Recent Advances in Protein-Protein Interactions.

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

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.

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.

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.

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.

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.

Alkyl triphenylphosphonium surfactants as nucleic acid carriers: complexation efficacy toward DNA decamers, interaction with lipid bilayers and cytotoxicity studies.

Herein, for the first time the complexation ability of a homological series of triphenylphosphonium surfactants (TPPB-n) toward DNA decamers has been explored. Formation of lipoplexes was confirmed by alternative techniques, including dynamic light scattering, indicating the occurrence of nanosized complexes (ca. 100-150 nm), and monitoring the charge neutralization of nucleotide phosphate groups and the fluorescence quenching of dye-intercalator ethidium bromide. The complexation efficacy of TPPB-surfactants toward an oligonucleotide (ONu) is compared with that of reference cationic surfactants. Strong effects of the alkyl chain length and the structure of the head group on the surfactant/ONu interaction are revealed, which probably occur via different mechanisms, with electrostatic and hydrophobic forces or intercalation imbedding involved. Phosphonium surfactants are shown to be capable of disordering lipid bilayers, which is supported by a decrease in the temperature of the main phase transition, Tm. This effect enhances with an increase in the alkyl chain length, indicating the integration of TPPB-n with lipid membranes. This markedly differs from the behavior of typical cationic surfactant cetyltrimethylammonium bromide, which induces an increase in the Tm value. It was demonstrated that the cytotoxicity of TPPB-n in terms of the MTT-test on a human cell line 293T nonmonotonically changes within the homological series, with the highest cytotoxicity exhibited by the dodecyl and tetradecyl homologs.

Protein Translational Diffusion and Intermolecular Interactions of Globular and Intrinsically Unstructured Proteins.

The study of intermolecular interactions of proteins has been an important problem for many years. This paper presents an approach to analyze different levels of protein interactions in solutions through a set of the second- and higher-order virial coefficients. The proposed approach is based on the diversified analysis of protein translational collective diffusion and self-diffusion obtained by dynamic light scattering and the pulsed-field gradient NMR (PFG NMR) spectroscopy experimental data. The experimental results were analyzed within the theoretical approach based on Vink's frictional formalism of nonequilibrium thermodynamics and the standard Derjaguin-Landau-Verwey-Overbeekb (DLVO) theory of interactions of colloid particles in electrolyte solutions. The second- and higher-order virial coefficients were obtained to estimate the pairwise and many-body intermolecular interactions in the solutions of globular α-chymotrypsin and intrinsically unstructured αS-casein. The second virial coefficients were calculated from the model of the protein-protein potential of mean force. The description of protein-protein interactions includes a set of interaction potentials: the attractive charge-dipole, dipole-dipole, the dispersion Hamaker, the mean force osmotic-attraction, and the repulsive charge-charge ones. It has been found that the major contribution to the intermolecular αS-casein interactions is made by the repulsive charge-charge potential, whereas for the case of α-chymotrypsin, the contributions from other types of interaction are of importance. It was determined that the model was well suited to describe the interactions of both globular and intrinsically disordered proteins. The suggested combination of Vink's approach and the DLVO theory is novel and holds much promise to make a profound analysis of the processes in systems containing various types of protein molecules.

NMR structure, conformational dynamics, and biological activity of PsDef1 defensin from Pinus sylvestris.

Plants have developed a complex defense response system against pests and pathogens. Defensins, produced by plants as part of their innate immune response, form the family of small, basic, cysteine-rich proteins with activity primarily directed against fungal pathogens. In addition, plant defensins can show antibacterial activity and protease and insect amylase inhibitory activities. However, in gymnosperms, only antifungal activity of defensins has been described thus far. Here, we report antibacterial and insect α-amylase inhibition activities for defensin PsDef1 from P. sylvestris, the first defensin from gymnosperms with a broad range of biological activities described. We also report the solution NMR structure of PsDef1 and its dynamics properties assessed by a combination of experimental NMR and computational techniques. Collectively, our data provide an insight into structure, dynamics, and functional properties of PsDef1 that could be common between defensins from this taxonomic group.

Structural basis for regulation of stability and activity in glyceraldehyde-3-phosphate dehydrogenases. Differential scanning calorimetry and molecular dynamics.

Tissue specific isoforms of human glyceraldehyde-3-phosphate dehydrogenase, somatic (GAPD) and sperm-specific (GAPDS), have been reported to display different levels of both stability and catalytic activity. Here we apply MD simulations to investigate molecular basis of this phenomenon. The protein is a tetramer where each subunit consists of two domains - catalytic and NAD-binding one. We demonstrated key residues responsible for intersubunit and interdomain interactions. Effect of several residues was studied by point mutations. Overall we considered three mutations (Glu96Gln, Glu244Gln and Asp311Asn) disrupting GAPDS-specific salt bridges. Comparison of calculated interaction energies with calorimetric enthalpies confirmed that intersubunit interactions were responsible for enhanced thermostability of GAPDS whereas interdomain interactions had indirect influence on intersubunit contacts. Mutation Asp311Asn was around 10Å far from the active center and corresponded to the closest natural substitution in the isoenzymes. MD simulations revealed that this residue had slight interaction with catalytic residues but influenced the hydrogen bond net and dynamics in active site. These effects can be responsible for a strong influence of this residue on catalytic activity. Overall, our results provide new insight into glyceraldehyde-3-phosphate dehydrogenase structure-function relationships and can be used for the engineering of mutant proteins with modified properties and for development of new inhibitors with indirect influence on the catalytic site.

