Crystal structure of the intrinsically flexible addiction antidote MazE

A specific camel VHH (variable domain of dromedary heavy chain antibody) fragment was used to crystallize the intrinsically flexible addiction antidote MazE. Only 45% of the polypeptide chain is found ordered in the crystal. The MazE monomer consisting of two beta-hairpins connected by a short alpha-helix has no hydrophobic core on its own and represents only one half of a typical protein domain. A complete domain structure is formed by the association of two chains, creating a hydrophobic core between two four-stranded beta-sheets. This hydrophobic core consists exclusively of short aliphatic residues. The folded part of MazE contains a novel DNA binding motif. A model for DNA binding that is consistent with the available biochemical data is presented.     

Recognition of the intrinsically flexible addiction antidote MazE by a dromedary single domain antibody fragment. Structure,thermodynamics of binding,stability, and influence on interactions with DNA

The Escherichia coli mazEF operon defines a chromosomal addiction module that programs cell death under various stress conditions. It encodes the toxic and long-lived MazF and the labile antidote MazE. The denaturation of MazE is a two-state reversible dimer-monomer transition. At lower concentrations the denatured state is significantly populated. This leads to a new aspect of the regulation of MazE concentration, which may decide about the life and death of the cell. Interactions of MazE with a dromedary antibody domain, cAbMaz1 (previously used as a crystallization aid), as well as with promoter DNA were studied using microcalorimetric and spectroscopic techniques. Unique features of cAbMaz1 enable a specific enthalpy-driven recognition of MazE and, thus, a significant stabilization of its dimeric native conformation. The MazE dimer and the MazE dimer-cAbMaz1 complex show very similar binding characteristics with promoter DNA, i.e. three binding sites with apparent affinities in micromolar range and highly exothermic binding accompanied by large negative entropy contributions. A working model for the MazE-DNA assembly is proposed on the basis of the structural and binding data. Both binding and stability studies lead to a picture of MazE solution structure that is significantly more unfolded than the structure observed in a crystal of the MazE-cAbMaz1 complex.     

Dominant Driving Forces in Human Telomere Quadruplex Binding-Induced Structural Alterations

Recently various pathways of human telomere (ht) DNA folding into G-quadruplexes and of ligand binding to these structures have been proposed. However, the key issue as to the nature of forces driving the folding and recognition processes remains unanswered. In this study, structural changes of 22-mer ht-DNA fragment (Tel22), induced by binding of ions (K⁺, Na⁺) and specific bisquinolinium ligands, were monitored by calorimetric and spectroscopic methods and by gel electrophoresis. Using the global model analysis of a wide variety of experimental data, we were able to characterize the thermodynamic forces that govern the formation of stable Tel22 G-quadruplexes, folding intermediates, and ligand-quadruplex complexes, and then predict Tel22 behavior in aqueous solutions as a function of temperature, salt concentration, and ligand concentration. On the basis of the above, we believe that our work sets the framework for better understanding the heterogeneity of ht-DNA folding and binding pathways, and its structural polymorphism.     

Vegetation of the Birjučij Island spit in the Azov Sea. Sand steppe vegetation

The syntaxa of the near-natural sand steppes (classFestucetea vaginatae) and their substitutes due to trampling (Chenopodietea) were studied in 1991 during the Ukrainian-Czech expedition to the Birju?ij Island Spit (Azov Sea, Ukraine). Within the allianceFestucion beckeri Vicherek 1972 (classFestucetea vaginatae Soó 1968 emend.Vicherek 1972, orderFestucetalia vaginatae Soó 1957) three associations and five communities without rank are described, covering the vegetation variability along gradients of sand stabilization/soil development and salinization/moisture. Further, two associations of the classChenopodietea, due to deer influence, are described. Four associations (Centaureo odessanae-Stipetum capillatae, Poo bulbosae-Caricetum colchicae, Secali-Cynodontetum dactyli andHeliotropio dolosi-Brometum japonici) are described as new.     

