Bulat Z. Idiyatullin

Physicochemical properties of complex rhamnogalacturonan I from gelatinous cell walls of flax fibers.

The physicochemical properties of flax fiber cell wall rhamnogalacturonan I (RG-I) and its fragments, obtained after galactanase treatment (fraction G1), were characterized. RG-I retains its hydrodynamic volume after its molecular weight decreases by approximately half, as revealed by SEC. Two techniques, DLS and NMR, with different principles of diffusion experiment were used to establish the reasons for this property of RG-I. Three possible types of particles were revealed by DLS depending on the concentration of the RG-I and G1 solutions (2-2.5, 15-20, and 150-200 nm). It was determined by BPP-LED experiments that the backbone of the RG-I was 1.3-1.9-fold more mobile than the side chains. The obtained data suggest a novel type of pectin spatial organization-the formation of RG-I associates with the backbone at the periphery and the interaction between the side chains to form a core zone.

Novel biomimetic systems based on amphiphilic compounds with a diterpenoid fragment: Role of counterions in self-assembly

Novel biomimetic systems are designed based on cationic surfactants composed of an isosteviol moiety and different counterions, namely bromide (S1) and tosylate (S2). The counterion structure is shown to play a crucial role in the surfactant association. A number of methods used provide evidence that only one type of aggregate, i.e., micelles are observed in the S2 systems, while a concentration-dependent association occurs in the case of S1. The DLS and fluorescence anisotropy measurements reveal that the micelle-vesicle-micelle transitions probably occur with the S1 system. The occurrence of small aggregates near the critical micelle concentration with radii of 2.5 nm is supported by NMR self-diffusion data. The Orange OT solubilization results strongly support the idea of a second threshold in the S1 system around 0.025 mM and provide evidence that hydrophobic domains occur in the aggregates. The latter property and the capacity to integrate with the lipid bilayer make it possible to suggest the newly synthesized surfactants as effective nanocontainers for hydrophobic guests.

Association of sodium dodecyl sulfate in aqueous solutions according to chemical shifts in 1H NMR spectra

Proton chemical shifts of different atomic groups in sodium dodecyl sulfate (SDS) have been studied by 1H NMR spectroscopy as functions of surfactant concentration in aqueous solutions. Three surfactant concentration ranges of the chemical shifts have been revealed. The first range corresponds to the premicellar solutions, the second one is in the vicinity of critical micelle concentration (CMC1), and the third range corresponds to high surfactant concentrations, at which intermicellar interactions play a significant role. The parameters of SDS association (CMC1 and CMC2) determined based on the concentration dependences of the chemical shifts are in satisfactory agreement with the data available from the literature. The concept of critical dimerization concentration (CDC) has been introduced for the first concentration range. The values of CDC and dimerization constant K2(210 × 60 dm3/mol) have been estimated within the framework of the two-state model.

Structure and properties of aqueous dispersions of sodium dodecyl sulfate with carbon nanotubes

The dispersing action of the surfactant (sodium dodecyl sulfate, SDS) on the carbon nanotubes (CNT) in aqueous medium has been studied. Electron microscopy, molecular docking, NMR and IR spectroscopies were applied to determine the physical-chemical properties of CNT dispersions in SDS—water solutions. It was established that micellar adsorption of the surfactant on the surface of carbon material and solubilization of SDS in aqueous medium contribute to improving CNT dispersing in water solutions. It was shown that the non-polar hydrocarbon radicals of a single surfactant molecule form the highest possible number of contacts with the graphene surface. Upon increase of the SDS in solution these radicals form micelles connected with the surface of the nanotubes. At the sufficiently high SDS concentration the nanotube surface becomes covered with an adsorbed layer of surfactant micelles. Water molecules and sodium cations are concentrated in spaces between micelles. The observed pattern of micellar adsorption is somewhat similar to a loose bilayer of surfactant molecules.

Structure and dynamics of concentrated micellar solutions of sodium dodecyl sulfate

In micellar solutions of sodium dodecyl sulfate, as the concentration of surfactants increases, the spheroid shape of the micelles changes from almost spherical to ellipsoidal with increasing ratio of half-axes ratio, and further the transition to cylindrical micelles occurs. The micelles in an aqueous solution can directly contact (compact aggregates) or be separated from one another by layers of intermicellar medium (periodical colloid structures). In the latter case, the thickness of the layer can significantly exceed the micelle size, and then no mutual correlation in micelle arrangement is observed. According to the data of small-angle X-ray scattering, the relationship between the surfactant concentration and formation of “quasi-crystalline” micellar structure is nonlinear, which can be due to both micelle aggregation processes and nonuniformity of their structure. The possible influence of ordered micellar structures on the diffusion mobility of micelles is shown.

Conformational Flexibility and Self-Association of Fibrinogen in Concentrated Solutions

We studied the hydrodynamic behavior of fibrinogen, a blood plasma protein involved in blood clotting, in a broad 0.3-60 mg/mL range of concentration and 5-42 °C temperature using pulsed-field gradient 1H NMR-diffusometry. Arrhenius plots revealed the activation energy for fibrinogen diffusion Ed = 21.3 kJ/mol at 1.4 mg/mL and 28.4 kJ/mol at 38 mg/mL. We found a dramatic slowdown in fibrinogen self-diffusion with concentration beginning at 1.7-3.4 mg/mL, which deviated from the standard hard-particle behavior, suggesting a remarkable intermolecular entanglement. This concentration dependence was observed regardless of the absence or presence of the GPRP peptide (inhibitor of fibrin polymerization), and also in samples free of fibrin oligomers. By contrast, diffusivity of fibrinogen variant I-9 with truncated C-terminal portions of the Aα chains was much less concentration-dependent, indicating the importance of intermolecular linkages formed by the αC regions. Theoretical models combined with all-atom molecular dynamics simulations revealed partially bent fibrinogen solution conformations that interpolate between a flexible chain and a rigid rod observed in the crystal. The results obtained illuminate the important role of the αC regions in modulating the fibrinogen molecular shape through formation of weak intermolecular linkages that control the bulk properties of fibrinogen solutions.

