Solution structure of a hydrophobic analogue of the winter flounder antifreeze protein

Symmetrization in the Calculation Pipeline of Gauss Function-Based Modeling of Hydrophobicity in Protein Structures

In this paper, we show, discuss, and compare the effects of symmetrization in two calculation subroutines of the Fuzzy Oil Drop model, a coarse-grained model of density of hydrophobicity in proteins. In the FOD model, an input structure is enclosed in an axis-aligned ellipsoid called a drop. Two profiles of hydrophobicity are then calculated for its residues: theoretical (based on the 3D Gauss function) and observed (based on pairwise hydrophobic interactions). Condition of the hydrophobic core is revealed by comparing those profiles through relative entropy, while analysis of their local differences allows, in particular, determination of the starting location for the search for protein–protein and protein–ligand interaction areas. Here, we improve the baseline workflow of the FOD model by introducing symmetry to the hydrophobicity profile comparison and ellipsoid bounding procedures. In the first modification (FOD–JS), Kullback–Leibler divergence is enhanced with its Jensen–Shannon variant. In the second modification (FOD-PCA), the molecule is optimally aligned with the axes of the coordinate system via principal component analysis, and the size of its drop is determined by the standard deviation of all its effective atoms, making it less susceptible to structural outliers. Tests on several molecules with various shapes and functions confirm that the proposed modifications improve the accuracy, robustness, speed, and usability of Gauss function-based modeling of the density of hydrophobicity in protein structures.

Antiviral Peptides (AVPs) of Marine Origin as Propitious Therapeutic Drug Candidates for the Treatment of Human Viruses

The marine environment presents a favorable avenue for potential therapeutic agents as a reservoir of new bioactive natural products. Due to their numerous potential pharmacological effects, marine-derived natural products—particularly marine peptides—have gained considerable attention. These peptides have shown a broad spectrum of biological functions, such as antimicrobial, antiviral, cytotoxic, immunomodulatory, and analgesic effects. The emergence of new virus strains and viral resistance leads to continuing efforts to develop more effective antiviral drugs. Interestingly, antimicrobial peptides (AMPs) that possess antiviral properties and are alternatively regarded as antiviral peptides (AVPs) demonstrate vast potential as alternative peptide-based drug candidates available for viral infection treatments. Hence, AVPs obtained from various marine organisms have been evaluated. This brief review features recent updates of marine-derived AVPs from 2011 to 2021. Moreover, the biosynthesis of this class of compounds and their possible mechanisms of action are also discussed. Selected peptides from various marine organisms possessing antiviral activities against important human viruses—such as human immunodeficiency viruses, herpes simplex viruses, influenza viruses, hepatitis C virus, and coronaviruses—are highlighted herein.

APPTEST is a novel protocol for the automatic prediction of peptide tertiary structures

Good knowledge of a peptide's tertiary structure is important for understanding its function and its interactions with its biological targets. APPTEST is a novel computational protocol that employs a neural network architecture and simulated annealing methods for the prediction of peptide tertiary structure from the primary sequence. APPTEST works for both linear and cyclic peptides of 5-40 natural amino acids. APPTEST is computationally efficient, returning predicted structures within a number of minutes. APPTEST performance was evaluated on a set of 356 test peptides; the best structure predicted for each peptide deviated by an average of 1.9Å from its experimentally determined backbone conformation, and a native or near-native structure was predicted for 97% of the target sequences. A comparison of APPTEST performance with PEP-FOLD, PEPstrMOD and PepLook across benchmark datasets of short, long and cyclic peptides shows that on average APPTEST produces structures more native than the existing methods in all three categories. This innovative, cutting-edge peptide structure prediction method is available as an online web server at https://research.timmons.eu/apptest, facilitating in silico study and design of peptides by the wider research community.

Ice-binding proteins: a remarkable ice crystal regulator for frozen foods

Ice crystal growth during cold storage presents a quality problem in frozen foods. The development of appropriate technical conditions and ingredient formulations is an effective method for frozen food manufacturers to inhibit ice crystals generated during storage and distribution. Ice-binding proteins (IBPs) have great application potential as ice crystal growth inhibitors. The ability of IBPs to retard the growth of ice crystals suggests that IBPs can be used as a natural ice conditioner for a variety of frozen products. In this review, we first discussed the damage caused by ice crystals in frozen foods during freezing and frozen storage. Next, the methods and technologies for production, purification and evaluation of IBPs were summarized. Importantly, the present review focused on the characteristics, structural diversity and mechanisms of IBPs, and the application advances of IBPs in food industry. Finally, the challenges and future perspectives of IBPs are also discussed. This review may provide a better understanding of IBPs and their applications in frozen products, providing some valuable information for further research and application of IBPs.

Why do antifreeze proteins require a solenoid?

