Ekaterina Smirnova

Ectothiorhodospira variabilis, sp. nov., an alkaliphilic and halophilic purple sulfur bacterium from soda lakes

During studies of moderately halophilic strains of Ectothiorhodospira from steppe soda lakes, we found a novel group of bacteria related to Ectothiorhodospira haloalkaliphila with salt optima at 50-80 g NaCl l(-1). Phylogenetic analysis using 16S rRNA gene sequences of strains from soda lakes in Mongolia, Egypt and Siberia revealed separation of the group of new isolates from other Ectothiorhodospira species, including the closely related Ect. haloalkaliphila. DNA-DNA hybridization studies demonstrated that the new isolates form a homogeneous group at the species level, but at the same time are distinct from related species such as Ect. haloalkaliphila, Ect. vacuolata, Ect. shaposhnikovii and Ect. marina. The new isolates are considered to be strains of a novel species, for which the name Ectothiorhodospira variabilis sp. nov. is proposed, with the type strain WN22(T) (=VKM B-2479(T) =DSM 21381(T)). Photosynthetic pigments of the novel species are bacteriochlorophyll a and carotenoids of the spirilloxanthin series with spirilloxanthin and derivatives thereof, together with small amounts of lycopene and rhodopin. Gas vesicles are formed by most of the strains, particularly in media containing yeast extract (0.5 g l(-1)) and acetate (0.5-2.0 g l(-1)). Sequence analysis of nifH (nitrogenase) and cbbL (RuBisCO) confirmed the assignment of the strains to the genus Ectothiorhodospira and in particular the close relationship to Ect. haloalkaliphila. The novel species Ect. variabilis is found in soda lakes separated by great geographical distances and is an alkaliphilic and halophilic bacterium that tolerates salt concentrations up to 150-200 g NaCl l(-1).

pH-responsive modulation of insulin aggregation and structural transformation of the aggregates

Over the past two decades, much information has appeared on electrostatically driven molecular mechanisms of protein self-assembly and formation of aggregates of different morphology, varying from soluble amorphous structures to highly-ordered amyloid-like fibrils. Protein aggregation represents a special tool in biomedicine and biotechnology to produce biological materials for a wide range of applications. This has awakened interest in identification of pH-triggered regulators of transformation of aggregation-prone proteins into structures of higher order. The objective of the present study is to elucidate the effects of low-molecular-weight biogenic agents on aggregation and formation of supramolecular structures of human recombinant insulin, as a model therapeutic protein. Using dynamic light scattering, turbidimetry, circular dichroism, fluorescence spectroscopy, atomic force microscopy, transmission electron microscopy, and nuclear magnetic resonance, we have demonstrated that the amino acid l-arginine (Arg) has the striking potential to influence insulin aggregation propensity. It was shown that modification of the net charge of insulin induced by changes in the pH level of the incubation medium results in dramatic changes in the interaction of the protein with Arg. We have revealed the dual effects of Arg, highly dependent on the pH level of the solution - suppression or acceleration of the aggregation of insulin at pH 7.0 or 8.0, respectively. These effects can be regulated by manipulating the pH of the environment. The results of this study may be of interest for development of appropriate drug formulations and for the more general insight into the functioning of insulin in living systems, as the protein is known to release by exocytosis from pancreatic beta cells in a pH-dependent manner.

Calibration of CryojetHT and Cobra Plus Cryosystems used in X-ray diffraction studies

CryoJetHT (Oxford Instruments) and Cobra Plus (Oxford Cryosystems) cryosystems, which are used for sample cooling in X-ray diffraction experiments, have been calibrated. It is shown that the real temperature in the vicinity of the sample differs significantly (the deviation is as high as 8–10 K at low temperatures) from the temperature recorded by authorized sensors of these systems. The calibration results are confirmed by measurements of the unit-cell parameters of GdFe3(BO3)4 single crystal in the temperature range of its phase transition. It is shown that, to determine the real temperature of a sample, one must perform an independent calibration of cryosystems rather than rely on their ratings.

Transient transformation of oligomeric structure of alpha-crystallin during its chaperone action

New evidence for dynamic behavior and flexible oligomeric structure of the molecular chaperone α-crystallin is presented. Based on the results of laser dynamic light scattering, centrifugal ultrafiltration, size exclusion chromatography, analytical ultracentrifugation and electrophoresis in polyacrylamide gel, addition of α-crystallin to fully reduced α-lactalbumin, used as a model protein substrate, at the stage of its start aggregate formation results in dissociation of multimeric structure of α-crystallin. In addition to large oligomers, transient low-sized assemblies are formed with the apparent molecular mass of 50-55 kDa that corresponds to the α-crystallin dimeric form associated with destabilized monomeric α-lactalbumin. This phenomenon is suggested to represent an essential component of a transient protective mechanism tuning the stressed protein to binding sites on the exposed surface of the chaperone dimers.

