Underused Marine Resources: Sudden Properties of Cod Skin Gelatin Gel.

The main object of this work was to characterize the structure and properties of laboratory-made fish gelatin from cod skin in comparison with known commercial gelatins of fish and mammalian origin. This is one way we can contribute to the World Food Program and characterize foodstuff resources from alternative natural sources. Our research was based on the combination of an expanded set of complementary physical-chemical methods to study the similarities and distinctions of hydrogels from traditional and novel gelatin sources from underused marine resources. In this work, we have compared the morphology, supramolecular structure and colloid properties of two commercial (mammalian and fish) gelatins with gelatin we extracted from cold-water cod skin in laboratory conditions. The obtained results are novel, showing that our laboratory-produced fish gelatin is much closer to the mammalian one in terms of such parameters as thermal stability and strength of structural network under temperature alterations. Especially interesting are our experimental observations comparing both fish gelatins: it was shown that the laboratory-extracted cod gelatin is essentially more thermally stable compared to its commercial analogue, being even closer in its rheological properties to the mammalian one.

Protein translational diffusion as a way to detect intermolecular interactions.

In this work, we analyze the information on the protein intermolecular interactions obtained from macromolecular diffusion. We have shown that the most hopeful results are given by our approach based on analysis of protein translational self-diffusion and collective diffusion obtained by dynamic light scattering and pulsed-field gradient NMR (PFG NMR) spectroscopy with the help of Vink's approach to analyze diffusion motion of particles by frictional formalism of non-equilibrium thermodynamics and the usage of the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of colloid particles interactions in electrolyte solutions. Early we have shown that integration of Vink's theory with DLVO provides a reliable basis for uniform interpreting of PFG NMR and DLS experiments on concentration dependence of diffusion coefficients. Basic details of theoretical and mathematical procedures and a broad analysis of experimental attestation of proposed conception on proteins of various structural form, size, and shape are presented. In the present review, the main capabilities of our approach obtain the details of intermolecular interactions of proteins with different shapes, internal structures, and mass. The universality of Vink's approach is experimentally shown, which gives the appropriate description of experimental results for proteins of complicated structure and shape.

Ions-Induced Alginate Gelation According to Elemental Analysis and a Combinatorial Approach.

This study considers the potential of elemental analysis of polysaccharide ionotropic gels in elucidating the junction zones for different divalent cations. The developed algorithm ensures the correct separation of contributions from physically adsorbed and structure-forming ionic compounds, with the obtained results scaled to alginate C12 block. Possible versions of chain association into dimers and their subsequent integration into flat junction zones were analyzed within the framework of the "egg-box" model. The application of combinatorial analysis made it possible to derive theoretical relations to find the probability of various types of egg-box cell occurrences for alginate chains with arbitrary monomeric units ratio µ = M/G, which makes it possible to compare experimental data for alginates of different origins. Based on literature data and obtained chemical formulas, the possible correspondence of concrete biopolymer cells to those most preferable for filling by alkaline earth cations was established. The identified features of elemental composition suggest the formation of composite hydrated complexes with the participation of transition metal cations. The possibility of quantitatively assessing ordered secondary structures formed due to the physical sorption of ions and molecules from environment, correlating with the sorption capabilities of Me2+ alginate, was established.

Sulfated Polysaccharides as a Fighter with Protein Non-Physiological Aggregation: The Role of Polysaccharide Flexibility and Charge Density.

Proteins can lose native functionality due to non-physiological aggregation. In this work, we have shown the power of sulfated polysaccharides as a natural assistant to restore damaged protein structures. Protein aggregates enriched by cross-ß structures are a characteristic of amyloid fibrils related to different health disorders. Our recent studies demonstrated that model fibrils of hen egg white lysozyme (HEWL) can be disaggregated and renatured by some negatively charged polysaccharides. In the current work, using the same model protein system and FTIR spectroscopy, we studied the role of conformation and charge distribution along the polysaccharide chain in the protein secondary structure conversion. The effects of three carrageenans (κ, ι, and λ) possessing from one to three sulfate groups per disaccharide unit were shown to be different. κ-Carrageenan was able to fully eliminate cross-ß structures and complete the renaturation process. ι-Carrageenan only initiated the formation of native-like ß-structures in HEWL, retaining most of the cross-ß structures. In contrast, λ-carrageenan even increased the content of amyloid cross-ß structures. Furthermore, κ-carrageenan in rigid helical conformation loses its capability to restore protein native structures, largely increasing the amount of amyloid cross-ß structures. Our findings create a platform for the design of novel natural chaperons to counteract protein unfolding.