Proteins whose presence prevents water from freezing in living organisms at temperatures below 0 °C are referred to as antifreeze proteins. This group includes molecules of varying size (from 30 to over 300 aa) and variable secondary/supersecondary conformation. Some of these proteins also contain peculiar structural motifs called solenoids. We have applied the fuzzy oil drop model in the analysis of four categories of antifreeze proteins: 1 - very small proteins, i.e. helical peptides (below 40 aa); 2 - small globular proteins (40-100 aa); 3 - large globular proteins (>100 aa) and 4 - proteins containing solenoids. The FOD model suggests a mechanism by which antifreeze proteins prevent freezing. In accordance with this theory, the presence of the protein itself produces an ordering of water molecules which counteracts the formation of ice crystals. This conclusion is supported by analysis of the ordering of hydrophobic and hydrophilic residues in antifreeze proteins, revealing significant variability - from perfect adherence to the fuzzy oil drop model through structures which lack a clearly defined hydrophobic core, all the way to linear arrangement of alternating local minima and maxima propagating along the principal axis of the solenoid (much like in amyloids). The presented model - alternative with respect to the ice docking model - explains the antifreeze properties of compounds such as saccharides and fatty acids. The fuzzy oil drop model also enables differentiation between amyloids and antifreeze proteins.

Balance between hydration enthalpy and entropy is important for ice binding surfaces in Antifreeze Proteins

Antifreeze Proteins (AFPs) inhibit the growth of an ice crystal by binding to it. The detailed binding mechanism is, however, still not fully understood. We investigated three AFPs using Molecular Dynamics simulations in combination with Grid Inhomogeneous Solvation Theory, exploring their hydration thermodynamics. The observed enthalpic and entropic differences between the ice-binding sites and the inactive surface reveal key properties essential for proteins in order to bind ice: While entropic contributions are similar for all sites, the enthalpic gain for all ice-binding sites is lower than for the rest of the protein surface. In contrast to most of the recently published studies, our analyses show that enthalpic interactions are as important as an ice-like pre-ordering. Based on these observations, we propose a new, thermodynamically more refined mechanism of the ice recognition process showing that the appropriate balance between entropy and enthalpy facilitates ice-binding of proteins. Especially, high enthalpic interactions between the protein surface and water can hinder the ice-binding activity.

Antifreeze peptides and glycopeptides, and their derivatives: potential uses in biotechnology

Antifreeze proteins (AFPs) and glycoproteins (AFGPs), collectively called AF(G)Ps, constitute a diverse class of proteins found in various Arctic and Antarctic fish, as well as in amphibians, plants, and insects. These compounds possess the ability to inhibit the formation of ice and are therefore essential to the survival of many marine teleost fishes that routinely encounter sub-zero temperatures. Owing to this property, AF(G)Ps have potential applications in many areas such as storage of cells or tissues at low temperature, ice slurries for refrigeration systems, and food storage. In contrast to AFGPs, which are composed of repeated tripeptide units (Ala-Ala-Thr)_n with minor sequence variations, AFPs possess very different primary, secondary, and tertiary structures. The isolation and purification of AFGPs is laborious, costly, and often results in mixtures, making characterization difficult. Recent structural investigations into the mechanism by which linear and cyclic AFGPs inhibit ice crystallization have led to significant progress toward the synthesis and assessment of several synthetic mimics of AFGPs. This review article will summarize synthetic AFGP mimics as well as current challenges in designing compounds capable of mimicking AFGPs. It will also cover our recent efforts in exploring whether peptoid mimics can serve as structural and functional mimics of native AFGPs.

NOT THAT RIGID MIDGETS AND NOT SO FLEXIBLE GIANTS: ON THE ABUNDANCE AND ROLES OF INTRINSIC DISORDER IN SHORT AND LONG PROTEINS

Intrinsically disordered proteins or proteins with disordered regions are very common in nature. These proteins have numerous biological functions which are complementary to the biological activities of traditional ordered proteins. A noticeable difference in the amino acid sequences encoding long and short disordered regions was found and this difference was used in the development of length-dependent predictors of intrinsic disorder. In this study, we analyze the scaling of intrinsic disorder in eukaryotic proteins and investigate the presence of length-dependent functions attributed to proteins containing long disordered regions.

Solution structures, dynamics, and ice growth inhibitory activity of peptide fragments derived from an antarctic yeast protein

Exotic functions of antifreeze proteins (AFP) and antifreeze glycopeptides (AFGP) have recently been attracted with much interest to develop them as commercial products. AFPs and AFGPs inhibit ice crystal growth by lowering the water freezing point without changing the water melting point. Our group isolated the Antarctic yeast Glaciozyma antarctica that expresses antifreeze protein to assist it in its survival mechanism at sub-zero temperatures. The protein is unique and novel, indicated by its low sequence homology compared to those of other AFPs. We explore the structure-function relationship of G. antarctica AFP using various approaches ranging from protein structure prediction, peptide design and antifreeze activity assays, nuclear magnetic resonance (NMR) studies and molecular dynamics simulation. The predicted secondary structure of G. antarctica AFP shows several α-helices, assumed to be responsible for its antifreeze activity. We designed several peptide fragments derived from the amino acid sequences of α-helical regions of the parent AFP and they also showed substantial antifreeze activities, below that of the original AFP. The relationship between peptide structure and activity was explored by NMR spectroscopy and molecular dynamics simulation. NMR results show that the antifreeze activity of the peptides correlates with their helicity and geometrical straightforwardness. Furthermore, molecular dynamics simulation also suggests that the activity of the designed peptides can be explained in terms of the structural rigidity/flexibility, i.e., the most active peptide demonstrates higher structural stability, lower flexibility than that of the other peptides with lower activities, and of lower rigidity. This report represents the first detailed report of downsizing a yeast AFP into its peptide fragments with measurable antifreeze activities.