Dynamics and thermodynamic properties of CXCL7 chemokine.

Chemokines form a family of signaling proteins mainly responsible for directing the traffic of leukocytes, where their biological activity can be modulated by their oligomerization state. We characterize the dynamics and thermodynamic stability of monomer and homodimer structures of CXCL7, one of the most abundant platelet chemokines, using experimental methods that include circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy, and computational methods that include the anisotropic network model (ANM), molecular dynamics (MD) simulations and the distance constraint model (DCM). A consistent picture emerges for the effects of dimerization and Cys5-Cys31 and Cys7-Cys47 disulfide bonds formation. The presence of disulfide bonds is not critical for maintaining structural stability in the monomer or dimer, but the monomer is destabilized more than the dimer upon removal of disulfide bonds. Disulfide bonds play a key role in shaping the characteristics of native state dynamics. The combined analysis shows that upon dimerization flexibly correlated motions are induced between the 30s and 50s loop within each monomer and across the dimer interface. Interestingly, the greatest gain in flexibility upon dimerization occurs when both disulfide bonds are present, and the homodimer is least stable relative to its two monomers. These results suggest that the highly conserved disulfide bonds in chemokines facilitate a structural mechanism that is tuned to optimally distinguish functional characteristics between monomer and dimer.

The Low-Waste Grafting Copolymerization Modification of Chitosan Is a Promising Approach to Obtaining Materials for Food Applications.

Chitosan takes second place of the most abundant polysaccharides naturally produced by living organisms. Due to its abundance and unique properties, such as its polycationic nature, ability to form strong elastic porous films, and antibacterial potential, it is widely used in the food industry and biomedicine. However, its low solubility in both water and organic solvents makes its application difficult. We have developed an environmentally friendly method for producing water-soluble graft copolymers of chitosan and poly (N-vinylpyrrolidone) with high grafting efficiency and a low yield of by-products. By using AFM, SEM, TGA, DSC, and XRD, it has been demonstrated that the products obtained have changed properties compared to the initial chitosan. They possess a smoother surface and lower thermal stability but are sufficient for practical use. The resulting copolymers have a higher viscosity than the original chitosan, making them a promising thickener and stabilizer for food gels. Moreover, the copolymers exhibit an antibacterial effect, suggesting their potential use as a component in smart food packaging.

Supramolecular design of biocompatible nanocontainers based on amphiphilic derivatives of a natural compound isosteviol.

Two diterpenoid surfactants with ammonium head groups and bromide (S1) or tosylate (S2) counterions have been synthesized. Exploration of these biomimetic species made it possible to demonstrate that even minor structural changes beyond their chemical nature may dramatically affect their solution behavior. While their aggregation thresholds differ inconsiderably, morphological behavior and affinity to lipid bilayer are strongly dependent on the counterion nature. Compound S2 demonstrates properties of typical surfactants and forms small micelle-like aggregates above critical micelle concentration. For surfactant S1, two critical concentrations and two types of aggregates occur. Structural transitions have been observed between small micelles and aggregates with higher aggregation numbers and hydrodynamic diameter of ca. 150 nm. Unlike S2, surfactant S1 is shown to integrate with liposomes based on dipalmitoylphosphatidylcholine, resulting in a decrease of the temperature of the main phase transition. Both surfactants demonstrate an effective complexation capacity toward oligonucleotide (ONu), which is supported by recharging the surfactant-ONu complexes and the ethidium bromide exclusion at a low N/P ratio. Meanwhile, a very weak complexation of plasmid DNA with the surfactants has been revealed in the gel electrophoresis experiment. The DNA transfer to bacterial cells mediated by the surfactant S1 is shown to depend on the protocol used. In the case of the electroporation, the inhibition of the cell transformation occurs in the presence of the surfactant, while upon the chemical treatment no surfactant effect has been observed. The variability in the morphology, the biocompatibility, the nanoscale dimension and the high binding capacity toward the DNA decamer make it possible to nominate the designed surfactants as promising carriers for biosubstrates or as a helper surfactant for the mixed liposome-surfactant nanocontainers.

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.

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.

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.

The α-helix to ß-sheet transition in stretched and compressed hydrated fibrin clots.

Fibrin is a protein polymer that forms the viscoelastic scaffold of blood clots and thrombi. Despite the critical importance of fibrin deformability for outcomes of bleeding and thrombosis, the structural origins of the clot's elasticity and plasticity remain largely unknown. However, there is substantial evidence that unfolding of fibrin is an important part of the mechanism. We used Fourier transform infrared spectroscopy to reveal force-induced changes in the secondary structure of hydrated fibrin clots made of human blood plasma in vitro. When extended or compressed, fibrin showed a shift of absorbance intensity mainly in the amide I band (1600-1700 cm(-1)) as well as in the amide II and III bands, indicating an increase of the ß-sheets and a corresponding reduction of the α-helices. The structural conversions correlated directly with the strain or pressure and were partially reversible at the conditions applied. The additional absorbance observed at 1612-1624 cm(-1) was characteristic of the nascent interchain ß-sheets, consistent with protein aggregation and fiber bundling during clot deformation observed using scanning electron microscopy. We conclude that under extension and/or compression an α-helix to ß-sheet conversion of the coiled-coils occurs in the fibrin clot as a part of forced protein unfolding.