Krzysztof Brzezinski

High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 Å

The crystal structure of a Z-DNA hexamer duplex d(CGCGCG)2 determined at ultra high resolution of 0.55 Å and refined without restraints, displays a high degree of regularity and rigidity in its stereochemistry, in contrast to the more flexible B-DNA duplexes. The estimations of standard uncertainties of all individually refined parameters, obtained by full-matrix least-squares optimization, are comparable with values that are typical for small-molecule crystallography. The Z-DNA model generated with ultra high-resolution diffraction data can be used to revise the stereochemical restraints applied in lower resolution refinements. Detailed comparisons of the stereochemical library values with the present accurate Z-DNA parameters, shows in general a good agreement, but also reveals significant discrepancies in the description of guanine-sugar valence angles and in the geometry of the phosphate groups.

Chemistry of Monomeric and Dinuclear Non-Oxido Vanadium(IV) and Oxidovanadium(V) Aroylazine Complexes: Exploring Solution Behavior

A series of mononuclear non-oxido vanadium(IV) [V(IV)(L(1-4))2] (1-4), oxidoethoxido vanadium(V) [V(V)O(L(1-4))(OEt)] (5-8), and dinuclear μ-oxidodioxidodivanadium(V) [V(V)2O3(L(1))2] (9) complexes with tridentate aroylazine ligands are reported [H2L(1) = 2-furoylazine of 2-hydroxy-1-acetonaphthone, H2L(2) = 2-thiophenoylazine of 2-hydroxy-1-acetonaphthone, H2L(3) = 1-naphthoylazine of 2-hydroxy-1-acetonaphthone, H2L(4) = 3-hydroxy-2-naphthoylazine of 2-hydroxy-1-acetonaphthone]. The complexes are characterized by elemental analysis, by various spectroscopic techniques, and by single-crystal X-ray diffraction (for 2, 3, 5, 6, 8, and 9). The non-oxido V(IV) complexes (1-4) are quite stable in open air as well as in solution, and DFT calculations allow predicting EPR and UV-vis spectra and the electronic structure. The solution behavior of the [V(V)O(L(1-4))(OEt)] compounds (5-8) is studied confirming the formation of at least two different types of V(V) species in solution, monomeric corresponding to 5-8, and μ-oxidodioxidodivanadium [V(V)2O3(L(1-4))2] compounds. The μ-oxidodioxidodivanadium compound [V(V)2O3(L(1))2] (9), generated from the corresponding mononuclear complex [V(V)O(L(1))(OEt)] (5), is characterized in solution and in the solid state. The single-crystal X-ray diffraction analyses of the non-oxido vanadium(IV) compounds (2 and 3) show a N2O4 binding set and a trigonal prismatic geometry, and those of the V(V)O complexes 5, 6, and 8 and the μ-oxidodioxidodivanadium(V) (9) reveal that the metal center is in a distorted square pyramidal geometry with O4N binding sets. For the μ-oxidodioxidodivanadium species in equilibrium with 5-8 in CH2Cl2, no mixed-valence complexes are detected by chronocoulometric and EPR studies. However, upon progressive transfer of two electrons, two distinct monomeric V(IV)O species are detected and characterized by EPR spectroscopy and DFT calculations.

Purification, crystallization and preliminary crystallographic studies of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).

By degrading S-adenosyl-L-homocysteine, which is a byproduct of S-adenosyl-L-methionine-dependent methylation reactions, S-adenosyl-L-homocysteine hydrolase (SAHase) acts as a regulator of cellular methylation processes. S-Adenosyl-L-homocysteine hydrolase from the leguminose plant yellow lupin (Lupinus luteus), LlSAHase, which is composed of 485 amino acids and has a molecular weight of 55 kDa, has been cloned, expressed in Escherichia coli and purified. Crystals of LlSAHase in complex with adenosine were obtained by the hanging-drop vapour-diffusion method using 20%(w/v) PEG 4000 and 10%(v/v) 2-propanol as precipitants in 0.1 M Tris-HCl buffer pH 8.0. The crystals were tetragonal, space group P4(3)2(1)2, with unit-cell parameters a = 122.4, c = 126.5 A and contained two protein molecules in the asymmetric unit, corresponding to the functional dimeric form of the enzyme. Atomic resolution (1.17 A) X-ray diffraction data have been collected using synchrotron radiation.