Controlled inactivation of Trichophyton rubrum using shaped electrical pulse bursts: Parametric analysis

The dermatophytes infect the skin by adherence to the epidermis followed by germination, growth, and penetration of the fungal hyphae within the cells. The aim of this study was to investigate the efficacy of the pulsed electric fields (PEF) of controlled inactivation of Trichophyton rubrum (ATCC 28188). In this work, we have used bursts of the square wave PEF pulses of different intensity (10–30 kV/cm) to induce the irreversible inactivation in vitro. The electric field pulses of 50 µs and 100 µs have been generated in bursts of 5, 10, and 20 pulses with repetition frequency of 1 Hz. The dynamics of the inactivation using different treatment parameters were studied and the inactivation map for the T. rubrum has been defined. Further, the combined effect of PEF with the antifungal agents itraconazole, terbinafine, and naftifine HCl was investigated. It has been demonstrated that the combined effect results in the full inactivation of T. rubrum colony. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1056–1060, 2016     

Specific potassium binding stabilizes pI258 arsenate reductase from Staphylococcus aureus

Arsenate reductase (ArsC) from Staphylococcus aureus plasmid pI258 catalyzes the reduction of arsenate to arsenite and plays a role in bacterial heavy metal resistance. The high resolution x-ray structure of ArsC reveals the atomic details of the K+ binding site situated next to the catalytic P-loop structural motif of this redox enzyme. A full thermodynamic study of the binding characteristics of a series of monovalent cations (Li+, Na+, K+, Rb+, and Cs+) and their influence on the thermal stability of ArsC was performed with isothermal titration calorimetry, circular dichroism spectroscopy, and differential scanning calorimetry. Potassium has the largest affinity with a Ka of 3.8 x 10(3) m(-1), and the effectiveness of stabilization of ArsC by monovalent cations follows the binding affinity order: K+ > Rb+ > Cs+ > Na+ > Li+. A mutagenesis study on the K+ binding side chains showed that Asn-13 and Asp-65 are essential for potassium binding, but the impact on the stability of ArsC was the most extreme when mutating Ser-36. Additionally, the thermal stabilization by K+ is significantly reduced in the case of the ArsC E21A mutant, showing the importance of a Glu-21-coordinated water molecule in its contact with K+. Although potassium is not essential for catalysis, in its presence the kcat/KM increases with a factor of 5. Altogether, the interaction of K+ with specific residues in ArsC is an enthalpydriven process that stabilizes ArsC and increases the specific activity of this redox enzyme.     

Synthesis of 2-(3-(3,5-bis(trifluoromethyl)phenyl)thioureido)-3-((dimethylamino)methyl)camphor organocatalysts

In a stereo-divergent synthesis, three novel camphor-derived bifunctional thiourea organocatalysts 7-9 have been prepared in five steps starting from (+)-camphor. In addition, borneol-derived bifunctional thiourea organocatalysts 19/19' have been prepared in three steps from (1S)-(+)-camphorquinone. Novel organocatalysts 7-9, 19/19' have been evaluated in a model reaction of Michael addition of dimethyl malonate to trans-β-nitrostyrene with low to moderate enantioselectivities (20%-60% ee). Configuration of all novel compounds has been meticulously determined using nuclear magnetic resonance (NMR) techniques.     

Structural and Thermodynamic Characterization of Vibrio fischeri CcdB

CcdB_Vfi from Vibrio fischeri is a member of the CcdB family of toxins that poison covalent gyrase-DNA complexes. In solution CcdB_Vfi is a dimer that unfolds to the corresponding monomeric components in a two-state fashion. In the unfolded state, the monomer retains a partial secondary structure. This observation correlates well with the crystal and NMR structures of the protein, which show a dimer with a hydrophobic core crossing the dimer interface. In contrast to its F plasmid homologue, CcdB_Vfi possesses a rigid dimer interface, and the apparent relative rotations of the two subunits are due to structural plasticity of the monomer. CcdB_Vfi shows a number of non-conservative substitutions compared with the F plasmid protein in both the CcdA and the gyrase binding sites. Although variation in the CcdA interaction site likely determines toxin-antitoxin specificity, substitutions in the gyrase-interacting region may have more profound functional implications.     

New molybdenum(V) complexes based on the {Mo2O4} structural core with esters or anions of malonic and succinic acid