Effects of Homogeneous and Heterogeneous Crowding on Translational Diffusion of Rigid Bovine Serum Albumin and Disordered Alfa-Casein.

Intracellular environment includes proteins, sugars, and nucleic acids interacting in restricted media. In the cytoplasm, the excluded volume effect takes up to 40% of the volume available for occupation by macromolecules. In this work, we tested several approaches modeling crowded solutions for protein diffusion. We experimentally showed how the protein diffusion deviates from conventional Brownian motion in artificial conditions modeling the alteration of medium viscosity and rigid spatial obstacles. The studied tracer proteins were globular bovine serum albumin and intrinsically disordered α-casein. Using the pulsed field gradient NMR, we investigated the translational diffusion of protein probes of different structures in homogeneous (glycerol) and heterogeneous (PEG 300/PEG 6000/PEG 40,000) solutions as a function of crowder concentration. Our results showed fundamentally different effects of homogeneous and heterogeneous crowded environments on protein self-diffusion. In addition, the applied "tracer on lattice" model showed that smaller crowding obstacles (PEG 300 and PEG 6000) create a dense net of restrictions noticeably hindering diffusing protein probes, whereas the large-sized PEG 40,000 creates a "less restricted" environment for the diffusive motion of protein molecules.

Complexation of Bromelain, Ficin, and Papain with the Graft Copolymer of Carboxymethyl Cellulose Sodium Salt and N-Vinylimidazole Enhances Enzyme Proteolytic Activity.

This study investigates the features of interactions between cysteine proteases (bromelain, ficin, and papain) and a graft copolymer of carboxymethyl cellulose sodium salt with N-vinylimidazole. The objective is to understand the influence of this interactions on the proteolytic activity and stability of the enzymes. The enzymes were immobilized through complexation with the carrier. The interaction mechanism was examined using Fourier-transform infrared spectroscopy and flexible molecular docking simulations. The findings reveal that the enzymes interact with the functional groups of the carrier via amino acid residues, resulting in the formation of secondary structure elements and enzyme's active sites. These interactions induce modulation of active site of the enzymes, leading to an enhancement in their proteolytic activity. Furthermore, the immobilized enzymes demonstrate superior stability compared to their native counterparts. Notably, during a 21-day incubation period, no protein release from the conjugates was observed. These results suggest that the complexation of the enzymes with the graft copolymer has the potential to improve their performance as biocatalysts, with applications in various fields such as biomedicine, pharmaceutics, and biotechnology.

Phase Behavior of Aqueous Mixtures of Sodium Alginate with Fish Gelatin: Effects of pH and Ionic Strength.

The phase behavior of aqueous mixtures of fish gelatin (FG) and sodium alginate (SA) and complex coacervation phenomena depending on pH, ionic strength, and cation type (Na+, Ca2+) were studied by turbidimetric acid titration, UV spectrophotometry, dynamic light scattering, transmission electron microscopy and scanning electron microscopy for different mass ratios of sodium alginate and gelatin (Z = 0.01-1.00). The boundary pH values determining the formation and dissociation of SA-FG complexes were measured, and we found that the formation of soluble SA-FG complexes occurs in the transition from neutral (pHc) to acidic (pHφ1) conditions. Insoluble complexes formed below pHφ1 separate into distinct phases, and the phenomenon of complex coacervation is thus observed. Formation of the highest number of insoluble SA-FG complexes, based on the value of the absorption maximum, is observed at рHopt and results from strong electrostatic interactions. Then, visible aggregation occurs, and dissociation of the complexes is observed when the next boundary, pHφ2, is reached. As Z increases in the range of SA-FG mass ratios from 0.01 to 1.00, the boundary values of рНc, рHφ1, рHopt, and рHφ2 become more acidic, shifting from 7.0 to 4.6, from 6.8 to 4.3, from 6.6 to 2.8, and from 6.0 to 2.7, respectively. An increase in ionic strength leads to suppression of the electrostatic interaction between the FG and SA molecules, and no complex coacervation is observed at NaCl and CaCl2 concentrations of 50 to 200 mM.

