystals has attracted attention because ice and water are ubiquitous in the environment and play critical roles in natural processes. Hexagonal ice, I(h), is the most common form of ice among 15 known crystalline phases of ice. In this work we report the results of an extensive and systematic molecular dynamics study of the temperature dependence of the crystal growth on the three primary crystal faces of hexagonal ice, the basal {0001} face, the prism {1010} face, and the secondary prism {1120} face, utilizing the TIP4P-2005 water model. New insights into the nature of its anisotropic growth are uncovered. It is demonstrated that the ice growth is indeed anisotropic; the growth and melting of the basal face are the slowest of the three faces, its maximum growth rates being 31% and 43% slower, respectively, than those of the prism and the secondary prism faces. It is also shown that application of periodic boundary conditions can lead to varying size effect for different orientations of an ice crystal caused by the anisotropic physical properties of the crystal, and results in measurably different thermodynamic melting temperatures in three systems of similar, yet moderate, size. Evidence obtained here provides the grounds on which to clarify the current understanding of ice growth on the secondary prism face of ice. We also revisit the effect of the integration time step on the crystal growth of ice in a more thorough and systematic way. Careful evaluation demonstrates that increasing the integration time step size measurably affects the free energy of the bulk phases and shifts the temperature dependence of the growth rate curve to lower temperatures by approximately 1 K when the step is changed from 1 fs to 2 fs, and by 3 K when 3 fs steps are used. A thorough investigation of the numerical aspects of the simulations exposes important consequences of the simulation parameter choices upon the delicate dynamic balance that is involved in ice crystal growth.     

Mimicking the Ice Recrystallization Activity of Biological Antifreezes. When is a New Polymer “Active”?

Antifreeze proteins and ice‐binding proteins have been discovered in a diverse range of extremophiles and have the ability to modulate the growth and formation of ice crystals. Considering the importance of cryoscience across transport, biomedicine, and climate science, there is significant interest in developing synthetic macromolecular mimics of antifreeze proteins, in particular to reproduce their property of ice recrystallization inhibition (IRI). This activity is a continuum rather than an “on/off” property and there may be multiple molecular mechanisms which give rise to differences in this observable property; the limiting concentrations for ice growth vary by more than a thousand between an antifreeze glycoprotein and poly(vinyl alcohol), for example. The aim of this article is to provide a concise comparison of a range of natural and synthetic materials that are known to have IRI, thus providing a guide to see if a new synthetic mimic is active or not, including emerging materials which are comparatively weak compared to antifreeze proteins, but may have technological importance. The link between activity and the mechanisms involving either ice binding or amphiphilicity is discussed and known materials assigned into classes based on this.     

苏氨酸在昆虫抗冻蛋白抗冻活性中的作用

设计系列昆虫抗冻蛋白CfAFP突变体, 通过分子动力学模拟确定各突变体与冰晶的最佳作用模式, 并用半经验分子轨道方法AM1和PM3研究了其与冰晶的相互作用. 结果表明, TXT面上的苏氨酸在蛋白与冰晶相互识别和结合过程中十分关键, 对CfAFP与冰晶间相互作用的贡献大, 用其它疏水或亲水氨基酸残基替换都将削弱抗冻蛋白与冰晶的相互作用强度, 从而降低蛋白的抗冻活性. 但是, 在维系蛋白和冰晶结构匹配的基础上, 疏水基团的增加加强了抗冻蛋白与冰晶的结合, 从而增加蛋白的抗冻活性.     

Growth inhibition at the ice prismatic plane induced by a spruce budworm antifreeze protein: a molecular dynamics simulation study

A molecular dynamics simulation was conducted to investigate the growth kinetics at the ice prismatic interface to which a spruce budworm antifreeze protein was bound. Two initial binding conformations of the protein at the interface--one energetically stable and the other energetically unstable--were examined. For both binding conformations, the growth of ice was observed around the protein. A sharp decrease in the rate of ice growth was observed around the protein that initially had the energetically stable binding conformation. Simulation results suggest that the observed decrease in the ice growth rate was attributable to melting point depression caused by the Gibbs-Thomson effect. The protein that initially had the energetically unstable binding conformation markedly relaxed so as to stably bind to the prismatic plane interface of the grown ice; thereafter, a decrease in the ice growth rate was observed as well. However, the binding conformation that the protein approached during the relaxation was different from that of the protein that initially had the energetically stable binding conformation. Thus, the simulation indicates the existence of two binding conformations for inducing a decrease in the ice growth rate. The results are possibly related to the hyperactivity of a spruce budworm antifreeze protein in real systems.     