Structure of Scots pine defensin 1 by spectroscopic methods and computational modeling.

Defensins are part of the innate immune system in plants with activity against a broad range of pathogens, including bacteria, fungi and viruses. Several defensins from conifers, including Scots pine defensin 1 (Pinus sylvestris defensin 1, (PsDef1)) have shown a strong antifungal activity, however structural and physico-chemical properties of the family, needed for establishing the structure-dynamics-function relationships, remain poorly characterized. We use several spectroscopic and computational methods to characterize the structure, dynamics, and oligomeric state of PsDef1. The three-dimensional structure was modeled by comparative modeling using several programs (Geno3D, SWISS-MODEL, I-TASSER, Phyre(2), and FUGUE) and verified by circular dichroism (CD) and infrared (FTIR) spectroscopy. Furthermore, FTIR data indicates that the structure of PsDef1 is highly resistant to high temperatures. NMR diffusion experiments show that defensin exists in solution in the equilibrium between monomers and dimers. Four types of dimers were constructed using the HADDOCK program and compared to the known dimer structures of other plant defensins. Gaussian network model was used to characterize the internal dynamics of PsDef1 in monomer and dimer states. PsDef1 is a typical representative of P. sylvestris defensins and hence the results of this study are applicable to other members of the family.

Gelation of rhamnogalacturonan I is based on galactan side chain interaction and does not involve chemical modifications

The article presents the structural principles of microwave-induced formation of new gel type from pectic rhamnogalacturonan I (RG-I). The backbone of gel-forming RG-I does not contain consecutive galacturonic residues and modifying groups that can be the cause of junction zone formation as it occurs in course of classical ways of pectin gelation. Microwave irradiation does not cause destruction and chemical modifications of RG-I. Removal of half of galactan chains from RG-I leads to loss of gelling capability pointing out on their leading role in this process. Rising of intensity of the bands attributed to galactose and glycosidic linkages in RG-I gel comparing to solution where this polymer exists as molecule associate indicates that the spatial organization of galactans in gel is changed. A model of the RG-I gelation is proposed: being destabilized at volumetric microwave heating RG-I associates are repacked forming network where RG-I molecules are entangled by galactan chains.

The Folding of the Specific DNA Recognition Subdomain of the Sleeping Beauty Transposase Is Temperature-Dependent and Is Required for Its Binding to the Transposon DNA

The reaction of DNA transposition begins when the transposase enzyme binds to the transposon DNA. Sleeping Beauty is a member of the mariner family of DNA transposons. Although it is an important tool in genetic applications and has been adapted for human gene therapy, its molecular mechanism remains obscure. Here, we show that only the folded conformation of the specific DNA recognition subdomain of the Sleeping Beauty transposase, the PAI subdomain, binds to the transposon DNA. Furthermore, we show that the PAI subdomain is well folded at low temperatures, but the presence of unfolded conformation gradually increases at temperatures above 15°C, suggesting that the choice of temperature may be important for the optimal transposase activity. Overall, the results provide a molecular-level insight into the DNA recognition by the Sleeping Beauty transposase.

Micellar catalytic effect as a factor of lipase activity regulation

238 Lipases (triacylglycerol hydrolase, EC 3.1.1.3) are a diverse family of enzymes that hydrolyze ester bonds of fat [1]. Lipases are widely distributed in mammals, plants, yeast, and bacteria. They are also widely used in the cleaning products, in food technology, and in paper manufacturing. Lipases are hydrophilic, whereas their substrates are hydrophobic molecules. It is known [2, 3] that the lipase activity increases sharply at substrate concentrations above the solubility limit; i.e., with the appearance of fat droplets in the system and, therefore, an interface. This phenomenon is called interfacial activation. Models that attempt to draw a molecular basis to this phenomenon are divided into two categories—enzyme and substrate models [3, 4]. The enzyme model [3, 5] is based on the conformational transition associated with structural changes in the vicinity of the enzyme active site occurr ring during the interaction with the surface of the subb strate fat droplet. The substrate model considers the regulation of the lipolytic activity through the changes in the local concentration of the substrate and its availl ability for the active site of the enzyme [3, 4]. Both mechanisms are associated with the properties of the surface of substrate particles, which can be modified by various amphiphilic substances. Quite often, such modifiers are represented by bile salts. They play an important role in the physiological processes of lipid metabolism and, owing to their amphiphilic structure, can modify the surface of substrate fat droplets [6]. The purpose of this study was to find arguments in favor of each of the mechanisms of lipase interfacial activation. A number of bile salts differing in hydroo philic and lipophilic properties were tested as a factor that regulates the level of lipolytic activity. We showed that the regulatory effect of the interface on the lipolyy tic activity is mainly determined by the micellar cataa lytic effect, namely, the ability of a microheterogee neous medium to support local reaction contact of substances that are poorly compatible in a homogee neous solution. In this work, we used lipase from Candida rugosa, sodium cholate (NaC), sodium deoxycholate (NaDC), and sodium chenodeoxycholate (NaCDC) from Sigma (United States). pNitrophenyl ester of lauric (dodee canoic) acid (pNPL, 98.9%, MP Biomedicals LLC) was used as a substrate. Kinetic measurements were performed with a Lambda 25 spectrophotometer (Perkin Elmer, United States) with a thermostated sample compartment. The rate of pNPL hydrolysis was monitored by the changes in …