Binding site optimisation for artificial enzymes by diffusion NMR of small molecules

A binding site optimisation protocol for the design of artificial enzymes based on "small molecule-small molecule" binding studies by diffusion NMR is presented. Since the reaction chosen was the hydrolysis of ester 1 ([4-(4-carboxy-1-oxobutyl)-aminobenzyl]-phenethyl ester), an analogous phosphonate ester 2 ([4-(4-carboxy-1-oxobutyl)-aminobenzyl]-phosphonic phenethyl ester) was selected as a suitable transition state analogue (TSA). The key objective of the NMR studies was to find a unit with functional groups capable of binding to the acidic sites of the TSA. Nine dipeptides, mainly with basic and hydroxyl groups, were used and their affinity to the TSA was studied by measuring the change in the diffusion coefficient, D(pep), upon binding by pulse field gradient NMR. The value of D(pep) at 298 K in D(2)O at pD 5, 7 and 10 was measured both in free solution, and mixtures containing one dipeptide and the TSA. As both components are low molecular weight species with M < 500, a TSA-to-dipeptide ratio of 10:1 was used to detect significant changes in D(pep). The results revealed that dipeptides with basic residues show higher affinity to the TSA than those with hydroxyl or aliphatic side chains in aqueous solutions. The dipeptide showing the most significant relative change in D(pep) was H-Arg-Arg-OH, and the binding constant was estimated to be 86 L M(-1) by measuring D(pep) at varying concentrations of the TSA. In addition, binding of the TSA to a new water-soluble polymer with a polyallylamine backbone and randomly distributed Arg-Arg binding sites was examined, and the binding constant was estimated to be > or =1500 L M(-1). As confirmed by further catalytic activity tests, polymers containing Arg-Arg as a binding site are capable of significant rate accelerations in the hydrolysis of ester 1.     

Etude comparative de l'alkylation des tetraphenylporphyrines de l'etain et de leurs formes reduites par les reactifs de grignard

A comparative study of alkylation by Grignard reagents of PSn(OH)₂ (P = tetraphenylporphyrin (TPP), tetraphenylchlorine (TPC), tetraphenylisobacteriochlorine (TPiBC)) shows that dialkylstannylisobacteriochlorines are the most easily obtained. The presence of transition metals in the magnesium crystals directs the reaction towards reduction of the macrocycle instead of alkylation on tin. This is supplementary proof for the intervention of a single electron transfer mechanism (SET) in alkylation of a macrocycle by Grignard reagents.These results fit very well with earlier electrochemical experiments and the measurements of the reduction potentials of the Group IVB metalloporphyrins and their reduced forms.     

A phenolate-induced trans influence: crystallographic evidence for unusual asymmetric coordination of an alpha-diimine in ternary complexes of iron(III) possessing biologically relevant hetero-donor N-centered tripodal ligands

Three mononuclear ternary complexes of iron(III) with an alpha-diimine (bipy or phen) and a derivative of N,N-bis(2-hydroxybenzyl)glycinate (L3-) have been synthesized and characterized by magnetic susceptibility measurements, electron paramagnetic resonance (EPR) spectroscopy, vibrational spectroscopy, and electronic absorption spectroscopy. Single-crystal X-ray structure determinations of the pseudo-octahedral complexes [Fe(bipy)L] x MeCN [L = (3,5-Br2)-L3- or (5,3-Cl,Me)-L3-] revealed a considerable and consistent distortion in the coordination of bipy to iron(III) attributable largely to electronic effects. In both crystal structures, the Fe-N(pyridyl) bond trans to the phenolate oxygen is 0.133 A longer than the other one positioned trans to the tertiary amine nitrogen, a relatively weaker donor. This coordination behavior of bipy is of structural interest and has not been observed previously for iron(III). The electronic and EPR spectra of the compounds [Fe(L'-L')L] x MeCN (L'-L' = bipy or phen) are consistent with the spin state of the central metal atom (S = 5/2). The charge-transfer transitions arising from the strong interactions of the phenolate moieties with the ferric ion have been identified as phenolate (p(pi)) --> iron(III) (d(pi*)) (lambda(max) approximately 500 nm, epsilon approximately 3000 M(-1) cm(-1)) and phenolate (p(pi)) --> iron(III) (d(sigma*) (lambda(max) approximately 320 nm, epsilon approximately 5200 M(-1) cm(-1)). The presence of the phenolate moieties in the quadridentate hetero-donor tripodal ligands, H3L, lends these iron(III) ternary complexes the potential to model the specific metal-coordination, metal-substrate interactions, and physicochemical behaviors of several iron-tyrosinate proteins.     