Ion-Induced Polysaccharide Gelation: Peculiarities of Alginate Egg-Box Association with Different Divalent Cations.

Structural aspects of polysaccharide hydrogels based on sodium alginate and divalent cations Ba2+, Ca2+, Sr2+, Cu2+, Zn2+, Ni2+ and Mn2+ was studied using data on hydrogel elemental composition and combinatorial analysis of the primary structure of alginate chains. It was shown that the elemental composition of hydrogels in the form of freezing dried microspheres gives information on the structure of junction zones in the polysaccharide hydrogel network, the degree of filling of egg-box cells by cations, the type and magnitude of the interaction of cations with alginate chains, the most preferred types of alginate egg-box cells for cation binding and the nature of alginate dimers binding in junction zones. It was ascertained that metal-alginate complexes have more complicated organization than was previously desired. It was revealed that in metal-alginate hydrogels, the number of cations of various metals per C12 block may be less than the limiting theoretical value equal to 1 for completely filled cells. In the case of alkaline earth metals and zinc, this number is equal to 0.3 for calcium, 0.6 for barium and zinc and 0.65-0.7 for strontium. We have determined that in the presence of transition metals copper, nickel and manganese, a structure similar to an egg-box is formed with completely filled cells. It was determined that in nickel-alginate and copper-alginate microspheres, the cross-linking of alginate chains and formation of ordered egg-box structures with completely filled cells are carried out by hydrated metal complexes with complicated composition. It was found that an additional characteristic of complex formation with manganese cations is the partial destruction of alginate chains. It has been established that the existence of unequal binding sites of metal ions with alginate chains can lead to the appearance of ordered secondary structures due to the physical sorption of metal ions and their compounds from the environment. It was shown that hydrogels based on calcium alginate are most promising for absorbent engineering in environmental and other modern technologies.

Carboxymethyl Cellulose-Based Polymers as Promising Matrices for Ficin Immobilization.

The present work is devoted to research on the interaction between carboxymethyl cellulose sodium salt and its derivatives (graft copolymer of carboxymethyl cellulose sodium salt and N,N-dimethyl aminoethyl methacrylate) with cysteine protease (ficin). The interaction was studied by FTIR and by flexible molecular docking, which have shown the conjugates' formation with both matrices. The proteolytic activity assay performed with azocasein demonstrated that the specific activities of all immobilized ficin samples are higher in comparison with those of the native enzyme. This is due to the modulation of the conformation of ficin globule and of the enzyme active site by weak physical interactions involving catalytically valuable amino acids. The results obtained can extend the practical use of ficin in biomedicine and biotechnology.

Recent Advances in Protein-Protein Interactions.

Protein-protein interactions (PPIs) lead to formation of complexes and aggregates between a pair or multiple protein molecules [...].

Novel Biocatalysts Based on Bromelain Immobilized on Functionalized Chitosans and Research on Their Structural Features.

