New heterocyclic beta-sheet ligands with peptidic recognition elements

A detailed and comprehensive overview is presented about the design, modeling, and synthesis, as well as spectroscopic characterization, of a new class of beta-sheet ligands. The characteristic feature of these compounds is a peptidic chimeric structure formed from a specific combination of aminopyrazolecarboxylic acids with naturally occurring alpha-amino acids. These hybrid peptides are designed with the aid of molecular modeling to exist mainly in an extended conformation. All their hydrogen bond donors and acceptors can be aligned at the bottom face in such a way that a perfect complementarity toward beta-sheets is obtained. Thus the aminopyrazoles impart rigidity and a highly efficient DAD sequence for the recognition of whole dipeptide fragments, whereas the natural alpha-amino acids are designed to mimick recognition sites in proteins, ultimately leading to sequence-selective protein recognition. The synthetic protocols either rely upon solution phase peptide coupling with a PMB protecting group strategy or solid-phase peptide coupling based on the Fmoc strategy, using the same protecting group. In solution, a key building block was prepared by catalytic reduction of a nitropyrazolecarboxylic acid precursor. Subsequently, it was (N-1)-protected with a PMB group, and elongated by HCTU- or T3P-assisted peptide coupling with dipeptide fragments, followed by PyClop-assisted coupling with another nitropyrazolecarboxylic acid building block. Final simultaneous deprotection of all PMB groups with hot TFA completed the high-yield protocol, which works racemization-free. After preparing a similar key building block with an Fmoc protection at N-3, we developed a strategy suitable for automated synthesis of larger hybrid ligands on a peptide synthesizer. Attachment of the first amino acid to a polystyrene resin over the Sieber amide linker is followed by an iterative sequence consisting of Fmoc deprotection with piperidine and subsequent coupling with natural alpha-amino acid via HATU/HOAt. High yields of free hybrid peptides are obtained after mild acidic cleavage from the resin, followed by deprotection of the PMB groups with hot TFA. The new aminopyrazole peptide hybrid compounds were characterized by various spectroscopic measurements including CD spectra, VT, and ROESY NMR experiments. All these accumulated data indicate the absence of any intramolecular hydrogen bonds and strongly support an extended conformation in solution, ideal for docking on to solvent-exposed beta-sheets in proteins. Initial results from aggregation tests of pathological proteins with these and related ligands look extremely promising.     

Spectrophotometric behaviour of quinolinium oxime-palladium(II) complexes

Summary It has been established that 1-(2-phenyl-2-hydroxyiminoethyl)-1-quinolinium chloride, 1-(2-phenyl-2-hydroxyiminoethyl)-1-isoqui-nolinium chloride, 1-(2-phenyl-2-hydroxyiminoethyl)-1-(4-methyl)-quinolinium chloride and 1-(2-phenyl-2-hydroxyiminoethyl)-1-(6-methyl)quinolinium chloride react with palladium(II) chloride in the pH range 3.3–7.1 and form yellow water-soluble 11 complexes with maximum absorbance at 413 nm. The conditional stability constants of the complexes at the optimum pH of 6.5 are all about 10^4.7, and the molar absorptivities are in the range 2.2–2.6×10³ l·l mole^–1·cm^–1 at pH 6.5 and 413 nm. Beer's law is obeyed up to 3–4×10^–4 M oxime concentration, depending on the oxime determined.     

Quantum chemical investigation of the electronic spectra of the keto, enol, and keto-imine tautomers of cytosine

The low-lying excited singlet states of the keto, enol, and keto-imine tautomers of cytosine have been investigated employing a combined density functional/multireference configuration interaction (DFT/MRCI) method. Unconstrained geometry optimizations have yielded out-of-plain distorted structures of the pi --> pi and n --> pi excited states of all cytosine forms. For the keto tautomer, the DFT/MRCI adiabatic excitation energy of the pi --> pi state (4.06 eV including zero-point vibrational energy corrections) supports the resonant two-photon ionization (R2PI) spectrum (Nir et al. Phys. Chem. Chem. Phys. 2002, 5, 4780). On its S1 potential energy surface, a conical intersection between the 1pipi state and the electronic ground state has been identified. The barrier height of the reaction along a constrained minimum energy path amounts to merely 0.2 eV above the origin and explains the break-off of the R2PI spectrum. The 1pipi minimum of the enol tautomer is found at considerably higher excitation energies (4.50 eV). Because of significant geometry shifts with respect to the ground state, long vibrational progressions are expected, in accord with experimental observations. For the keto-imine tautomer, a crossing of the 1pipi potential energy surface with the ground-state surface has been found, too. Its n --> pi minimum (3.27 eV) is located well below the conical intersection between the pi --> pi and S0 states, but it will be difficult to observe because of its small transition moment. The identified conical intersections of the pi --> pi excited states of the keto cytosine tautomers are made responsible for the ultrafast decay to the electronic ground states and thus may explain their subpicoseconds lifetimes.     

