Time-resolved measurements of the photolysis and recombination of adenosylcobalamin bound to glutamate mutase

Femtosecond to nanosecond transient absorption spectroscopy is used to investigate the photolysis of 5'-deoxyadenosylcobalamin (coenzyme B12, AdoCbl) bound to glutamate mutase. The photochemistry of AdoCbl is found to be inherently dependent upon the environment of the cofactor. Excitation of AdoCbl bound to glutamate mutase results in formation of a metal-to-ligand charge transfer intermediate state which decays to form cob(II)alamin with a time constant of 105 ps. This observation is in contrast to earlier measurements in water where the photohomolysis proceeds through an intermediate state in which the axial dimethylbenzimidazole ligand appears to have dissociated, and measurements in ethylene glycol where prompt bond homolysis is observed (Yoder, L. M.; Cole, A. G.; Walker, L. A., II; Sension, R. J. J. Phys. Chem. B 2001, 105, 12180-12188). The quantum yield for formation of stable radical pairs in the enzyme is found to be phi = 0.05 +/- 0.03, and the resulting intrinsic rate constants for geminate recombination and "cage escape" are 1.0 +/- 0.1 and 0.05 +/- 0.03 ns(-1), respectively. The rate constant for geminate recombination is 30% less than that observed for AdoCbl in water or ethylene glycol. This reduction is insufficient to account for the 10(12)-fold increase in the homolysis rate observed when substrate is bound to the protein. Finally, the protein provides a cage to prevent diffusive loss of the adenosyl radical; however, the ultimate yield for long-lived radicals is determined by the evolution from a singlet to a triplet radical pair as proposed for AdoCbl in ethylene glycol.     

AIScore chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes

In this work we report on a novel scoring function that is based on the LUDI model and focuses on the prediction of binding affinities. AIScore extends the original FlexX scoring function using a chemically diverse set of hydrogen-bonded interactions derived from extensive quantum chemical ab initio calculations. Furthermore, we introduce an algorithmic extension for the treatment of multifurcated hydrogen bonds (XFurcate). Charged and resonance-assisted hydrogen bond energies and hydrophobic interactions as well as a scaling factor for implicit solvation were fitted to experimental data. To this end, we assembled a set of 101 protein-ligand complexes with known experimental binding affinities. Tightly bound water molecules in the active site were considered to be an integral part of the binding pocket. Compared to the original FlexX scoring function, AIScore significantly improves the prediction of the binding free energies of the complexes in their native crystal structures. In combination with XFurcate, AIScore yields a Pearson correlation coefficient of R P = 0.87 on the training set. In a validation run on the PDBbind test set we achieved an R P value of 0.46 for 799 attractively scored complexes, compared to a value of R P = 0.17 and 739 bound complexes obtained with the FlexX original scoring function. The redocking capability of AIScore, on the other hand, does not fully reach the good performance of the original FlexX scoring function. This finding suggests that AIScore should rather be used for postscoring in combination with the standard FlexX incremental ligand construction scheme.     

Statistical analysis of serum protein electrophoresis results in External Quality Assessment schemes

The goal of External Quality Assessment (EQA) schemes is to ensure that results obtained on a particular specimen in a given clinical laboratory are compatible with those obtained by other laboratories on the same specimen. Serum protein electrophoresis is a laboratory test consisting of five fractions (albumin, α₁, α₂, β and γ globulins), which sum up to 100% of total proteins. So far, in EQA schemes the five fractions have been analyzed separately as for ordinary tests like glucose or cholesterol. This approach does not consider the fractions as a whole and the linear relationship between them. A statistical approach has been developed to analyze EQA electrophoresis results from a global standpoint by using robust multivariate method to eliminate the effect of outlying profiles. As illustrated on electrophoretic data from the Belgian EQA scheme, the novel approach improves the detection of poor performing laboratories. The method will be implemented in the Belgian EQA scheme on a routine basis.     

Stepwise conversion of a single source precursor into crystalline AlN by transamination reaction

Ammonolysis of the monomeric, base-stabilized trisaminoalane Me₃N-Al[N(H)Dipp)]₃ (Dipp=2,6-ⁱPr₂-C₆H₃) yielded Al-N oligomers, which were characterized in detail by solid state NMR spectroscopy (¹H, ¹³C, ¹⁵N, ²⁷Al) and TGA/DTA. Pyrolysis of as-prepared oligomers at different temperatures in an argon steam yielded carbon-containing black solids, whereas pyrolysis under a steady flow of NH₃ produced pure aluminum nitride (AlN). The role of the pyrolysis temperature and the influence of NH₃ on the formation of crystalline materials were investigated. As-prepared AlN was characterized by solid state NMR spectroscopy (¹⁵N, ²⁷Al), X-ray diffraction (XRD), transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS). Theoretical calculations were performed in order to identify potential reaction intermediates.     