Enzyme immobilization on various carriers represents an effective approach to improve their stability, reusability, and even change their catalytic properties. Here, we show the mechanism of interaction of cysteine protease bromelain with the water-soluble derivatives of chitosan-carboxymethylchitosan, N-(2-hydroxypropyl)-3-trimethylammonium chitosan, chitosan sulfate, and chitosan acetate-during immobilization and characterize the structural features and catalytic properties of obtained complexes. Chitosan sulfate and carboxymethylchitosan form the highest number of hydrogen bonds with bromelain in comparison with chitosan acetate and N-(2-hydroxypropyl)-3-trimethylammonium chitosan, leading to a higher yield of protein immobilization on chitosan sulfate and carboxymethylchitosan (up to 58 and 65%, respectively). In addition, all derivatives of chitosan studied in this work form hydrogen bonds with His158 located in the active site of bromelain (except N-(2-hydroxypropyl)-3-trimethylammonium chitosan), apparently explaining a significant decrease in the activity of biocatalysts. The N-(2-hydroxypropyl)-3-trimethylammonium chitosan displays only physical interactions with His158, thus possibly modulating the structure of the bromelain active site and leading to the hyperactivation of the enzyme, up to 208% of the total activity and 158% of the specific activity. The FTIR analysis revealed that interaction between N-(2-hydroxypropyl)-3-trimethylammonium chitosan and bromelain did not significantly change the enzyme structure. Perhaps this is due to the slowing down of aggregation and the autolysis processes during the complex formation of bromelain with a carrier, with a minimal modification of enzyme structure and its active site orientation.

κ-Carrageenan Hydrogel as a Matrix for Therapeutic Enzyme Immobilization.

During the last few decades, polysaccharide hydrogels attract more and more attention as therapeutic protein delivery systems due to their biocompatibility and the simplicity of the biodegradation of natural polymers. The protein retention by and release from the polysaccharide gel network is regulated by geometry and physical interactions of protein with the matrix. In the present work, we studied the molecular details of interactions between κ-carrageenan and three lipases, namely the lipases from Candida rugosa, Mucor javanicus, and Rhizomucor miehei-which differ in their size and net charge-upon protein immobilization in microparticles of polysaccharide gel. The kinetics of protein release revealed the different capability of κ-carrageenan to retain lipases, which are generally negatively charged; that was shown to be in line with the energy of interactions between polysaccharides and positively charged epitopes on the protein surface. These data create a platform for the novel design of nanocarriers for biomedical probes of enzymatic origin.

Supramolecular Structure and Mechanical Performance of κ-Carrageenan-Gelatin Gel.

In this work, by means of complex physicochemical methods the structural features of a composite κ-carrageenan-gelatin system were studied in comparison with initial protein gel. The correlation between the morphology of hydrogels and their mechanical properties was demonstrated through the example of changes in their rheological characteristics. The experiments carried out with PXRD, SAXS, AFM and rheology approaches gave new information on the structure and mechanical performance of κ-carrageenan-gelatin hydrogel. The combination of PXRD, SAXS and AFM results showed that the morphological structures of individual components were not observed in the composite protein-polysaccharide hydrogels. The results of the mechanical testing of initial gelatin and engineered κ-carrageenan-gelatin gel showed the substantially denser parking of polymer chains in the composite system due to a significant increase in intermolecular protein-polysaccharide contacts. Close results were indirectly followed from the SAXS estimations-the driving force for the formation of the common supramolecular structural arrangement of proteins and polysaccharides was the increase in the density of network of macromolecular chains entanglements; therefore, an increase in the energy costs was necessary to change the conformational rearrangements of the studied system. This increase in the macromolecular arrangement led to the growth of the supramolecular associate size and the growth of interchain physical bonds. This led to an increase in the composite gel plasticity, whereas the enlargement of scattering particles made the novel gel system not only more rigid, but also more fragile.

Effect of Protein-Protein Interactions on Translational Diffusion of Spheroidal Proteins.

One of the commonly accepted approaches to estimate protein-protein interactions (PPI) in aqueous solutions is the analysis of their translational diffusion. The present review article observes a phenomenological approach to analyze PPI effects via concentration dependencies of self- and collective translational diffusion coefficient for several spheroidal proteins derived from the pulsed field gradient NMR (PFG NMR) and dynamic light scattering (DLS), respectively. These proteins are rigid globular α-chymotrypsin (ChTr) and human serum albumin (HSA), and partly disordered α-casein (α-CN) and ß-lactoglobulin (ß-Lg). The PPI analysis enabled us to reveal the dominance of intermolecular repulsion at low ionic strength of solution (0.003-0.01 M) for all studied proteins. The increase in the ionic strength to 0.1-1.0 M leads to the screening of protein charges, resulting in the decrease of the protein electrostatic potential. The increase of the van der Waals potential for ChTr and α-CN characterizes their propensity towards unstable weak attractive interactions. The decrease of van der Waals interactions for ß-Lg is probably associated with the formation of stable oligomers by this protein. The PPI, estimated with the help of interaction potential and idealized spherical molecular geometry, are in good agreement with experimental data.

