Molecular Factors of Ice Growth Inhibition for Hyperactive and Globular Antifreeze Proteins: Insights from Molecular Dynamics Simulation

Head-to-Tail Cyclization Enhances Ice-Growth Inhibition by Linear Threonine Oligomers

Developing short antifreeze peptides with low immunogenicity is considered to be a promising strategy for improving cryopreservation. Inspired by the design principles of cyclic peptide drugs characterized by high stability and strong affinity, we propose to use the cyclization strategy as a principle for the design of antifreeze peptides, aiming to enhance their structural stability and ice-binding ability, thereby significantly improving their antifreeze activity. In this study, we choose linear threonine oligomers (L-(Thr)n), composed of common and biocompatible threonine residues, to investigate the mechanism and efficacy of cyclization. Molecular dynamics (MD) simulations are used to compare the ice-growth inhibition ability of a series of linear oligomers and their corresponding cyclic counterparts (49 molecular systems) on different ice planes, resulting in 80.8 μs MD trajectories. A detailed analysis of conformational changes during inhibition and their correlation with inhibitory efficiency reveals that conformational variability is detrimental to the binding of L-(Thr)n to ice, while β-sheet-like conformation has a significant advantage in inhibiting ice growth and is identified as a key factor for the superior performance of cyclized oligomers (C-(Thr)n) over their linear counterparts. Encouragingly, we find that C-(Thr)12 exhibits the most prominent performance, surpassing previously reported cyclic peptides of similar size due to its enhanced structural stability, superior ice binding, coverage, and antiengulfment capabilities. This study provides valuable insights into the design of small-sized ice-growth inhibitors through head-to-tail cyclization of linear oligomers. However, it should be noted that our findings are based purely on computational simulations, and experimental validation in actual cryopreservation conditions remains necessary.

Cooperative Role of Conformation and Ice-Binding Groups in Ice Growth Inhibition of Antifreeze Glycoproteins

The antifreeze mechanism of antifreeze glycoproteins (AFGPs) remains incompletely understood, which limits the design of new antifreeze molecules for practical applications. For instance, the ice growth inhibition of AFGP8 (the shortest AFGPs) is primarily driven by hydrophobic methyl and hydrogen-bonding hydroxyl groups. However, altering the C3-β linkage in the disaccharide moiety of AFGP8, denoted as variant GP8-LacNAc, significantly reduces its antifreeze activity. This challenges the conventional understanding of the antifreeze activity of AFGP8 because no group is removed. Here, we revisit the antifreeze mechanism using molecular dynamics simulations of two AFGPs as an example, revealing the relation between conformation, ice-binding group, and ice growth inhibition activity. The PPII helix is not the reason for the weak activity of GP8-LacNAc, while the cooperativity of the conformation and group matters. AFGP8 maintains a dominant conformation with all four disaccharides on the same side, which maximizes the binding with ice. While GP8-LacNAc undergoes frequent conformational transitions, leading to a methyl-hydroxyl distance mismatch with the ice surface. Our results reveal the cooperative role of conformation and ice-binding groups, providing new insights into the antifreeze mechanism of flexible proteins.

Development of Macromolecular Cryoprotectants for Cryopreservation of Cells

Cryopreservation is a common way for long-term storage of therapeutical proteins, erythrocytes, and mammalian cells. For cryoprotection of these biosamples to keep their structural integrity and biological activities, it is essential to incorporate highly efficient cryoprotectants. Currently, permeable small molecular cryoprotectants such as glycerol and dimethyl sulfoxide dominate in cryostorage applications, but they are harmful to cells and human health. As acting in the extracellular space, membrane-impermeable macromolecular cryoprotectants, which exert remarkable membrane stabilization against cryo-injury and are easily removed post-thaw, are promising candidates with biocompatibility and feasibility. Water-soluble hydroxyl-containing polymers such as poly(vinyl alcohol) and polyol-based polymers are potent ice recrystallization inhibitors, while polyampholytes, polyzwitterions, and bio-inspired (glyco)polypeptides can significantly increase post-thaw recovery with reduced membrane damages. In this review, the synthetic macromolecular cryoprotectants are systematically summarized based on their synthesis routes, practical utilities, and cryoprotective mechanisms. It provides a valuable insight in development of highly efficient macromolecular cryoprotectants with valid ice recrystallization inhibition activity for highly efficient and safe cryopreservation of cells.

