Interaction of zinc finger ZNF191(243—368) and its I323 W and R327W mutants with oligonucleotides by florescence spectrum

Two mutants of the zinc finger protein, ZNF191 (243–368) I323W and R327W, are successfully obtained by site-directed mutagenesis. The fluorescence spectrum is used to study the interaction between these two mutants and the oligonucleotides. The influence of the mutation on the interaction has been studied using ethidium bromide (EB) as the fluorescence probe. The binding constants of the I323W-DNA and R327W-DNA have been calculated and the possible binding models have been discussed.     

Theoretical prediction on vibrational spectra of [Ar...Ar-H]<Superscript>+</Superscript>

Centrosymmetric linear [Ar-H-Ar]⁺ and asymmetric linear [Ar---Ar-H]⁺ are two stable configurations of [Ar₂H]⁺. Based on the global potential energy surface of [Ar₂H]⁺ provided by our group recently, we calculated the vibrational spectra of [Ar---Ar-H]⁺ with total angular momentum J = 0 by time-dependent quantum mechanical method, and the influence of quantum tunneling effect on vibrational spectra was found. With the help of the observation on the eigenstate functions and the modified potential energy surface, assignments were made to the spectra. The strong coupling between the excited bending mode of [Ar-H-Ar]⁺ and the vibrational states of [Ar---Ar-H]⁺ was discussed.     

Determination of S-carboxymethyl-L-cysteine and some of its metabolites in urine and serum by high-performance liquid chromatography using fluorescent pre-column labelling.

Pre-column labelling techniques are described for the determination of S-carboxymethyl-L-cysteine (CMC) and its metabolites in urine and plasma samples by high-performance liquid chromatography (HPLC) without prior extraction. All substances containing an amino group were converted into fluorescent fluorenylmethyl derivatives with 9-fluorenylmethyloxycarbonyl chloride (FMOC). Deaminated or N-acetylated carbocysteine metabolites were coupled with 1-pyrenyldiazomethane (PDAM) to give fluorescent PDAM esters. Similar results were obtained with the two commercially available and stable diazomethane derivatives PDAM and 9-anthryldiazomethane (ADAM). Following double derivatization with PDAM and FMOC, in a single chromatographic run with two fluorescence detectors connected in series, amines and amino(carboxylic) acids could be detected by their FMOC residues and, simultaneously, carboxylic acids were detected as fluorescent PDAM esters. The (R) and (S) enantiomers of the sulphoxides of CMC, of methylcysteine and of N-acetyl CMC were separated, although the reversed-phase HPLC system did not contain a chiral additive or stationary phase designed for the separation of enantiomers. The methods do not include liquid extraction steps and can therefore be performed either manually or automatically using an HPLC autosampler. These methods were used for the investigation of a disputed pharmacogenetic polymorphism of S-oxidation of CMC in humans, which until now has most often been studied using paper chromatography. The described techniques were applied to the determination of CMC and its metabolites in human urine and plasma samples.     

Construction of 4D-QSAR Models for Use in the Design of Novel p38-MAPK Inhibitors

The p38-mitogen-activated protein kinase (p38-MAPK) plays a key role in lipopolysaccharide-induced tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1) release during the inflammatory process, emerging as an attractive target for new anti-inflammatory agents. Four-dimensional quantitative structure-activity relationship (4D-QSAR) analysis [Hopfinger et al., J. Am. Chem. Soc., 119 (1997) 10509] was applied to a series of 33 (a training set of 28 and a test set of 5) pyridinyl-imidazole and pyrimidinyl-imidazole inhibitors of p38-MAPK, with IC50 ranging from 0.11 to 2100 nM [Liverton et al., J. Med. Chem., 42 (1999) 2180]. Five thousand conformations of each analogue were sampled from a molecular dynamics simulation (MDS) during 50 ps at a constant temperature of 303 K. Each conformation was placed in a 2 angstroms grid cell lattice for each of three trial alignments. 4D-QSAR models were constructed by genetic algorithm (GA) optimization and partial least squares (PLS) fitting, and evaluated by leave-one-out cross-validation technique. In the best models, with three to six terms, the adjusted cross-validated squared correlation coefficients, Q2adj, ranged from 0.67 to 0.85. Model D (Q2adj = 0.84) was identified as the most robust model from alignment 1, and it is representative of the other best models. This model encompasses new molecular regions as containing pharmacophore sites, such as the amino-benzyl moiety of pyrimidine analogs and the N1-substituent in the imidazole ring. These regions of the ligands should be further explored to identify better anti-inflammatory inhibitors of p38-MAPK.     

