Identifying Ice-Binding Proteins in Nature

Organisms inhabiting freezing terrestrial, polar, and alpine environments survive because they have evolved adaptations to tolerate sub-freezing temperatures. Among these adaptations are ice-binding proteins (IBPs) which in the case of fishes and some insects have antifreeze properties which allow them to avoid freezing even at their lowest environmental temperatures. Other organisms, including some insects, microorganisms, and plants, tolerate freezing and also contain IBPs. Unlike fish and insects, their antifreeze properties (hysteresis) are minimal, but most are potent ice recrystallization inhibitors (IRIs). Microbes secrete IBPs into their immediate environment where they are thought to modify ice growth in a way that ensures a liquidous habitat in the ice and also reduces ice recrystallization. With plants, IBPs are found in the small amount of apoplastic fluid associated with the extracellular spaces and show a weak hysteresis but are potent IRIs.Techniques are described for drawing blood and hemolymph from fish and insects, respectively, in order to determine whether there is a hysteresis present (separation of the freezing and melting points) indicative of an antifreeze protein. For microbes, which secrete very small amounts of IBPs into their environment, a technique is described where their spent growth media causes the pitting of the basal plane of an ice crystal at a temperature slightly below the media freezing point. In plants, IBPs are isolated from the apoplastic fluids of the leaves by vacuum infiltration of a fluid into the extracellular spaces and then recovering the fluid by centrifugation.The pitting of the basal plane again can be used to verify the presence of IBPs in the concentrated apoplastic fluid.The techniques describe how to collect fluids from a variety of organisms to determine if IBPs are present using nanoliter osmometry or using the ice basal plane pitting technique.

Multiscale Molecular Dynamics Simulations of Ice-Binding Proteins

Ice-binding proteins (IBPs) are a diverse class of proteins that are essential for the survival of organisms in cold conditions. IBPs are diverse in their function and can prevent or promote ice growth and selectively bind to specific crystallographic planes of the growing ice lattice. Moreover, IBPs are widely utilized to modulate ice crystal growth and recrystallization in the food industry and as cryoprotectants to preserve biological matter. A key unresolved aspect of the mode of action is how the ice-binding sites of these proteins distinguish between ice and water and interact with multiple crystal facets of the ice. The use of molecular dynamics (MD) simulation allows us to thoroughly investigate the binding mechanism and energetics of ice-binding proteins, to complement and expand on the mechanistic understandings gained from experiments. In this chapter, we describe a series of molecular dynamics simulation methodologies to investigate the mechanism of action of ice-binding proteins. Specifically, we provide detailed instructions to set up MD simulations to study the binding and interaction of ice-binding proteins using atomistic and coarse-grained simulations.

Investigating the Interaction Between Ice-Binding Proteins and Ice Surfaces Using Microfluidic Devices and Cold Stages

Ice-binding proteins (IBPs) protect organisms living in sub-freezing conditions by inhibiting ice growth in fish and insects, limiting ice recrystallization in plants, and assisting bacteria to adhere to ice. The mechanisms by which these proteins bind to ice and inhibit its growth have been studied both experimentally and using molecular dynamic simulations. A unique experimental technique developed to test and characterize the interactions between IBPs and ice using a combination of a microfluidic device, cold stages with millikelvin temperature resolution, fluorescence-labeled IBPs, and fluorescence microscopy is described herein. The main advantage of this technique is the ability to exchange the solution around micron-sized ice crystals and characterize their binding to and inhibition of ice.

Ice Isn't the Only Crystal in Town: Structure Determination of Ice-Binding Proteins via X-Ray Crystallography

Ice-binding proteins (IBPs) are proteins that have the remarkable ability to bind to ice, and their study has intrigued researchers for decades. This chapter explores the importance of structural biology in understanding IBPs and highlights the significant contributions of IBPs to the field of structural biology. The structures of various IBPs from different organisms have been elucidated, revealing key elements involved in ice binding. Structural biology techniques, including nuclear magnetic resonance (NMR) spectroscopy, transmission electron cryo-microscopy (cryo-EM), and X-ray crystallography, play crucial roles in solving protein structures. This article focuses on X-ray crystallography as a tool for investigating IBP structures, providing insights into its theoretical and practical aspects, experimental workflows, and common pitfalls to avoid.

The Nanoliter Osmometer: Thermal Hysteresis Measurement

The nanoliter osmometer is one of the most common tools in the study of ice-binding proteins (IBPs). It is used not only to measure the thermal hysteresis activity of IBPs but also to explore ice shaping, ice adhesion, and ice growth and melting rates and patterns. The advantage of the nanoliter osmometer for the IBP study and for studying single ice crystals lies in the small sample volume, in the range of nanoliters. Such a small volume enables precise determination and control of the temperature with precision in the range of millidegrees. This chapter describes in detail the process of determination of thermal hysteresis using a nanoliter osmometer operated by a LabVIEW interface. We describe the preparation of suitable capillaries and sample injection, which is a challenging step in the measurement. We then describe the procedure of single crystal formation and the determination of the melting and freezing temperatures. Insights on crucial parameters are emphasized.