Alginate-Based Hydrogel as Delivery System for Therapeutic Bacterial RNase.

To deliver therapeutic proteins into a living body, it is important to maintain their target activity in the gastrointestinal tract after oral administration. Secreted ribonuclease from Bacillus pumilus (binase) has antitumor and antiviral activity, which makes it a promising therapeutic agent. This globular protein of small molecular weight (12.2 kDa) is considered as a potential agent that induces apoptosis of tumor cells expressing certain oncogenes, including colorectal and duodenum cancer. The most important problem of its usage is the preservation of its structure and target activity, which could be lost during oral administration. Here, we developed alginate microspheres reinforced with divalent cations and analyzed the enzyme release from them. Using methods of scanning electron microscopy, measurements of fluorescence, enzyme catalytic activity, and determination of viability of the duodenum adenocarcinoma tumor cell line, we characterized obtained microspheres and chose calcium as a biogenic ion-strengthening microsphere structure. Among such modified additivities as beta-casein, gelatin, and carbon nanotubes introduced into microspheres, only gelatin showed a pronounced increase in their stability and provided data on the prolonged action of enzyme release from microspheres into tumor cell culture medium during 48 h in an amount of about 70% of the loaded quantity.

Chitosan Graft Copolymers with N-Vinylimidazole as Promising Matrices for Immobilization of Bromelain, Ficin, and Papain.

This work aims to synthesize graft copolymers of chitosan and N-vinylimidazole (VI) with different compositions to be used as matrices for the immobilization of cysteine proteases-bromelain, ficin, and papain. The copolymers are synthesized by free radical solution copolymerization with a potassium persulfate-sodium metabisulfite blend initiator. The copolymers have a relatively high frequency of grafting and yields. All the synthesized graft copolymers are water-soluble, and their solutions are characterized by DLS and laser Doppler microelectrophoresis. The copolymers are self-assembled in aqueous solutions, and they have a cationic nature and pH-sensitivity correlating to the VI content. The FTIR data demonstrate that synthesized graft copolymers conjugate cysteine proteases. The synthesized copolymer adsorbs more enzyme macromolecules compared to non-modified chitosan with the same molecular weight. The proteolytic activity of the immobilized enzymes is increased up to 100% compared to native ones. The immobilized ficin retains up to 97% of the initial activity after a one-day incubation, the immobilized bromelain retains 69% of activity after a 3-day incubation, and the immobilized papain retains 57% of the initial activity after a 7-day incubation. Therefore, the synthesized copolymers can be used as matrices for the immobilization of bromelain, ficin, and papain.

Interaction-Induced Structural Transformations in Polysaccharide and Protein-Polysaccharide Gels as Functional Basis for Novel Soft-Matter: A Case of Carrageenans.

Biocompatible, nontoxic, and biodegradable polysaccharides are considered as a promising base for bio-inspired materials, applicable as scaffolds in regenerative medicine, coatings in drug delivery systems, etc. The tunable macroscopic properties of gels should meet case-dependent requirements. The admixture of proteins to polysaccharides and their coupling in more sophisticated structures opens an avenue for gel property tuning via physical cross-linking of components and the modification of gel network structure. In this review recent success in the conformational studies of binary protein-polysaccharide gels is summarized with the main focus upon carrageenans. Future perspectives and challenges in rational design of novel polysaccharide-based materials are outlined.

Morphology of Ionic Micelles as Studied by Numerical Solution of the Poisson Equation.