Antifreeze Polysaccharides from Wheat Bran: The Structural Characterization and Antifreeze Mechanism

Exploring a novel natural cryoprotectant and understanding its antifreeze mechanism allows the rational design of future sustainable antifreeze analogues. In this study, various antifreeze polysaccharides were isolated from wheat bran, and the antifreeze activity was comparatively studied in relation to the molecular structure. The antifreeze mechanism was further revealed based on the interactions of polysaccharides and water molecules through dynamic simulation analysis. The antifreeze polysaccharides showed distinct ice recrystallization inhibition activity, and structural analysis suggested that the polysaccharides were arabinoxylan, featuring a xylan backbone with a majority of Araf and minor fractions of Manp, Galp, and Glcp involved in the side chain. The antifreeze arabinoxylan, characterized by lower molecular weight, less branching, and more flexible conformation, could weaken the hydrogen bonding of the surrounding water molecules more evidently, thus retarding the transformation of water molecules into the ordered ice structure.

On the engulfment of antifreeze proteins by ice

Antifreeze proteins (AFPs) are remarkable biomolecules that suppress ice formation at trace concentrations. To inhibit ice growth, AFPs must not only bind to ice crystals, but also resist engulfment by ice. The highest supercooling, [Formula: see text], for which AFPs are able to resist engulfment is widely believed to scale as the inverse of the separation, [Formula: see text], between bound AFPs, whereas its dependence on the molecular characteristics of the AFP remains poorly understood. By using specialized molecular simulations and interfacial thermodynamics, here, we show that in contrast with conventional wisdom, [Formula: see text] scales as [Formula: see text] and not as [Formula: see text]. We further show that [Formula: see text] is proportional to AFP size and that diverse naturally occurring AFPs are optimal at resisting engulfment by ice. By facilitating the development of AFP structure-function relationships, we hope that our findings will pave the way for the rational design of AFPs.

Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice

Using molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water, which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation and distance relative to the surface of ice, which enables the effective binding (via hydrogen bonds) of the molecule with the nascent ice surface. Our results show that the final adsorption of the AFP III molecule on the surface of ice is not achieved by chaotic diffusion movements, but it is preceded by a remote, water-mediated interaction between the IBS and the surface of ice. The key factor that determines the existence of this interaction is the ability of water molecules to spontaneously form large, high-volume aggregates that can be anchored to both the IBS of the AFP molecule and the surface of ice. The results presented in this work for AFP III are in full agreement with the ones obtained by us previously for hyperactive CfAFP, which indicates that the mechanism of the remote interaction of these molecules with ice remains unchanged despite significant differences in the molecular structure of their ice binding sites. For that reason, we can expect that also other types of AFPs interact with the ice surface according to an analogous mechanism.

Molecular dynamics simulation as a promising approach for computational study of liquid crystal-based aptasensors

As a potent computational methodology, molecular dynamics (MD) simulation provides advantageous knowledge about biological compounds from the molecular viewpoint. In particular, MD simulation gives exact information about aptamer strands, such as the short synthetic oligomers, their orientation, binding sites, folding-unfolding state, and conformational re-arrangement. Also, the effect of the different chemicals and biochemicals as the components of aptamer-based sensors (aptasensors) on the aptamer-target interaction can be investigated by MD simulation. Liquid crystals (LCs) as soft substances with characteristics of both solid anisotropy and liquid fluidity are new candidates for designing label-free aptasensors. To now, diverse aptasensors have been developed experimentally based on the optical anisotropy, fluidity, and long-range orientational order of LCs. Here, we represent a computational model of an LC-based aptasensor through a detailed MD simulation study. The different parameters are defined and studied to achieve a comprehensive understanding of the computational design of the LC-based aptasensor, including the density of LCs, their orientation angle, and lognormal distribution in the absence and presence of aptamer strands, both aptamer and target molecules with various concentrations, and interfering substance. As a case study, the tobramycin antibiotic is considered the target molecule for the computational model of the LC-based aptasensor.