Synthesis, Structure, and Antimicrobial Activity of Complexes of Pt(II), Pd(II), and Ni(II) with the Condensation Product of 2-(Diphenylphosphino)benzaldehyde and Semioxamazide

Summary. Complexes of Pt(II), Pd(II), and Ni(II) with the condensation derivative of 2-(diphenylphosphino)benzaldehyde and semioxamazide were synthesized, characterized, and their antimicrobial activity was evaluated. The ligand and the complexes were characterized by spectroscopic methods with the particular accent on NMR spectral analysis. For the palladium(II) complex, the crystal structure was determined by X-ray analysis. In all the complexes the ligand is coordinated as a tridentate via a P, N, O donor set. The Pd(II) and Pt(II) complexes have a square planar geometry, whereas the geometry of the Ni(II) complex is tetrahedral. The ligand showed antibacterial and antifungal activity, which was enhanced upon complexation.     

Accreditation of GMO detection laboratories: Improving the reliability of GMO detection

Reliable and efficient methods for detecting genetically modified organisms (GMOs) are essential for establishing an effective system for traceability all along the supply chain from seed producers to final consumers. The latter is especially meaningful in European Union and other countries where strict legislations on GMOs were set up. Performance of the methods used in laboratories around the world should be uniform, in order to obtain reliable and comparable results. Accreditation is a suitable system for harmonising procedures in each testing laboratory. In this paper, key elements for the accreditation of molecular biology methods for GMO detection according to ISO/IEC 17025 are described. The procedures described are also valuable for the accreditation of molecular methods for all laboratory diagnostics where qualitative and quantitative characterisation of nucleic acids is needed.     

Sodium citrate dihydrate doped with Mn3+ ions

Sodium citrate dihydrate doped with Mn³⁺ ions, namely trisodium(I) managnese(III) citrate(3−) dihydrate, [Na₃Mn_0.011(C₆H₅O₇)(H₂O)₂]_n, was obtained during attempts to prepare some complex Mn^III citrates from a concentrated strong alkaline solution containing Na⁺, Mn³⁺ and citrate ions. The compound is isostructural with the recently described Na₃(C₆H₅O₇)·2H₂O [Fischer & Palladino (2003). Acta Cryst. E 59 , m1080–m1082]. The essential difference between these two structures is the presence of a very small proportion (0.205 wt%) of Mn³⁺ ions, which are positioned at the special 4e Wyckoff position in C2/c, where they are in a highly distorted octahedral environment of O atoms from two citrate anions.     

Simulations and Velocity Measurements for a Microparticle in an Evanescent Field

We report theoretical calculations and experimental data for guiding of polystyrene microspheres in the evanescent field of an optical waveguide. The waveguides used in our experiments were made using Cs⁺ ion-exchange in soda lime glass, which gives efficient trapping and high guiding velocities. The computations were done using a generalized version of Mie scattering theory, which gives good agreement with our experimental results. © 2005 The Optical Society of Japan     

Identification of Tmem10/Opalin as a novel marker for oligodendrocytes using gene expression profiling

Background  

During the development of the central nervous system, oligodendrocytes generate large amounts of myelin, a multilayered insulating membrane that ensheathes axons, thereby allowing the fast conduction of the action potential and maintaining axonal integrity. Differentiation of oligodendrocytes to myelin-forming cells requires the downregulation of RhoA GTPase activity.     

The Crystal Structure of the NH4NCS Complex of Nonactin

The NH₄NCS complex of the macrotetrolide antibiotic nonactin crystallizes in the space group P1 , a = 12.565, b = 13.115, c = 14.999 Å, α= 91.22, β= 90.10, γ= 104.97°. The X-ray crystal structure analysis shows that the NH ion is coordinated by hydrogen bonds to the four ether oxygen atoms (NH … O, 2.86 Å). These four atoms and the four carbonyl oxygen atoms (N … O, 3.08 Å) enclose the NH ion in a somewhat distorted cube.