Synthesis of Carbon–Nitrogen–Phosphorous Materials with an Unprecedented High Amount of Phosphorous toward an Efficient Fire‐Retardant Material

Phosphorus incorporation into carbon can greatly modify its chemical, electronic, and thermal stability properties. To date this has been limited to low levels of phosphorus. Now a simple, large‐scale synthesis of carbon–nitrogen–phosphorus (CNP) materials is reported with tunable elemental composition, leading to excellent thermal stability to oxidation and fire‐retardant properties. The synthesis consists of using monomers that are liquid at high temperatures as the reaction precursors. The molten‐state stage leads to good monomer miscibility and enhanced reactivity at high temperatures and formation of CNP materials with up to 32 wt % phosphorus incorporation. The CNP composition and fire‐retardant properties can be tuned by modifying the starting monomers ratio and the final calcination temperature. The CNP materials demonstrate great resistance to oxidation and excellent fire‐retardant properties, with up to 90 % of the materials preserved upon heating to 800 °C in air.     

Synthesis,biological activity,and conformational analysis of CD-ring modified trans-decalin 1 alpha,25-dihydroxyvitamin D analogs

A novel series of analogs of 1,25-dihydroxyvitamin D3, the hormonally active metabolite of vitamin D3, characterised by the presence of a trans-fused decalin CD-ring system, possesses surprising biological activities in combination with specific structural modifications in the flexible parts of the molecule, when compared with the natural hydrindane derivatives. (1) A large difference in biological activity is observed between the 20-epimeric trans-decalin analogs that follows a pattern opposite to what is usually observed for the natural ring size. (2) Several trans-decalin analogs that are modified in the seco-B-ring region, including previtamin derivatives, possess a pronounced vitamin D-like activity, whereas the corresponding hydrindane derivatives are inactive. The molecular origin of this behavior is still under study.     

Molecular Level Characterization of the Structure and Interactions in Peptide‐Functionalized Metal–Organic Frameworks

We use density functional theory, newly parameterized molecular dynamics simulations, and last generation ¹⁵N dynamic nuclear polarization surface enhanced solid‐state NMR spectroscopy (DNP SENS) to understand graft–host interactions and effects imposed by the metal–organic framework (MOF) host on peptide conformations in a peptide‐functionalized MOF. Focusing on two grafts typified by MIL‐68‐proline ( ‐Pro ) and MIL‐68‐glycine‐proline ( ‐Gly‐Pro ), we identified the most likely peptide conformations adopted in the functionalized hybrid frameworks. We found that hydrogen bond interactions between the graft and the surface hydroxyl groups of the MOF are essential in determining the peptides conformation(s). DNP SENS methodology shows unprecedented signal enhancements when applied to these peptide‐functionalized MOFs. The calculated chemical shifts of selected MIL‐68‐NH‐ Pro and MIL‐68‐NH‐ Gly‐Pro conformations are in a good agreement with the experimentally obtained ¹⁵N NMR signals. The study shows that the conformations of peptides when grafted in a MOF host are unlikely to be freely distributed, and conformational selection is directed by strong host–guest interactions.     

Preparation of Useful Buiding-Blocks for the Synthesis of 7-Azanorbornylprostanoids

The Diels-Alder adduct 4 of an N-protected pyrrole with dimethyl acetylenedicarboxylate can be transformed to 5 and 6 by short sequences which differenciate the two ester groups; these compounds are interesting starting materials for the synthesis of potential thromboxane A₂ antagonists as well as other bio-active compounds.     

Protection of aluminum hydroxide during lyophilisation as an adjuvant for freeze-dried vaccines

Lyophilisation of an aluminum hydroxide adjuvant containing formulation for use in vaccine development has been investigated. Novel formulation approaches using disaccharides, polysaccharides, polyols and polymers have been investigated as stabilising excipients to prevent aluminum hydroxide adjuvant from aggregation during a freeze–thaw cycle or the lyophilisation process itself. Amorphous character of the lyophilisates was investigated by wide angle X-ray diffraction. Sedimentation assay, particle size analysis and optical microscopy could show that aluminum adjuvant gel character of selected formulations could be maintained within acceptable quality or stayed the same in some cases. In principle, it could be demonstrated that not less than 10% excipient is necessary to yield good results within applied analytics evaluating the excipients’ protecting qualities. Based on results obtained by this study, the formulations containing trehalose at a concentration of 15 or 20%, dextran, PVP K 25, HES 450 and 200, saccharose and sorbitole along with polysorbate 80 and buffer promise to be good candidates for the protection of aluminum adjuvanted vaccines during exposure to coldness stresses as during freezing or lyophilisation.