Medicago truncatula histidine-containing phosphotransfer protein: Structural and biochemical insights into the cytokinin transduction pathway in plants.

Histidine‐containing phosphotransfer proteins (HPts) take part in hormone signal transduction in higher plants. The overall pathway of this process is reminiscent of the two‐component system initially identified in prokaryotes. HPts function in histidine–aspartate phosphorelays in which they mediate the signal from sensory kinases (usually membrane proteins) to RRs in the nucleus. Here, we report the crystal structure of an HPt protein from Medicago truncatula (MtHPt1) determined at 1.45 Å resolution and refined to an R‐factor of 16.7% using low‐temperature synchrotron‐radiation X‐ray diffraction data. There is one MtHPt1 molecule in the asymmetric unit of the crystal lattice with P212121 symmetry. The protein fold consists of six α helices, four of which form a C‐terminal helix bundle. The coiled‐coil structure of the bundle is stabilized by a network of S–aromatic interactions involving highly conserved sulfur‐containing residues. The structure reveals a solvent‐exposed side chain of His79, which is the phosphorylation site, as demonstrated by autoradiography combined with site‐directed mutation. It is surrounded by highly conserved residues present in all plant HPts. These residues form a putative docking interface for either the receiver domain of the sensory kinase, or for the RR. The biological activity of MtHPt1 was tested by autoradiography. It demonstrated phosphorylation by the intracellular kinase domain of the cytokinin receptor MtCRE1. Complex formation between MtHPt1 and the intracellular fragment of MtCRE1 was confirmed by thermophoresis, with a dissociation constant Kd of 14 μm.

Triple helical collagen-like peptide interactions with selected polyphenolic compounds.

Because collagen is the most abundant component of connective tissue, it is an excellent biomaterial in numerous medical applications. However, the utility of collagen is limited by its low mechanical strength in aqueous solutions and its susceptibility to proteolytic degradation in vivo. To improve the physical properties of collagen and to enhance its chemical resistance, it is necessary to stabilize its structure through chemical or physical modifications. In this study, we analyzed the interactions of a model molecule, a synthetic triple helical collagen-like peptide, with polyphenols such as curcumin, rutin, quercetin, naringin, and hypericin. Interactions between the peptide and polyphenolic compounds were analyzed using various techniques. The layer-by-layer assembly processes of a gold surface using the peptide and polyphenols was performed via surface plasmon resonance (SPR), atomic force microscopy (AFM), and ellipsometry. SPR screening of polyphenols was conducted in real time to select compounds that bind to the collagen-like peptide and could thus be applied to the stabilization of collagen. Selected polyphenols, especially naringin and hypericin, demonstrated notable binding to the peptide. To determine the nature of these interactions, experiments were supplemented with crystallographic studies and molecular docking of plant metabolites and collagen-like peptides.

Relative configuration, absolute configuration and absolute structure of three isomeric 8-benzyl-2-[(4-bromophenyl)(hydroxy)methyl]-8-azabicyclo[3.2.1]octan-3-ones.

The title compounds, C21H22BrNO2, are isomeric 8-benzyl-2-[(4-bromophenyl)(hydroxy)methyl]-8-azabicyclo[3.2.1]octan-3-ones. Compound (I), the (±)-exo,syn-(1RS,2SR,5SR,9SR) isomer, crystallizes in the hexagonal space group R-3, while compounds (II) [the (+)-exo,anti-(1R,2S,5S,9R) isomer] and (III) [the (±)-exo,anti-(1RS,2SR,5SR,9RS) isomer] crystallize in the orthorhombic space groups P212121 and Pna21, respectively. The absolute configuration was determined for enantiomerically pure (II). For the noncentrosymmetric crystal of (III), its absolute structure was established. In the crystal structures of (I) and (II), an intramolecular hydrogen bond is formed between the hydroxy group and the heterocyclic N atom. In the crystal structure of racemic (III), hydrogen-bonded chains of molecules are formed via intermolecular O-H...O interactions. Additionally, face-to-edge π-π interactions are present in the crystal structures of (I) and (II). In all three structures, the piperidinone rings adopt chair conformations and the N-benzyl substituents occupy the equatorial positions.

