Anna Brzuszkiewicz

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 0.55u2009Å 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.

On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin.

Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C(α) and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5u2005Å and more than one third were conserved within 0.1u2005Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments.

To scavenge or not to scavenge: that is the question

Analysis of a series of diffraction data sets measured from four native as well as four nicotinic acid-soaked crystals of trypsin at 100 K shows a high variability in radiation-sensitivity among individual crystals for both nicotinic acid-soaked and native crystals. The level of radiation-sensitivity and the extent of its variability is statistically indistinguishable between the two conditions. This suggests that this potential scavenger does not have any statistically significant effect on the amount of radiation damage incurred in the crystals on X-ray irradiation. This is in contrast to previous results [Kauffmann et al. (2006), Structure, 14, 1099-1105] where only one crystal specimen was used for each condition (native and nicotinic acid-soaked).

Thiophosphorylated bis-thioureas for competitive bulk liquid membrane transport of some metal ions

Eight N-thiophosphorylated bis-thioureas of the common formula Z[NHC(S)NHP(S)(OiPr) 2] 2 [Z = (1), 1,2-C 6H 4 (2), 1,3-C 6H 4 (3), 1,4-C 6H 4 (4), CH 2(1,4-C 6H 4) 2 (5), O(1,4-C 6H 4) 2 (6), S(1,4-C 6H 4) 2 (7), CH 2(1,4-C 6H 10) 2 (8)] have been synthesized and characterized by NMR spectroscopy and elemental analysis. Molecular structures of 3, 4, 5·0.5C 6H 14, 6·CH 2Cl 2 and 8 were elucidated by X-ray diffraction revealing two linear intramolecular hydrogen bonds. Their crystal structures are stabilized by four intermolecular hydrogen bonds, which in turn lead to a polymeric chain formation. Competitive transport experiments involving metal ions from an aqueous source phase through a chloroform membrane into an aqueous receiving phase have been carried out using 1-8 as the ionophore present in the organic phase.

Structure of EstA esterase from psychrotrophic Pseudoalteromonas sp. 643A covalently inhibited by monoethylphosphonate.

The crystal structure of the esterase EstA from the cold-adapted bacterium Pseudoalteromonas sp. 643A was determined in a covalently inhibited form at a resolution of 1.35 A. The enzyme has a typical SGNH hydrolase structure consisting of a single domain containing a five-stranded beta-sheet, with three helices at the convex side and two helices at the concave side of the sheet, and is ornamented with a couple of very short helices at the domain edges. The active site is located in a groove and contains the classic catalytic triad of Ser, His and Asp. In the structure of the crystal soaked in diethyl p-nitrophenyl phosphate (DNP), the catalytic serine is covalently connected to a phosphonate moiety that clearly has only one ethyl group. This is the only example in the Protein Data Bank of a DNP-inhibited enzyme with covalently bound monoethylphosphate.

Systematic coordination chemistry and cytotoxicity of copper(II) complexes with methyl substituted 4-nitropyridine N-oxides.

Three new nitrato copper(II) complexes of dimethyl substituted 4-nitropyridine N-oxide were synthesized and characterized by elemental analysis, magnetic, spectroscopic, thermal and X-ray methods, respectively. They were isolated as trans isomers, mononuclear (μ=1.70-1.88 BM), five (1-2) and four (3) coordinate species of general formula [Cu(NO3)2(H2O)L2] where L=2,3-dimethyl-, 2,5-dimethyl-4-nitropyridine N-oxide and [Cu (NO3)2L2], L=3,5-dimethyl-4-nitropyridine N-oxide, respectively. The X-ray crystal structure of (1) (L=2,3-dimethyl-4-nitropyridine N-oxide) was determined. The organic ligands, the complexes and copper hexaqua ion as a reference were tested in vitro on the cytotoxic activity against human cancer cell lines: MCF-7 (breast), SW-707 (colon) and P-388 (murine leukemia). The complexes are relatively strong cytotoxic agents towards P-388 cell line. Comparative analysis was performed for all known copper(II) complexes containing methyl derivatives of the 4-nitropyridine N-oxide on the basis of their composition, structure and cytotoxic activities. To obtain the typical structure for these species (i.e., 4-coordinate mononuclear of the type trans-[Cu(inorganic anion)2L2]), two methyl groups must be situated on both sides of nitrogen atom(s) (i.e., NO and NO2) in the ligand. The biological activity was found to be strongly dependent upon the number of the methyl groups and the type of cell line. The best cytotoxic results were found for the complexes without substituents or with one methyl group. Generally, for all cell lines, the complexation increased cytotoxicity when compared with the free ligands.