A series of malonato complexes of molybdenum(V) was prepared by reacting (PyH)₅[MoOCl₄(H₂O)]₃Cl₂ or (PyH)_n[MoOBr₄]_n with malonic acid (H₂mal) or a half-neutralized acid, hydrogen malonate (Hmal⁻), at ambient conditions: (PyH)₃[Mo₂O₄Cl₄(μ₂-Hmal)] · CH₃CN (1), (PyH)₃[Mo₂O₄Br₄(μ₂-Hmal)] · CH₃CN (2), (PyH)₂[Mo₂O₄Cl(η²-mal)(μ₂-Hmal)Py] (3), (3,5-LutH)₂(H₃O) [Mo₂O₄(η²-mal)₂(μ₂-Hmal)] (4), (PyH)[Mo₂O₄Cl₂(μ₂-Memal)Py₂] (5), (3,5-LutH)[Mo₂O₄Cl₂(μ₂-Memal)(3,5-Lut)₂] (6), (PyH)[Mo₂O₄Cl₂(μ₂-Etmal)Py₂] (7), (3,5-LutH)[Mo₂O₄Cl₂(μ₂-Prmal)(3,5-Lut)₂] (8) and [{Mo₂O₄(μ₂-Memal)Py₂}₂(μ₂-OCH₃)₂] (9) (where Py = pyridine, C₅H₅N; PyH⁺ = pyridinium cation, C₅H₅NH⁺; 3,5-Lut = 3,5-lutidine, C₇H₉N; 3,5-LutH⁺ = 3,5-lutidinium cation, C₇H₉NH⁺; mal²⁻ = malonate, ⁻OOCCH₂COO⁻; Memal⁻ = monomethyl malonate, ⁻OOCCH₂COOCH₃; Etmal⁻ = monoethyl malonate, ⁻OOCCH₂COOC₂H₅ and Prmal⁻ = monopropyl malonate, ⁻OOCCH₂COOC₃H₇). The complex anions of compounds 1-8 have a common structural feature: a dinuclear, singly metal-metal bonded {Mo₂O₄}²⁺ core with the carboxylate moiety of the malonato ligand coordinated in a syn-syn bidentate bridging manner to the pair of metal atoms. The remaining four coordination sites of the {Mo₂O₄}²⁺ core are occupied with halides in 1 and 2, with halides/pyridine ligands in 5-8, with a pair of bidentate malonate ions in 4 and with the combination of all in 3. The neutral molecules of 9 consist of two {Mo₂O₄}²⁺ cores linked with a pair of methoxide ions into a chain-like, tetranuclear cluster. An esterification of malonic acid was observed to take place in the reaction mixtures containing alcohols. Solvothermal reactions with malonic acid carried out at 115 °C produced anionic acetato complexes as found in (PyH)[Mo₂O₄Cl₂(μ₂-OOCCH₃)Py₂] · Py (10), (PyH)[Mo₂O₄Cl₂(μ₂-OOCCH₃)Py₂] (11), (3,5-LutH)[Mo₂O₄Cl₂(μ₂-OOCCH₃)(3,5-Lut)₂] (12) and (4-MePyH)₃[Mo₂O₄Cl₂(μ₂-OOCCH₃)(4-MePy)₂]₂Cl (13) (4-MePy = 4-methylpyridine, C₆H₇N). The acetate coordinated in the syn-syn bidentate bridging mode in all. Reactions of (PyH)₅[MoOCl₄(H₂O)]₃Cl₂ with succinic acid (H₂suc) at ambient conditions resulted in a complex with a half-neutralized acid, (PyH)[Mo₂O₄Cl₂(μ₂-Hsuc)Py₂] · Py (14) (Hsuc⁻ = hydrogen succinate, ⁻OOC(CH₂)₂COOH), while those carried out at 115 °C in a tetranuclear succinato complex, (4-MePyH)₂[{Mo₂O₄Cl₂(4-MePy)₂}₂(μ₄-suc)] (15) (suc²⁻ = succinate, ⁻OOC(CH₂)₂COO⁻). The tetranuclear anion of 15 consists of two {Mo₂O₄}²⁺ cores covalently linked with a tetradentate succinato ligand. The compounds were fully characterized by infrared vibrational spectroscopy, elemental analyses and X-ray diffraction studies.     

Synthesis of Novel Camphor‐Derived Bifunctional Thiourea Organocatalysts

Synthesis and catalyst performance of 2,3‐ (types B and C ) and 2,8‐disubstituted (type D ) thiourea bifunctional organocatalysts was attempted. The synthesis of catalyst of type B has, so far, not been realized, while catalysts of type C , i.e., the 2,3‐exo‐ and the 2‐endo‐3‐exo‐thiourea catalysts, were prepared in six steps starting from (+)‐camphor. The catalysts of type D were prepared from (+)‐camphor in eight steps. All the potential catalysts as well as most of the intermediate products were carefully structurally characterized. The thiourea bifunctional organocatalysts were tested in a model reaction of Michael addition of dimethyl malonate to trans‐β‐nitrostyrene. Chirality 27:39–52, 2015. © 2014 Wiley Periodicals, Inc.