S-adenosyl-L-homocysteine hydrolase from a hyperthermophile (Thermotoga maritima) is expressed in Escherichia coli in inactive form – Biochemical and structural studies

Thermotoga maritima is a hyperthermophilic bacterium but its genome encodes a number of archaeal proteins including S-adenosyl-L-homocysteine hydrolase (SAHase), which regulates cellular methylation reactions. The question of proper folding and activity of proteins of extremophilic origin is an intriguing problem. When expressed in E.coli and purified (as a homotetramer) at room temperature, the hyperthermophilic SAHase from T.maritima was inactive. ITC study indicated that the protein undergoes heat-induced conformational changes, and enzymatic activity assays demonstrated that these changes are required to attain enzymatic activity. To explain the mechanism of thermal activation, two crystal structures of the inactive form of T. maritima SAHase (iTmSAHase) were determined for an incomplete binary complex with the reduced cofactor (NADH), and in a mixture of binary complexes with NADH and with adenosine. In contrast to active SAHases, in iTmSAHase only two of the four subunits contain a bound cofactor, predominantly in its non-reactive, reduced state. Moreover, the closed-like conformation of the cofactor-containing subunits precludes substrate delivery to the active site. The two other subunits cannot be involved in the enzymatic reaction either; although they have an open-like conformation, they do not contain the cofactor, whose binding site may be occupied by an adenosine molecule. The results suggest that this enzyme, when expressed in mesophilic cells, is arrested in the activity-incompatible conformation revealed by its crystal structures.

Carbon nano-onion composites: Physicochemical characteristics and biological activity

ABSTRACT Carbon nano-onion/surfactant (CNO/surfactant) composites offer the possibility to easily produce the soluble nanostructures. That approach combines the hydrophilicity of surfactants with the robustness of carbon structures to produce composites with superior and unusual physicochemical properties. We used the following surfactants: hexadecyltrimethylammonium bromide (CTAB), sodium dodecyl sulfate (SDS), sodium dodecyl benzene sulfonate (SDBS), 4-(1,1,3,3-tetramethylbutyl)phenyl-polyethylene glycol (Triton X-100), and polyethylene glycol sorbitan monolaurate (Tween 20) to non-covalently modify CNO surfaces. The existence of stable CNO composites are clearly evidenced by direct transmission electron microscopy observations, which are also supported by thermogravimetric analyses. Dynamic light scattering and zeta potential confirmed their dispersion and stability. Additionally, the biological activity of well-dispersed CNO/surfactant composites against a strain of Escherichia coli was assayed. In vitro antimicrobial assays for the composites revealed that only the CNO/CTAB composite decreased cell viability. This activity could be assigned to the simple composite dissociation in water solutions, however antimicrobial properties of the composite are slightly better when compared with pure CTAB. This indicate some synergic effect with respect to the properties of the pure surfactant.

(2R)-8-Benzyl-2-[(S)-hy­droxy(phen­yl)meth­yl]-8-aza­bicyclo­[3.2.1]octan-3-one

The crystal of the title compound, C21H23NO2, was chosen from a conglomerate formed by a racemic mixture. An intramolecular hydrogen bond is formed between hydroxy group and heterocyclic N atom of the azabicyclo[3.2.1]octan-3-one system. The crystal structure is stabilized by C—H⋯O interactions between aliphatic C—H groups and the carbonyl O atom. For the title chiral crystal, the highly redundant and accurate diffraction data set collected with low energy copper radiation gave a Flack parameter of 0.12 (18) for anomalous scattering effects originating from O atoms.

Bis(2,2':6',2''-terpyridine)-ruthenium(II) bis-(perchlorate) hemihydrate.

The asymmetric unit of the title compound, [Ru(C15H11N3)2](ClO4)2·0.5H2O, contains one ruthenium–terpiridine complex cation, two perchlorate anions and one half-molecule of water. Face-to-face and face-to-edge π-stacking interactions between terpyridine units [centroid–centroid distances = 3.793 (2) and 3.801 (2)  Å] stabilize the crystal lattice The partially occupied water molecule interacts with two perchlorate ions via O—H⋯O hydrogen bonds. In the crystal lattice, the complex cations, perchlorate ion-water pairs and the second perchlorate anions are arranged into columns along b direction.