Synchrotron radiation circular dichroism spectroscopy of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides.

Synchrotron radiation circular dichroism (SRCD) spectra of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides and cyclic derivatives were measured in the vacuum ultraviolet region (down to 168 nm for sugars and 175 nm for adenine derivatives) and at different pH values (3, 6-7, 9-10) and temperatures (between 5 and 45 degrees C). The information content in the VUV region is important since the CD bands strongly depend on the chemical structure of the sugar, the presence and orientation of a phosphate group and the protonation state of adenine. On the other hand, single or double deprotonation of the phosphoric acid group has no influence on the spectra. We assign the vacuum ultraviolet (VUV) CD bands of the nucleoside and nucleotides to be due mainly to n-->pi* transitions in the adenine nucleobase based on a comparison with the absorption spectra. The CD bands of the sugars are due to n(O -->sigma*) transitions and are much smaller than the CD signal from the nucleotides in the VUV region. Bands are assigned to both pyranose and open-chain forms.     

Electron transfer dissociation of peptide anions

Ion/ion reactions of multiply deprotonated peptide anions with xenon radical cations result in electron abstraction to generate charge-reduced peptide anions containing a free-radical site. Peptide backbone cleavage then occurs by hydrogen radical abstraction from a backbone amide N to facilitate cleavage of the adjacent C-C bond, thereby producing a- and x-type product ions. Introduction of free-radical sites to multiply charged peptides allows access to new fragmentation pathways that are otherwise too costly (e. g., lowers activation energies). Further, ion/ion chemistry, namely electron transfer reactions, presents a rapid and efficient means of generating odd-electron multiply charged peptides; these reactions can be used for studying gas-phase chemistries and for peptide sequence analysis.     

A kinetic stability study of <Emphasis Type="Italic">M</Emphasis>N<Subscript>5</Subscript> (<Emphasis Type="Italic">M</Emphasis>=Li,Na, K,and Rb)

A structure and kinetic stability study on some complexes with the general formula MN₅, where M are the alkali-metal atoms, Li, Na, K, and Rb, has been carried by using hybrid density functional methods. Complex B (C_2v) with two points of attachment to the N₅ ring is the most energetically favored for all metals considered here. Pyramidal structures A (C_5v) are kinetically unstable and they rapidly rearrange to the most stable planar structures B. At the QCISD(T)/6-311 + G*//B3LYP/6-311 + G* + ZPE (B3LYP/6-311 + G*) level, the decomposition barrier heights of LiN₅-B, NaN₅–B, KN₅-B, and RbN₅-B are predicted to be 19.9, 22.0, 22.5, and 23.0 kcal/mol, respectively. In addition, the rate constants of the decomposition reaction MN₅-B MN₃ + N₂ (M + Li, Na, K, and Rb) are also predicted using conventional transition state theory and canonical variational transition state theory, respectively.     

The performance of density functional theory for LnF (Ln=Nd,Eu, Gd,Yb) and YbH

Different density functional theory (DFT) functionals have been evaluated by studying geometries and bond strengths of YbH, YbF, EuF, GdF, and NdF and compared with accurate CCSD(T) results and, when available, experiment. The agreement between the CCSD(T) results and experiment, when available, is good. The agreement is also good between bond strengths calculated at the DFT level using relativistic effective core potentials and the CCSD(T) results. However, the all-electron ADF calculations systematically overestimate binding energies. The geometries obtained by both the all-electron and the effective-core-potential-based DFT calculations are generally in good agreement with the CCSD(T) results.Contribution to the Björn Roos Honorary Issue     

Substituent control in the diastereoselectivity of dipolar cycloadditions of nitrones and their Zn(II) complexes with N-arylmaleimides

The π-π stacking interactions between maleimide's and nitrone's aromatic rings during the 1,3-dipolar cycloaddition were assumed to control the exo-endo selectivity of the reaction. The exo-endo ratios change during the reactions until they reach a constant value, which depends on the substituent. Electron-withdrawing groups favour the exo adduct while electron-donating groups favour the endo adduct. The nitrone ZnBr₂ complexes react much more slowly than the free nitrone and the cycloaddition is exo selective in all cases independent of the substituents on the maleimide's aromatic ring. Thermal retrocycloaddition of the cycloadducts produce the corresponding nitrones. The ring opening in the presence of secondary amines did not induce imine formation. endo Adducts were shown for the first time to be the stable paramagnetic compounds.