Formation of supramolecular structures of a native-like protein in the presence of amphiphilic peptides: Variations in aggregate morphology

A striking potential of the amphiphilic dipeptides, Arg‐Phe or Asp‐Phe, to induce aggregation of a model protein, alcohol dehydrogenase in its native‐like state, has been demonstrated under physiologically relevant conditions, using dynamic light scattering, fluorescence spectroscopy, circular dichroism, transmission electron‐ and atomic force microscopy. The peptide action resulted in accumulation of a variety of morphologically distinct supramolecular structures profoundly differing from those generated by the heat‐induced aggregation at the early stages of the process, when amyloid fibril assemblies were not detectable. The biogenic amphiphilic agents are suggested to act as regulators of structural transformations of native‐like proteins.

Can aggregation of insulin govern its fate in the intestine? Implications for oral delivery of the drug

The objective of this study is to elucidate the role of low-molecular weight biogenic agents, resembling dietary-derived products naturally occurring in the intestine, in the regulation of transformations of soluble aggregation-prone insulin into aggregates of higher order. In the course of model experiments, a striking potential of the amino acids L-arginine (Arg) and L-lysine (Lys) and a number of positively charged peptides to induce formation of heterogenic supramolecular structures of insulin was demonstrated under environment conditions where the protein aggregation in their absence was not observed. This phenomenon is assumed to be essential for elaboration of strategies of oral delivery of insulin to diabetic patients supplemented by controlling the pH values of the intestinal environment where the drug is released.

Algorithm and program for precise determination of unit-cell parameters of single crystal taking into account the sample eccentricity

A technique has been developed to refine the unit-cell parameters of single crystals with minimization of the influence of instrumental errors on the result. The corresponding computational procedure HuberUB is added to the software package of Huber-5042 diffractometer with a point detector and closedcycle helium cryostat Displex DE-202. The parameters of unit cell, its orientation, the goniometer zero angles, the sample eccentricity, the distances in the goniometer, and the radiation wavelength were refined by the nonlinear least-squares method, which allows imposition of constraints on the unit-cell parameters, depending on the crystal symmetry. The technique is approved on a LuB12 single crystal. The unit-cell parameters are determined in a temperature range of 20–295 K, with an absolute error not larger than 0.0004 Å (the relative error is of ~5 × 10–5). The estimates of the unit-cell parameters obtained by the proposed method are evidenced to be unbiased. Some specific features of the behavior of parameters in the ranges of 120–140 and 20–50 K are revealed, which correlate with the anomalies of the physical properties of the crystal.

Structure of Gd0.95Bi0.05Fe3(BO3)4 single crystals at 293 and 90 K

The structure of GdFe3(BO3)4 single crystals has been studied by X-ray diffraction at 293 and 90 K. The crystals are grown from a flux in the Bi2Mo3O12–B2O3–Li2MoO4–Gd2O3–Fe2O3 system. The results of chemical analysis and structural study show that these crystals contain bismuth as an impurity. It is found that bismuth atoms are located at gadolinium sites in the structure. A decrease in the temperature is accompanied by a lowering of the symmetry from sp. gr. R32 (at 293 K) to sp. gr. P3121 (at 90 K). The presence of two types of iron chains with different geometries at 90 K promotes a change in the magnetic properties of these crystals with a decrease in the temperature.

Crystal structure, phase transition and structural deformations in iron borate (Y0.95Bi0.05)Fe3(BO3)4 in the temperature range 90–500 K

An accurate X-ray diffraction study of (Y0.95Bi0.05)Fe3(BO3)4 single crystals in the temperature range 90-500 K was performed on a laboratory diffractometer and used synchrotron radiation. It was established that the crystal undergoes a diffuse structural phase transition in the temperature range 350-380 K. The complexity of localization of such a transition over temperature was overcome by means of special analysis of systematic extinction reflections by symmetry. The transition temperature can be considered to be Tstr ≃ 370 K. The crystal has a trigonal structure in the space group P3121 at temperatures of 90-370 K, and it has a trigonal structure in the space group R32 at 375-500 K. There is one type of chain formed by the FeO6 octahedra along the c axis in the R32 phase. When going into the P3121 phase, two types of nonequivalent chains arise, in which Fe atoms are separated from the Y atoms by a different distance. Upon lowering the temperature from 500 to 90 K, a distortion of the Y(Bi)O6, FeO6, B(2,3)O3 coordination polyhedra is observed. The distances between atoms in helical Fe chains and Fe-O-Fe angles change non-uniformly. A sharp jump in the equivalent isotropic displacement parameters of O1 and O2 atoms within the Fe-Fe chains and fluctuations of the equivalent isotropic displacement parameters of B2 and B3 atoms were observed in the region of structural transition as well as noticeable elongation of O1, O2, B2, B3, Fe1, Fe2 atomic displacement ellipsoids. It was established that the helices of electron density formed by Fe, O1 and O2 atoms may be structural elements determining chirality, optical activity and multiferroicity of rare-earth iron borates. Compression and stretching of these helices account for the symmetry change and for the manifestation of a number of properties, whose geometry is controlled by an indirect exchange interaction between iron cations that compete with the thermal motion of atoms in the structure. Structural analysis detected these changes as variations of a number of structural characteristics in the c unit-cell direction, that is, the direction of the helices. Structural results for the local surrounding of the atoms in (Y0.95Bi0.05)Fe3(BO3)4 were confirmed by EXAFS and Mössbauer spectroscopies.