Self-Assembled Nanostructures of Homo-Oligopeptide as a Potent Ice Growth Inhibitor

This study reports the formation of self-assembled nanostructures with homo-oligopeptides consisting of amino acids (i.e., alanine, threonine, valine, and tyrosine), the resulting morphologies (i.e., spherical shape, layered structure, and wire structure) in aqueous solution, and their potential as ice growth inhibitors. Among the homo-oligopeptides investigated, an alanine homo-oligopeptide (n = 5) with a spherical nanostructure showed the highest ice recrystallization inhibition (IRI) activity without showing a burst ice growth property and with low ice nucleation activity. The presence of nanoscale self-assembled structures in the solution showed superior IRI activity compared to an amino acid monomer because of the higher binding affinity of structures on the growing ice crystal plane. Simulation results revealed that the presence of nanostructures induced a significant inhibition of ice growth and increased lifetime of hydrogen bonding compared with unassembled homo-oligopeptide. These results envision extraordinary performance for self-assembled nanostructures as a desirable and potent ice growth inhibitor.

Preferential Ordering and Organization of Hydration Water Favor Nucleation of Ice by Ice-Nucleating Proteins over Antifreeze Proteins

Bacteria containing ice-nucleating proteins (INPs) evolved in nature to nucleate ice at the high sub-zero ambiance. The ability of the INPs to induce order in the hydration layer and their aggregation propensity appear to be key factors of their ice nucleation abilities. However, the mechanism of the process of ice nucleation by INPs is yet to be understood clearly. Here, we have performed all-atom molecular dynamics simulations and analyzed the structure and dynamics of the hydration layer around the proposed ice-nucleating surface of a model INP. Results are compared with the hydration of a topologically similar non-ice-binding protein (non-IBP) and another ice-growth inhibitory antifreeze protein (sbwAFP). We observed that the hydration structure around the ice-nucleating surface of INP is highly ordered and the dynamics of the hydration water are slower, compared to the non-IBP. Even the ordering of the hydration layer is more evident around the ice-binding surface of INP, compared to the antifreeze protein sbwAFP. Particularly with increasing repeat units of INP, we observe an increased population of ice-like water. Interestingly, the distances between the hydroxyl groups of the threonine ladder and its associated channel water of the ice-binding surface (IBS) of INP in the X and Y direction mimic the oxygen atom distances of the basal plane of hexagonal ice. However, the structural synergies between the hydroxyl group distances of the threonine ladder and its associated channel water of the IBS of sbwAFP and oxygen atom distances of the basal plane are less evident. This difference makes the IBS of the INP a better template for ice nucleation than AFP, although both of them bind to the ice surface efficiently.

Engulfment Avalanches and Thermal Hysteresis for Antifreeze Proteins on Supercooled Ice

Antifreeze proteins (AFPs) bind to the ice-water surface and prevent ice growth at temperatures below 0 °C through a Gibbs-Thomson effect. Each adsorbed AFP creates a metastable depression on the surface that locally resists ice growth, until ice engulfs the AFP. We recently predicted the susceptibility to engulfment as a function of AFP size, distance between AFPs, and supercooling [ J. Chem. Phys. 2023, 158, 094501]. For an ensemble of AFPs adsorbed on the ice surface, the most isolated AFPs are the most susceptible, and when an isolated AFP gets engulfed, its former neighbors become more isolated and more susceptible to engulfment. Thus, an initial engulfment event can trigger an avalanche of subsequent engulfment events, leading to a sudden surge of unrestrained ice growth. This work develops a model to predict the supercooling at which the first engulfment event will occur for an ensemble of randomly distributed AFP pinning sites on an ice surface. Specifically, we formulate an inhomogeneous survival probability that accounts for the AFP coverage, the distribution of AFP neighbor distances, the resulting ensemble of engulfment rates, the ice surface area, and the cooling rate. We use the model to predict thermal hysteresis trends and compare with experimental data.