An improved clean-up strategy for simultaneous analysis of polychlorinated dibenzo-p-dioxins (PCDD), polychlorinated dibenzofurans (PCDF), and polychlorinated biphenyls (PCB) in fatty food samples

The study and extension of a simple automated clean-up method for polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) to a broad range of polychlorinated biphenyls (PCB) is described. The isolation of seven PCDD, ten PCDF, and three coplanar PCB (cPCB) is extended to eight monoortho substituted PCB and seven so-called "marker PCB" (Aroclor 1260) for fatty food samples. This enables quantification of 35 compounds - including all congeners with a WHO toxic equivalent factor (TEF)--in a single extraction and single purification step. The chromatographic behaviour of mono-ortho PCB and marker PCB on a variety of adsorbents, including basic alumina, has been studied. Partitioning of analytes through multi-column sequences is described and correlated with their structural and electronic properties, by use of molecular modelling calculations. The fractionation process available with the Power-Prep automated clean-up system enables rapid independent analysis of the different groups of compounds. Gas chromatography with high resolution mass spectrometry (GC-HRMS) is used for the PCDD/F and cPCB fraction and quadrupole ion-storage tandem in time mass spectrometry (GC-QISTMS) for analysis of the remaining PCB. A comparison study was performed on quality-control samples and real fatty food samples to evaluate the robustness of the new strategy compared with a reference method. On the basis of this simultaneous clean-up, a rapid simplified strategy for PCDD/F and selected PCB analysis determination is proposed for fatty food samples.     

Simple tricyclohexylphosphine-palladium complexes as efficient catalysts for the Stille coupling of deactivated aryl chlorides

Simple, inexpensive tricyclohexylphosphine adducts of palladium show the highest activity yet observed in the Stille coupling of non-activated and deactivated aryl chlorides.     

PTV-LV-GC/MS/MS as screening and complementary method to HRMS for the monitoring of dioxin levels in food and feed

Recent developments in trapping efficiency inside ion trap mass spectrometer permitted to lower instrument detection limit (IDL). An IDL of 200 fg μl⁻¹ injected with a signal-to-noise ratio of 5:1 for tetrachlorodibenzo-p-dioxin (TCDD) was obtained by gas chromatography coupled to a quadrupole ion storage mass spectrometer in tandem mode (GC/MS/MS). Coupling large volume programmable temperature vaporizer (PTV-LV) injection to GC/MS/MS provides an alternative and complementary method to classical splitless-GC injection connected to high-resolution mass spectrometry (splitless-GC/HRMS) method for dioxin monitoring in food and feed.

An injection volume of 10 μl was found to be the best compromise between the sensitivity requirements and the robustness required for a high throughput method. PTV-LV-GC/MS/MS and Splitless-GC/HRMS were compared by performing analysis on five different matrices such as beef fat, yolk eggs, milk powder, animal feed and serum samples covering a concentration range of two orders of magnitude (i.e. 0.2–25 ng WHO-TEQ kg⁻¹). An analysis of variance (ANOVA) was carried out. Fisher tests pointed out that the method effect for all the 2,3,7,8 congeners was not significant, indicating that the null hypothesis (H₀: μ₁=μ₂=…=μ_n) was not rejected. Moreover, the interaction effects between methods and matrices were not significant for most of the 2,3,7,8 congeners. However, three congeners (2,3,7,8-TCDF; 1,2,3,4,7,8-HxCDD and 1,2,3,4,6,7,8-HpCDD) were characterized by P-values lower than the significance level (=0.05). In toxic equivalence (TEQ), the study showed that no significant bias was observed between the two methods. Consequently, PTV-LV-GC/MS/MS is an attractive technique and can be used as a cost effective complementary method to HRMS for dioxin levels monitoring in food and feed.     