Interaction of Antifreeze Proteins with Hydrocarbon Hydrates

Recombinant antifreeze proteins (AFPs), representing a range of activities with respect to ice growth inhibition, were investigated for their abilities to control the crystal formation and growth of hydrocarbon hydrates. Three different AFPs were compared with two synthetic commercial inhibitors, poly‐N‐vinylpyrrolidone (PVP) and HIW85281, by using multiple approaches, which included gas uptake, differential scanning calorimetry (DSC) temperature ramping, and DSC isothermal observations. A new method to assess the induction period before heterogeneous nucleation and subsequent hydrate crystal growth was developed and involved the dispersal of water in the pore space of silica gel beads. Although hydrate nucleation is a complex phenomenon, we have shown that it can now be carefully quantified. The presence of AFPs delayed crystallization events and showed hydrate growth inhibition that was superior to that of one of the benchmark commercial inhibitors, PVP. Nucleation and growth inhibition were shown to be independent processes, which indicates a difference in the mechanisms required for these two inhibitory actions. In addition, there was no apparent correlation between the assayed activities of the three AFPs toward hexagonal ice and the cubic structure II (sII) hydrate, which suggests that there are distinctive differences in the protein interactions with the two crystal surfaces.     

Ice-surface adsorption enhanced colligative effect of antifreeze proteins in ice growth inhibition

This Communication describes a mechanism to explain antifreeze protein's function to inhibit the growth of ice crystals. We propose that the adsorption of antifreeze protein (AFP) molecules on an ice surface induces a dense AFP-water layer, which can significantly decrease the mole fraction of the interfacial water and, thus, lower the temperature for a seed ice crystal to grow in a super-cooled AFP solution. This mechanism can also explain the nearly unchanged melting point for the ice crystal due to the AFP's ice-surface adsorption. A mathematical model combining the Langmuir theory of adsorption and the colligative effect of thermodynamics has been proposed to find the equilibrium constants of the ice-surface adsorptions, and the interfacial concentrations of AFPs through fitting the theoretical curves to the experimental thermal hysteresis data. This model has been demonstrated by using the experimental data of serial size-mutated beetle Tenebrio molitor (Tm) AFPs. It was found that the AFP's ice-surface adsorptions could increase the interfacial AFP's concentrations by 3 to 4 orders compared with those in the bulk AFP solutions.     

Growth inhibition mechanism of an ice-water interface by a mutant of winter flounder antifreeze protein: a molecular dynamics study

Molecular dynamics (MD) simulations of a growing ice-water interface of a pyramidal {2021} plane in the presence of a mutant of winter flounder antifreeze protein (AFP) were conducted. Simulation results indicated that the AFP was partially surrounded by ice grown at the pyramidal interface. The AFP stably bound to the interface only when AFP hydrophobic residues bound to ice. Simulation results also indicated a drastic decrease in the growth velocity of the ice surrounding the stably bound AFP, in agreement with ice growth inhibition processes that have been observed in real systems. We confirmed that the decrease in the growth velocity of ice was attributable to the melting point depression caused by the Gibbs-Thomson effect. Simulation results suggested that the growth of ice surrounding the AFP is needed to promote stable AFP binding to the interface and subsequent ice growth inhibition. MD simulations of a growing ice-water interface of a prismatic {10_10} plane were also conducted. Neither the stable binding of the AFP to the interface nor the decrease in the growth velocity occurred for the prismatic plane. These results agree with the fact that AFPs inhibit the growth of ice only on the pyramidal planes in real systems.     

甘油对冰晶生长抑制作用的分子动力学模拟

采用分子模拟方法研究了正交晶系冰晶(020)生长面在不同浓度甘油水溶液中的生长情况. 通过统计分析氢键数、 密度分布函数、 均方根偏差和原子间径向分布函数研究了水分子和甘油分子的动态行为. 结果表明, 甘油分子在水溶液中可与水分子形成大量氢键, 这使水分子间的氢键作用受到抑制, 降低了水分子的扩散性, 致使冰晶不易成核和生长; 另外, 一些甘油分子可代替水分子吸附在晶面上, 甚至占据晶格位点, 这种行为打破了冰晶的对称性并且降低了冰晶的生长速率. 因此, 甘油可同时在晶面和液相中抑制冰晶的生长.     

Aggregation of antifreeze protein and impact on antifreeze activity

Antifreeze protein type III aggregates once the concentration exceeds a critical value, the so-called critical aggregation concentration (CAC). It was found for the first time that the aggregation of antifreeze protein exerts a direct impact on the antifreeze efficiency. It follows from our measurements that the AFP III above CAC will enhance the antifreeze activity because of the increase of the kink kinetics barrier of surface integration. This is attributed to the optimal packing of AFP III molecules on the surface of the ice nucleus as well as ice crystals above CAC. This study will extend our understanding of the antifreeze mechanism of antifreeze protein monomers as well as antifreeze aggregates on ice nucleation and shed light on the selection of antifreeze agents.     

