Interaction-induced structural transformation of lysozyme and kappa-carrageenan in binary complexes.

The interactions between κ-carrageenan and hen egg-white lysozyme have been studied. In dilute solutions, the insoluble complexes with constant κ-carrageenan/lysozyme ratio of 0.3, or 12 disaccharide units per mole of protein are formed. FTIR-spectroscopy revealed that κ-carrageenan retains its unordered conformation and induces the rise of ß-structure in lysozyme. In the complexes formed in concentrated mixtures, κ-carrageenan adopts helical conformation and lysozyme retains its native-like structure. These complexes contain 21 disaccharide units per mole of protein. Molecular modeling showed that flexible coil and rigid double helix of κ-carrageenan have different binding patterns to lysozyme surface. The latter has a strong preference to positively charged spots in lysozyme α-domain while the former also interacts to protein ß-domain and stabilizes short-living ß-structures. The obtained results confirm the preference of unordered κ-carrageenan to ß-structure rich protein regions, which can be further used in the development of carrageenan-based protection of amyloid-like aggregation of proteins.

Structural insights in interactions between RNase from Bacillus Intermedius and rhamnogalacturonan I from potato.

Being biocompatible and biodegradable polymers, polysaccharides present a perspective material for drug delivery systems. This study aimed at unraveling the molecular details of interactions between rhamnogalacturonan I, brunched with galactan side chains, and RNase from Bacillus Intermedius, binase. FTIR- and NMR-spectroscopic analyses showed that binase interacts with side chains of the polysaccharide. In complexes with polysaccharide, the protein retains its native structure. The 2D-NMR techniques revealed eight protein residues responsive to polysaccharide binding. Further, computer simulations were carried out to provide the atomistic details of binase-polysaccharide complexes. Both blind and knowledge-based docking procedures elucidate the existence of epitopes on the binase surface with the preferential binding of galactan fragments. The refinement of these complexes by molecular dynamics simulations confirmed stable protein-polysaccharide interactions. The results of this study strengthen the knowledge on non-specific protein-carbohydrate interactions and outline the rhamnogalacturonan I as a possible matrix material for protein delivery systems.

Interplay between secondary structure and ion binding upon thermoreversible gelation of κ-carrageenan.

It is widely accepted that cation binding specifically favors chain ordering and gelling of κ-carrageenan. However, current insights into the exact sequence of binding and conformational rearrangements as well as into the structure of binding sites are controversial. In the present work, the FTIR-spectroscopy combined with the computer modelling has been used to reveal the relation between cation binding and the secondary structure transition upon thermoreversible gelation of the κ-carrageenan. Three states of sulfate groups were defined spectroscopically: one cation-free and two specific cation-bound states. The DFT calculations reveal two energetically inequivalent spatial structures of cation binding unit, formed due to the local conformational adjustment in neocarrabiose moiety. Besides a charge screening effect, the cation-bound conformation of neocarrabiose also favors the helix formation.

Molecular structure and properties of κ-carrageenan-gelatin gels.

Rheological studies, FTIR spectroscopy and a molecular docking approach were used to explore the structural basis of the peculiar physicochemical properties of gelatin gels modified with a κ-carrageenan admixture. Mixed gel properties are affected by the polysaccharide-to-gelatin ratio, Z, and can be divided into two categories. At low ratios, the strength of mixed gels varies insignificantly compared to gelatin due to the similar structures of the gels. Above the threshold content of κ-carrageenan (Z > 0.1), the storage modulus and yield stress of mixed gels are significantly enhanced. The nonadditivity and threshold character of the rheological properties could be the result of conformational ordering of both gelatin and κ-carrageenan, leading to the formation of additional junction zones in the gel network. According to molecular docking studies, the junctions could be formed as a result of complementary interactions between the gelatin triple helix and the κ-carrageenan double helix. The stack formation increases the interaction energy, which explains the strengthening of the gel network.

Localization of non-native D-glyceraldehyde-3-phosphate dehydrogenase in growing and apoptotic HeLa cells.

Monoclonal antibodies that could not bind native tetramers of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) but could bind to dimeric, monomeric, or denatured forms of GAPDH were used to investigate its intracellular localization. These antibodies distinctly stained the nucleus in growing HeLa cells. In the cytoplasm, non-native GAPDH was colocalized with actin filaments. Incubation of HeLa cells with tumor necrosis factor α (TNF-α) and the protein synthesis inhibitor emetine led to a drastic increase in the amount of the non-native GAPDH in the nuclei. Overproduction of Bcl-2 protein did not change the non-native GAPDH localization in the growing HeLa cells but prevented the development of apoptosis and the increase in the amount of non-native GAPDH in the nuclei upon incubation with TNF-α.

[Influence of dioxane on the hydration shell of polypeptides].

Our interest in modifying influence of the low-molecular organic compounds on the hydration shell of biopolymers is due to a well-known fact that the former can act as regulators of the enzymatic activity changed the hydration shell of the latter. Dioxane was chosen because of its wide application in non-aqueous biocatalysis. In the present study we investigate the mechanisms of the dioxane influence on water of the first hydration layer of the model polypeptides by FTIR-spectroscopy during simultaneous sorption of water-dioxane vapors into the polypeptide films at low water activity. It was found that modification of the hydration shell of the studied polypeptides was mainly due to the indirect ordering ofpolypeptide secondary structure at penetration of dioxane molecules at these conditions.