Structural and functional characterization of a multifunctional alanine-rich peptide analogue from Pleuronectes americanus

Recently, defense peptides that are able to act against several targets have been characterized. The present work focuses on structural and functional evaluation of the peptide analogue Pa-MAP, previously isolated as an antifreeze peptide from Pleuronectes americanus. Pa-MAP showed activities against different targets such as tumoral cells in culture (CACO-2, MCF-7 and HCT-116), bacteria (Escherichia coli ATCC 8739 and Staphylococcus aureus ATCC 25923), viruses (HSV-1 and HSV-2) and fungi (Candida parapsilosis ATCC 22019, Trichophyton mentagrophytes (28d&E) and T. rubrum (327)). This peptide did not show toxicity against mammalian cells such as erythrocytes, Vero and RAW 264.7 cells. Molecular mechanism of action was related to hydrophobic residues, since only the terminal amino group is charged at pH 7 as confirmed by potentiometric titration. In order to shed some light on its structure-function relations, in vitro and in silico assays were carried out using circular dichroism and molecular dynamics. Furthermore, Pa-MAP showed partial unfolding of the peptide changes in a wide pH (3 to 11) and temperature (25 to 95°C) ranges, although it might not reach complete unfolding at 95°C, suggesting a high conformational stability. This peptide also showed a conformational transition with a partial α-helical fold in water and a full α-helical core in SDS and TFE environments. These results were corroborated by spectral data measured at 222 nm and by 50 ns dynamic simulation. In conclusion, data reported here show that Pa-MAP is a potential candidate for drug design against pathogenic microorganisms due to its structural stability and wide activity against a range of targets.

Two domains of RD3 antifreeze protein diffuse independently

Antifreeze proteins (AFPs) make up a class of structurally diverse proteins that help to protect many organisms from freezing temperatures by inhibiting ice crystal growth at temperatures below the colligative freezing point. AFPs are typically small proteins with a relatively flat, slightly hydrophobic binding region that matches the lattice structure of a specific ice crystal plane. The only known two-domain AFP is RD3 from the Antarctic eel pout. It consists of two nearly identical type III domains connected by a nine-residue linker. This protein exhibits higher activity than the single-domain protein at low concentrations. The initial solution structure of RD3 revealed that the domains were aligned so that the binding regions were nearly coplanar, effectively doubling the surface area for binding. A more recent report suggests that the domains may not be aligned in solution but rather diffuse independently. To resolve the issue, we have measured the NMR residual dipolar couplings using alignment media of stretched gels and filamentous phage to determine the relative orientation of the domains. We find that the two domains of RD3 are free to move relative to each other, within the constraint of the flexible nine-residue linker. Our data show that there is no strongly preferred alignment in solution. Furthermore, the flexibility and length of the linker are sufficient to allow the two domains to have their binding faces in the same orientation and coplanar for simultaneous binding to an ice crystal surface.

Design and synthesis of alpha-helical peptides and mimetics

The alpha-helix is the most abundant secondary structural element in proteins and is an important structural domain for mediating protein-protein and protein-nucleic acid interactions. Strategies for the rational design and synthesis of alpha-helix mimetics have not matured as well as other secondary structure mimetics such as strands and turns. This perspective will focus on developments in the design, synthesis and applications of alpha-helices and mimetics, particularly in the last 5 years. Examples where synthetic compounds have delivered promising biological results will be highlighted as well as opportunities for the design of mimetics of the type I alpha-helical antifreeze proteins.

Antifreeze proteins at the ice/water interface: three calculated discriminating properties for orientation of type I proteins

Antifreeze proteins (AFPs) protect many plants and organisms from freezing in low temperatures. Of the different AFPs, the most studied AFP Type I from winter flounder is used in the current computational studies to gain molecular insight into its adsorption at the ice/water interface. Employing molecular dynamics simulations, we calculate the free energy difference between the hydrophilic and hydrophobic faces of the protein interacting with ice. Furthermore, we identify three properties of Type I "antifreeze" proteins that discriminate among these two orientations of the protein at the ice/water interface. The three properties are: the "surface area" of the protein; a measure of the interaction of the protein with neighboring water molecules as determined by the number of hydrogen bond count, for example; and the side-chain orientation angles of the threonine residues. All three discriminants are consistent with our free energy results, which clearly show that the hydrophilic protein face orientations toward the ice/water interface, as hypothesized from experimental and ice/vacuum simulations, are incorrect and support the hypothesis that the hydrophobic face is oriented toward the ice/water interface. The adsorption free energy is calculated to be 2-3 kJ/mol.