Dependence of 13C chemical shifts on the spatial interaction of protons,and its application in structural and conformational studies of oligo- and poly-saccharides

Regularities in the variation of chemical shifts and the glycosidation effects in the ¹³C-n.m.r. spectra of disaccharides were found to depend on the configuration at the anomeric centre of the glycosidating pyranose, and the absolute configuration of both pyranoses moieties. These empirical regularities are explained in terms of the spatial proton-proton interactions within the statistically averaged, or preferred, conformation near the glycosidic linkage. The applicability of these effects for the determination of the anomeric and absolute configuration and the sequence of pyranose residues in oligo- and poly-saccharides is discussed. The conformational properties of glycosidic linkages in disaccharides and disaccharide fragments of oligo- and poly-saccharides are compared on the basis of ¹³C-n.m.r. data.     

New insights into the interaction of ribosomal protein L1 with RNA

The RNA-binding ability of ribosomal protein L1 is of profound interest, since L1 has a dual function as a ribosomal structural protein that binds rRNA and as a translational repressor that binds its own mRNA. Here, we report the crystal structure at 2.6 A resolution of ribosomal protein L1 from the bacterium Thermus thermophilus in complex with a 38 nt fragment of L1 mRNA from Methanoccocus vannielii. The conformation of RNA-bound T.thermophilus L1 differs dramatically from that of the isolated protein. Analysis of four copies of the L1-mRNA complex in the crystal has shown that domain II of the protein does not contribute to mRNA-specific binding. A detailed comparison of the protein-RNA interactions in the L1-mRNA and L1-rRNA complexes identified amino acid residues of L1 crucial for recognition of its specific targets on the both RNAs. Incorporation of the structure of bacterial L1 into a model of the Escherichia coli ribosome revealed two additional contact regions for L1 on the 23S rRNA that were not identified in previous ribosome models.     

Formation of reactive halide species by myeloperoxidase and eosinophil peroxidase

The formation of chloro- and bromohydrins from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine following incubation with myeloperoxidase or eosinophil peroxidase in the presence of hydrogen peroxide, chloride and/or bromide was analysed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. These products were only formed below a certain pH threshold value, that increased with increasing halide concentration. Thermodynamic considerations on halide and pH dependencies of reduction potentials of all redox couples showed that the formation of a given reactive halide species in halide oxidation coupled with the reduction of compound I of heme peroxidases is only possible below a certain pH threshold that depends on halide concentration. The comparison of experimentally derived and calculated data revealed that Cl(2), Br(2), or BrCl will primarily be formed by the myeloperoxidase-H(2)O(2)-halide system. However, the eosinophil peroxidase-H(2)O(2)-halide system forms directly HOCl and HOBr.     

Ribosomal protein L1 recognizes the same specific structural motif in its target sites on the autoregulatory mRNA and 23S rRNA

The RNA-binding ability of ribosomal protein L1 is of profound interest since the protein has a dual function as a ribosomal protein binding rRNA and as a translational repressor binding its mRNA. Here, we report the crystal structure of ribosomal protein L1 in complex with a specific fragment of its mRNA and compare it with the structure of L1 in complex with a specific fragment of 23S rRNA determined earlier. In both complexes, a strongly conserved RNA structural motif is involved in L1 binding through a conserved network of RNA–protein H-bonds inaccessible to the solvent. These interactions should be responsible for specific recognition between the protein and RNA. A large number of additional non-conserved RNA–protein H-bonds stabilizes both complexes. The added contribution of these non-conserved H-bonds makes the ribosomal complex much more stable than the regulatory one.     

Uniparental Genetic Heritage of Belarusians: Encounter of Rare Middle Eastern Matrilineages with a Central European Mitochondrial DNA Pool

Ethnic Belarusians make up more than 80% of the nine and half million people inhabiting the Republic of Belarus. Belarusians together with Ukrainians and Russians represent the East Slavic linguistic group, largest both in numbers and territory, inhabiting East Europe alongside Baltic-, Finno-Permic- and Turkic-speaking people. Till date, only a limited number of low resolution genetic studies have been performed on this population. Therefore, with the phylogeographic analysis of 565 Y-chromosomes and 267 mitochondrial DNAs from six well covered geographic sub-regions of Belarus we strove to complement the existing genetic profile of eastern Europeans. Our results reveal that around 80% of the paternal Belarusian gene pool is composed of R1a, I2a and N1c Y-chromosome haplogroups – a profile which is very similar to the two other eastern European populations – Ukrainians and Russians. The maternal Belarusian gene pool encompasses a full range of West Eurasian haplogroups and agrees well with the genetic structure of central-east European populations. Our data attest that latitudinal gradients characterize the variation of the uniparentally transmitted gene pools of modern Belarusians. In particular, the Y-chromosome reflects movements of people in central-east Europe, starting probably as early as the beginning of the Holocene. Furthermore, the matrilineal legacy of Belarusians retains two rare mitochondrial DNA haplogroups, N1a3 and N3, whose phylogeographies were explored in detail after de novo sequencing of 20 and 13 complete mitogenomes, respectively, from all over Eurasia. Our phylogeographic analyses reveal that two mitochondrial DNA lineages, N3 and N1a3, both of Middle Eastern origin, might mark distinct events of matrilineal gene flow to Europe: during the mid-Holocene period and around the Pleistocene-Holocene transition, respectively.     