The existing concepts of the ionic micelle structure were specified. It was noted that the composition of dispersed phase particles in a liquid dispersion medium should necessarily include adsorbed counterions rigidly bound to these particles. By numerical solution of the Poisson equation for the two most often used approximations, the Poisson-Boltzmann (PB) model and the Jellium-approximation (JA), the electric potential decay from the Stern potential of dispersed phase particles was defined. A new methodological approach to analyze the reaction of micelle potential decay based on small variability of the CMC value was proposed. It made possible to determine the dimension parameter, which in the presence of weak thermal effects approximately corresponds to the micelle hydrodynamic radius, and to calculate the electrokinetic potential of micelles. The results of theoretical calculations were compared with our previous experimental data on the thickness of the SDS micelle hydrophilic layer obtained by SAXS. A good agreement between the calculated and measured values was obtained, and it was noted that for low concentrations the experimental values are more correctly described by the PB model, but for concentrations greater than 100 mM the JA model is more preferable. It was found that the slipping plane is located near the outer Stern plane and is separated from it only by a few molecular layers of water. The influence stronger than the thermal one can shift the slipping plane closer to the micelle core. Accordingly, the smallest hydrodynamic micelle size is determined by the outer Stern plane. The results of our work allowed us to conclude that the micelle is not something soft and watery, but according to its specified structure, it is a more solid-like particle than was previously assumed. The proposed approach can be extended to investigate other effects of a physicochemical nature, in particular, those observed with the addition of an external electrolyte or nanoparticles.

The Role of pH and Ionic Strength in the Attraction-Repulsion Balance of Fibrinogen Interactions.

Fibrinogen (Fg) self-assembly is sensitive to the physicochemical properties of an environment like pH and ionic strength. These parameters tune the direction and strength of noncovalent physical driving forces determining protein intermolecular interactions. The attraction-repulsion balance in intermolecular interactions of the multidomain protein Fg at pH values 3.5, 7.4, and 9.5 and varying ionic strengths of the water medium has been analyzed by the complex diffusive approach, proposed by us previously. The concentration dependence of protein collective diffusion was analyzed within the phenomenological approach, based on the frictional formalism of nonequilibrium thermodynamics proposed by H. Vink. The analysis of protein diffusion data has shown the fundamental difference in the physical nature and direction of interaction forces between protein molecules at different conditions. The paired interaction potential of protein molecules was characterized in terms of second virial coefficients and Hamaker constants within the Deryaguin-Landau-Verwey-Overbeek theory and the "porous" colloid particle model. Our results indicated the maximum Hamaker constant and dominance of the van der Waals attraction between Fg molecules at pH 7.4. The increase in pH up to 9.5 results in the zero values of the second virial coefficient and Hamaker constant, corresponding to the full reciprocal compensation for electrostatic repulsion and van der Waals attraction. In the acidic medium (pH 3.5), the strong electrostatic repulsion substantially exceeds the van der Waals attraction. A high ionic strength is characterized by a significant decrease of all intermolecular interactions, which is expressed in almost zero values of virial coefficients and the Hamaker constant. Thus, it is experimentally shown that the physiological conditions of the Fg environment (pH 7.4 and slight ionic strength) provide a high probability for peak physical attraction between fibrinogen molecules, which is used in nature to facilitate blood clotting.

Fibril fragments from the amyloid core of lysozyme: An accelerated molecular dynamics study.

Protein aggregation and formation of amyloid fibrils are associated with many diseases and present a ubiquitous problem in protein science. Hen egg white lysozyme (HEWL) can form fibrils both from the full length protein and from its fragments. In the present study, we simulated unfolding of the amyloidogenic fragment of HEWL encompassing residues 49-101 to study the conformational aspects of amyloidogenesis. The accelerated molecular dynamics approach was used to speed up the sampling of the fragment conformers under enhanced temperature. Analysis of conformational transformation and intermediate structures was performed. During the unfolding, the novel short-living and long-living ß-structures are formed along with the unstructured random coils. Such ß-structure enriched monomers can interact with each other and propagate into fibril-like forms. The stability of oligomers assembled from these monomers was evaluated in the course of MD simulations with explicit water. The residues playing a key role in fibril stabilization were determined. The work provides new insights into the processes occurring at the early stages of amyloid fibril assembly.