DSC study and computer modelling of the melting process in ice slurry

In order to understand the non-isothermal melting kinetics in the ice slurry, a differential scanning calorimetry (DSC) was used. Experimental results were compared to those obtained by a numerical simulation in which a general enthalpy method was applied. In this work the ice slurry studied consists of ice particles uniformly dispersed within a water-antifreeze liquid mixture. The effects of the heating rate and the initial antifreeze mass fraction are discussed. It has been found that the temperature gradients inside the sample of the solution become important if either heating rate increases or initial antifreeze mass fraction decreases.     

自由能计算揭示苏氨酸对抗冻蛋白与冰晶结合能力的影响

采用分子动力学模拟和自由能计算研究了中等活性黑麦草抗冻蛋白(Lolium perenne antifreeze protein, LpAFP)冰结合位点(Ice-binding site, IBS)上苏氨酸(Thr)含量对其吸附冰晶能力的影响. 构建了一系列LpAFP突变体结构, 使其IBS上苏氨酸含量逐步增加, 其中包括一个对IBS上11个位点的突变, 使每个β片段均具有Thr-x-Thr基序(x是非保守的氨基酸, 主要是疏水氨基酸). 利用重要性采样算法(WTM-eABF)计算了LpAFP及其突变体与冰晶结合过程的自由能变化, 该算法结合了Well-tempering metadynamics的“填谷”和扩展拉格朗日自适应偏置力方法的“削峰”的优点, 显著提高了算法的采样效率. 结果表明, LpAFP突变体的IBS苏氨酸含量越高, 其与冰的结合在能量上越有利. 当突变体具有重复Thr-x-Thr基序时, 其与冰的结合能力最强. 进一步分析表明, 苏氨酸含量越高, IBS结合的液态水分子越多, 与冰晶结合时锚定包合水稳定存在的时间就越长, 抗冻蛋白的IBS与冰面之间的氢键网络也越稳定, 从而提高了抗冻蛋白与冰的结合能力. 增加苏氨酸残基的含量是提高中等活性抗冻蛋白抗冻活性的方法.     

Burial of gas-phase HNO(3) by growing ice surfaces under tropospheric conditions

The uptake of gas-phase nitric acid by ice surfaces undergoing growth by vapor deposition has been performed for the first time under conditions of the free troposphere. The investigation was performed using a coated-wall flow tube coupled to a chemical ionization mass spectrometer, at nitric acid partial pressures between 10(-7) and 10(-6) hPa, at 214, 229 and 239 K. Ice surfaces were prepared as smooth ice films from ultra-pure water. During the experiments an excess flow of water vapor was added to the carrier gas flow and the existing ice surfaces grew by depositing water vapor. The average growth rates ranged from 0.7-5 microm min(-1), values similar to those which prevail in some portions of the atmosphere. With growing ice the long term uptake of nitric acid is significantly enhanced compared to an experiment performed at equilibrium, i.e. at 100% relative humidity (RH) with respect to ice. The fraction of HNO(3) that is deposited onto the growing ice surface is independent of the growth rate and may be driven by the solubility of the nitric acid in the growing ice film rather than by condensation kinetics alone.     

Influence of Sequential Modifications and Carbohydrate Variations in Synthetic AFGP Analogues on Conformation and Antifreeze Activity

Certain Arctic and Antarctic ectotherm species have developed strategies for survival under low temperature conditions that, among others, consist of antifreeze glycopeptides (AFGP). AFGP form a class of biological antifreeze agents that exhibit the ability to inhibit ice growth in vitro and in vivo and, hence, enable life at temperatures below the freezing point. AFGP usually consist of a varying number of (Ala‐Ala‐Thr)_n units (n=4–55) with the disaccharide β‐D ‐galactosyl‐(1→3)‐α‐N‐acetyl‐D ‐galactosamine glycosidically attached to every threonine side chain hydroxyl group. AFGP have been shown to adopt polyproline II helical conformation. Although this pattern is highly conserved among different species, microheterogeneity concerning the amino acid composition usually occurs; for example, alanine is occasionally replaced by proline in smaller AFGP. The influence of minor and major sequence mutations on conformation and antifreeze activity of AFGP analogues was investigated by replacement of alanine by proline and glycosylated threonine by glycosylated hydroxyproline. The target compounds were prepared by using microwave‐enhanced solid phase peptide synthesis. Furthermore, artificial analogues were obtained by copper‐catalyzed azide–alkyne cycloaddition (CuAAC): propargyl glycosides were treated with polyproline helix II‐forming peptides comprising (Pro‐Azp‐Pro)_n units (n=2–4) that contained 4‐azidoproline (Azp). The conformations of all analogues were examined by circular dichroism (CD). In addition, microphysical analysis was performed to provide information on their inhibitory effect on ice recrystallization.