Effect of herbicide tralkoxydim and 2-acylcyclohexane-1,3-diones on peroxidase activity

Effect of 2-acylcyclohexane-1,3-dione derivatives (tralkoxydim and its diketone precursors) on peroxidase-catalyzed oxidation of 3,3',5,5'-tetramethylbenzidine (TMB), o-phenylenediamine (PDA), and the phenol-4-aminoantipyrine (4-AAP) couple has been studied. This effect varies from horseradish peroxidase (HRP) inactivation to activation in the reactions of peroxidation ofTMB, PDA, and, to a lesser extent, the phenol-4-AAP couple. The diketone-mediated HRP activation depends strongly on pH, presence of dimethylformamide, the structures of tralkoxydim and other diketones, and the substrate nature. The type of activation in the course of peroxidation with the presence of tralkoxydim can be noncompetitive (PDA and TMB) or mixed (TMB) depending on conditions. The maximal level of the HRP activation mediated by diketones depends on their structure. It can reach 4000% of the initial HRP-catalyzed peroxidation rate for TMB and ca. 1000% for PDA. A test system is proposed for quantitative tralkoxydim assay at millimolar concentration. It includes HRP and TMB as the substrate with spectrometrical monitoring of the TMB peroxidation product at 655 nm.     

Molecular dynamics simulation of the size-dependent morphological stability of cubic shape silver nanoparticles

The morphological stability of sharp-edged silver nanoparticles is examined by the classical molecular dynamics (MD) simulations. The crystalline structure and the perfect fcc atom packing of a series of silver nanocubes (AgNC) of different sizes varying from 63 up to 1099 atoms are compared against quasi-spherical nanoparticles of the same sizes at temperature 303 K. Our MD simulations demonstrate that starting from the preformed perfect crystalline structures the cubic shape is preserved for AgNCs composed of 365–1099 atoms. Surprisingly, the rapid loss of the cubic shape morphology and transformation into the non-fcc-structure are found for smaller AgNCs composed of less than ~256 atoms. No such loss of the preformed crystalline structure is seen for quasi-spherical nanoparticles composed of 38–1007 atoms. The analysis of the temperature dependence and the binding energy of outermost Ag surface atoms suggests that the loss of the perfect cubic shape, rounding and smoothing of sharp edges and corners are driven by the tendency towards the increase in their coordination number. In addition, we revealed that AgNC₁₀₉₉ partially loses its sharp edges and corners in the aqueous environment; however, the polymer coating with poly(vinyl alcohol) (PVA) was able to preserve the well-defined cubic morphology. Finally, these results help improve the understanding of the role of surface capping agents in solution phase synthesis of Ag nanocubes.     

Chronic beta-adrenoreceptor activation increases cardiac cavity size through chamber remodeling and not via modifications in myocardial material properties

Chronic beta-adrenoreceptor (beta-AR) activation increases left ventricular (LV) cavity size by promoting a rightward shift in LV diastolic pressure-volume (P-V) relations in association with increases in low-tensile strength myocardial (non-cross-linked) collagen concentrations. Because diastolic P-V relations are determined by chamber remodeling as well as by myocardial material properties (indexed by myocardial stiffness), both of which are associated with modifications in myocardial collagen cross-linking, we evaluated whether chamber remodeling or alterations in myocardial material properties govern beta-AR-mediated modifications in diastolic P-V relations. The effects of chronic administration of isoproterenol (Iso; 0.04 mg.kg(-1).day(-1) from 12 to 19 mo of age) to spontaneously hypertensive rats (SHRs) on LV cavity dimensions, LV diastolic P-V relations, myocardial collagen characteristics, myocardial stiffness constants [e.g., the slope of the LV diastolic stress-strain relation (k)], and LV chamber and myocardial systolic function were assessed. SHRs at 19 mo of age had normal LV diastolic P-V relations, marked myocardial fibrosis (using a pathological score), increased myocardial cross-linked (insoluble to cyanogen bromide digestion) type I and type III collagen concentrations, and enhanced myocardial k values. Iso administration to SHRs resulted in enlarged LV cavity dimensions mediated by a rightward shift in LV diastolic P-V relations, increased volume intercept of the LV diastolic P-V relation, decreased LV relative wall thickness despite a tendency to augment LV hypertrophy, and increased non-cross-linked type I and type III myocardial collagen concentrations. Iso administration resulted in reduced pump function without modification of intrinsic myocardial systolic function. However, despite increasing myocardial non-cross-linked concentrations, Iso failed to alter myocardial k in SHRs. These results suggest that beta-AR-mediated rightward shifts in LV diastolic P-V relations, which induce decreased pump function, are mediated by chamber remodeling but not by modifications in myocardial material properties.