Electron-impact fragmentation of the bicyclo[4.1.0]heptane-2-one system: Correlations with photochemistry

The low resolution and complete high resolution mass spectra of a series of methyl and deuterium substituted bicyclo[4.1.0]heptane-2-one derivatives have been measured. An attempt has been made to test the operation of a fragmentation process analogous to the known photochemical rearrangement, and to determine if the substitution effects critical to the photorearrangement also influence the electron-impact process. The fragmentation pattern of these conjugated cyclopropyl ketones is detailed and the influence of the cyclopropyl ring is discussed. It is suggested that electron-impact-induced rearrangements which are analogous to photochemical transformations will be relatively low energy processes and will remain prominent at low ionizing voltages.     

Determination of (1)H homonuclear scalar couplings in unlabeled carbohydrates

The scarcity of structural information on carbohydrates results from combined difficulties to crystallize and the limitations in NMR analysis. Current methods for determining basic NMR parameters such as (1)H homonuclear scalar couplings are very limited, especially for large molecules such as polysaccharides, oligonucleotides, and the carbohydrate part of glycoproteins. In this paper, a NMR experiment for the determination of endocyclic (1)H homonuclear scalar couplings ((3)J(HH)) in unlabeled carbohydrates is presented. In addition to scalar couplings, cross-correlated dipole-dipole relaxation rates were measured for large polysaccharides. The measurement of all endocyclic homonuclear coupling constants within monosaccharide units is presented for lactose, a model disaccharide, and for a natural-abundance 2 MDa bacterial polysaccharide excreted by Streptococcus thermophilus Sfi39.     

Dynamic behavior of DNA base pairs containing 8-oxoguanine

The process by which DNA repair enzymes recognize and selectively excise damaged bases in duplex DNA is fundamental to our mechanistic understanding of these critical biological reactions. 8-Oxoguanine (8-oxoG) is the most common form of oxidative DNA damage; unrepaired, this lesion generates a G:C-->T:A mutation. Central to the recognition and repair of DNA damage is base extrusion, a process in which the damaged base lesion or, in some cases, its partner disengages from the helix and is bound to the enzyme's active site where base excision takes place. The conformation adopted by 8-oxoG in duplex DNA is affected by the base positioned opposite this lesion; conformational changes may also take place when the damaged base binds to its cognate repair enzyme. We performed unrestrained molecular dynamics simulations for several 13-mer DNA duplexes. Oligomers containing G:C and 8oxoG:C pairs adopted Watson-Crick geometries in stable B-form duplexes; 8oxoG showed increased local and global flexibility and a reduced barrier to base extrusion. Duplexes containing the G:A mismatch showed much larger structural fluctuations and failed to adopt a well-defined structure. For the 8oxoG:A mismatch that is recognized by the DNA glycosylase MutY, the damaged nucleoside underwent spontaneous and reproducible anti-->syn transitions. The syn conformation is thermodynamically preferred. Steric hindrance and unfavorable electrostatics associated with the 8oxoG O8 atom in the anti conformation were the major driving forces for this transition. Transition events follow two qualitatively different pathways. The overall anti-->syn transition rate and relative probability of the two transition paths were dependent on local sequence context. These simulations indicate that both the dynamic and equilibrium behavior of the duplex change as a result of oxidation; these differences may provide valuable new insight into the selective action of enzymes on damaged DNA.