N-[tert-Butoxycarbonylglycyl-(Z)-α,β-dehydrophenylalanylglycyl-(E)-α,β-dehydrophenylalanylphenylalanyl]- 4-nitroaniline ethanol solvate

The alpha,beta-dehydrophenylalanine residues influence the conformation of the title pentapeptide Boc0-Gly1-Delta(Z)Phe2-Gly3-Delta(E)Phe4-L-Phe5-p-NA ethanol solvate, C42H43N7O9.C2H5OH. The first unsaturated phenylalanyl (Delta(Z)Phe2) and the third glycyl (Gly3) residues form a type I beta turn, while the second unsaturated phenylalanyl (Delta(E)Phe4) and the last phenylalanyl (L-Phe5) residues are part of a type II beta turn. All the amino acids in the peptide are linked trans to one another. The crystal structure is stabilized by intra- and intermolecular hydrogen bonds.

Two phosphonodehydrotripeptides: Boc0–Gly1–Δ(Z)Phe2–α-Abu3PO3Me2 and Boc0–Gly1–Δ(Z)Phe2–α-Nva3PO3Et2

The present paper reports the crystal structures of two short phosphonotripeptides (one in two crystal forms) containing one ΔPhe (dehydrophenylalanine) residue, namely dimethyl (3-{[tert-butoxycarbonylglycyl-α,β-(Z)-dehydrophenylalanyl]amino}propyl)phosphonate, Boc(0)-Gly(1)-Δ(Z)Phe(2)-α-Abu(3)PO3Me2, C21H32N3O7P, (I), and diethyl (4-{[tert-butoxycarbonylglycyl-α,β-(Z)-dehydrophenylalanyl]amino}butyl)phosphonate, Boc(0)-Gly(1)-Δ(Z)Phe(2)-α-Nva(3)PO3Et2, as the propan-2-ol monosolvate 0.122-hydrate, C24H38N3O7P·C3H8O·0.122H2O, (II), and the ethanol monosolvate 0.076-hydrate, C24H38N3O7P·C2H6O·0.076H2O, (III). The crystals of (II) and (III) are isomorphous but differ in the type of solvent. The phosphono group is linked directly to the last Cα atom in the main chain for all three peptides. All the amino acids are trans linked in the main chains. The crystal structures exhibit no intramolecular hydrogen bonds and are stabilized by intermolecular hydrogen bonds only.

Spin-canted ferromagnetic behaviour and unusual thermal decomposition of [Co{MeO(O)CC6H4NHC(S)NP(S)(OiPr)2}2]

Reaction of the deprotonated N-thiophosphorylated thiourea o-MeO(O)CC 6H4NHC(S)NHP(S)(OiPr)2 (HL) with Co II leads to the [CoL2] complex, the structure of which was studied by IR, UV-Vis, diffuse reflectance and NMR spectroscopy, ESI +/- mass spectrometry and microanalysis. The thermal properties of [CoL2] in an air atmosphere were studied by means of simultaneous TG/DTA analyses with the observed unprecedented final residue corresponding to CoPS3. Investigation of the thermal dependence of the magnetic susceptibility has shown that [CoL2] behaves as a spin-canted ferromagnet. The molecular structures of [CoL2] at 100 and 173 K were elucidated by a single crystal X-ray diffraction analysis. The metal was found to be in a tetrahedral 1,5-S2S′2 environment formed by the C=S and P=S sulfur atoms.

N-[tert-Butoxycarbonylglycyl-(Z)-alpha,beta-dehydrophenylalanylglycyl-(E)-alpha,beta-dehydrophenylalanylphenylalanyl]-4-nitroaniline ethanol solvate.

The alpha,beta-dehydrophenylalanine residues influence the conformation of the title pentapeptide Boc0-Gly1-Delta(Z)Phe2-Gly3-Delta(E)Phe4-L-Phe5-p-NA ethanol solvate, C42H43N7O9.C2H5OH. The first unsaturated phenylalanyl (Delta(Z)Phe2) and the third glycyl (Gly3) residues form a type I beta turn, while the second unsaturated phenylalanyl (Delta(E)Phe4) and the last phenylalanyl (L-Phe5) residues are part of a type II beta turn. All the amino acids in the peptide are linked trans to one another. The crystal structure is stabilized by intra- and intermolecular hydrogen bonds.