Measurement of Ice-Binding Protein Inhibition of Non-ice Crystal Growth

The kinetic hydrate inhibitor (KHI) was developed to prevent the formation of undesirable gas hydrate crystals in natural gas pipelines. Studies of antifreeze proteins (AFPs) are gaining attention in the natural gas research field due to their performance in crystal growth inhibition, excellent biodegradation, and low toxicity. Studies of AFPs may provide clues for developing future commercial KHIs used offshore. This chapter presents a simple method of evaluating AFP inhibitory performance as a KHI on tetrahydrofuran (THF) hydrate growth with a unidirectional growth apparatus.

Antifreeze proteins for low-temperature preservation in reproductive medicine: A systematic review over the last three decades

Antifreeze proteins (AFPs) are synthesized by diverse non-mammalian species, allowing them to survive in severely cold environments. Since the 1990s, the scientific literature reports their use for low-temperature preservation of germplasm. The aim of this systematic review was to compile available scientific evidence regarding the use of AFP for low-temperature preservation of several reproductive specimens. Internet databases were consulted using the terms: "antifreeze protein" OR "AFP" OR "antifreeze glycoprotein" OR "AFGP" OR "ice-binding protein" OR "IBP" OR "thermal hysteresis protein" AND "cryopreservation". From 56 articles, 87 experiments testing AFPs in low-temperature preservation of gametes, embryos or reproductive tissues/cells were fully analyzed and outcomes were annotated. A positive outcome was considered as a statistically significant improvement on any parameter evaluated after low-temperature preservation with AFP, whereas a negative outcome included worsening of any evaluated parameter, in comparison to untreated groups or groups treated with a lower concentration of AFP. The findings indicated that research on the use of AFP as a cryoprotectant for reproductive specimens has increased markedly over the past decade. Some experiments reported both positive and negative results, which depended, on AFP concentration in the preservation media. Variation in the outcomes associated with species was also observed. Among the 66 experiments conducted in mammals, 77.3% resulted in positive, and 28.8% in negative outcomes after the use of AFP. In fishes, positive and negative outcomes were observed in 71.4% and 33.3% of 21 experiments, respectively. Most positive outcomes included preserving cell post-warming survival. The beneficial effect of AFP supports its use in cryobiological approaches used in human and veterinary medicines and animal protein industry. Moreover, combination of different AFP types, or AFP with antioxidants, or even the use of AFP-biosimilar, comprise some promising approaches to be further explored in cryopreservation.

Effect of pH on the activity of ice-binding protein from Marinomonas primoryensis

The ability of an ice-binding protein (IBP) from Marinomonas primoryensis (MpIBP) to influence ice crystal growth and structure in nonphysiological pH environments was investigated in this work. The ability for MpIBP to retain ice interactivity under stressed environmental conditions was determined via (1) a modified splat assay to determine ice recrystallization inhibition (IRI) of polycrystalline ice and (2) nanoliter osmometry to evaluate the ability of MpIBP to dynamically shape the morphology of a single ice crystal. Circular dichroism (CD) was used to relate the IRI and DIS activity of MpIBP to secondary structure. The results illustrate that MpIBP secondary structure was stable between pH 6 and pH 10. It was found that MpIBP did not interact with ice at pH ≤ 4 or pH ≥ 13. At 6 ≤ pH ≥ 12 MpIBP exhibited a reduction in grain size of ice crystals as compared to control solutions and demonstrated dynamic ice shaping at 6 ≤ pH ≥ 10. The results substantiate that MpIBP retains some secondary structure and function in non-neutral pH environments; thereby, enabling its potential utility in nonphysiological materials science and engineering applications.

Characterization of Ice-Binding Proteins from Sea-Ice Microalgae

Several species of polar microalgae are able to live and thrive in the extreme environment found within sea ice, where ice crystals may reduce the organisms' living space and cause mechanical damage to the cells. Among the strategies adopted by these organisms to cope with the harsh conditions in their environment, ice-binding proteins (IBPs) seem to play a key role and possibly contribute to the success of microalgae in sea ice. Indeed, IBPs from microalgae predominantly belong to the so-called "DUF 3494-IBP" family, which today represents the most widespread IBP family. Since IBPs have the ability to control ice crystal growth, their mechanism of function is of interest for many potential applications. Here, we describe methods for a classical determination of the IBP activity (thermal hysteresis, recrystallization inhibition) and further methods for protein activity characterization (ice pitting assay, determination of the nucleating temperature).