Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.     

Heterogeneous platinum catalytic aerobic oxidation of cyclopentane-1,2-diols to cyclopentane-1,2-diones

A method for the aerobic oxidation of cyclopentane-1,2-diols to the corresponding diketones over a commercial heterogeneous Pt/C catalyst is described. Unsubstituted and 3- or 4-substituted cyclopentane-1,2-diols are oxidized to 1,2-dicarbonyl compounds in good yields under the reported optimized reaction conditions (atmospheric air, 1 mol % of catalyst, 1 equiv of LiOH, aqueous solvents and 60 °C temperature). The method is applicable for producing cyclopentane-1,2-diketones in a scalable manner.     

A validated stability-indicating LC method for simultaneous determination of quinapril and hydrochlorothiazide in pharmaceutical samples

A stability-indicating liquid chromatographic method was developed and validated for simultaneous determination of quinapril and hydrochlorothiazide in drug substances and dosage forms. Chromatographic separation of quinapril, hydrochlorothiazide and its degradation products was achieved on a RP-18 column, using acetonitrile and phosphate buffer (pH 4.6) as mobile phase in a gradient mode and detection at 216 nm. Stress testing was performed under hydrolytic, oxidative, thermal and photolytic conditions. The degradation products were well resolved from main peaks, proving the stability-indicating power of the method. The assay was linear for quinapril and hydrochlorothiazide concentrations of 40–200 µg mL^?1 and 25–125 µg mL^?1, respectively. The developed method was selective, accurate and precise for quinapril and hydrochlorothiazide determination. This method was used to quantify both drugs in combined commercial tablets. The results showed that the proposed method was found to be suitable for quantitative determination and the stability study of quinapril and hydrochlorothiazide in pharmaceutical samples.      

Relaxing mixed integer optimal control problems using a time transformation

Mixed integer control systems are used to model dynamical behavior that can change instantly, for example a driving car with different gears. Changing a gear corresponds to an instant change of the differential equation what is achieved in the model by changing the value of the integer control function. The optimal control of a mixed integer control system by a discretize-then-optimize approach leads to a mixed integer optimization problem that is not differentiable with respect to the integer variables, such that gradient based optimization methods can not be applied. In this work, differentiability with respect to all optimization variables is achieved by reformulating the mixed integer optimal control problem (MIOCP). A fixed integer control function and a time transformation are introduced. The combination of both allows to change the sequence of active differential equations by partially deactivating the fixed integer control function. In contrast to other works, here different fixed integer control functions are taken into account. Advantages of so called control consistent (CC) fixed integer control functions are discussed and confirmed on a numerical example. (© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Contribution of Cytosine‐Containing Cyclobutane Dimers to DNA Damage Produced by Photosensitized Triplet–Triplet Energy Transfer

Mutagenic cyclobutane pyrimidine dimers (CPDs) can be induced in DNA through either direct excitation or photosensitized triplet–triplet energy transfer (TTET). In the latter pathway, thymines are expected to receive the excitation energy from the photosensitizer and react with adjacent pyrimidines. By using state‐of‐the art analytical tools, we provide herein additional information on the formation of cytosine‐containing CPDs. We thus determined the yield of all possible CPDs upon TTET in a series of natural DNAs with various base compositions. We show that the distribution of CPDs cannot be explained only by excitation of individual thymines. We propose that the mechanism for TTET involves at least dinucleotides as the minimal targets. The observation of the formation of cytosine–cytosine CPDs also suggests that additional pathways are involved in this photosensitized reaction.     

Mapping Multivalency and Differential Affinities within Large Intrinsically Disordered Protein Complexes with Segmental Motion Analysis

Intrinsically disordered proteins (IDPs) can bind to multiple interaction partners. Numerous binding regions in the IDP that act in concert through complex cooperative effects facilitate such interactions, but complicate studying IDP complexes. To address this challenge we developed a combined fluorescence correlation and time‐resolved polarization spectroscopy approach to study the binding properties of the IDP nucleoporin153 (Nup153) to nuclear transport receptors (NTRs). The detection of segmental backbone mobility of Nup153 within the unperturbed complex provided a readout of local, region‐specific binding properties that are usually masked in measurements of the whole IDP. The binding affinities of functionally and structurally diverse NTRs to distinct regions of Nup153 can differ by orders of magnitudes—a result with implications for the diversity of transport routes in nucleocytoplasmic transport.     

Die Verteilung von Molybdänsäure-Brenzcatechin-Komplexen zwischen wäßrigen Lösungen und organischen Lösungsmitteln

Molybdic-acid catechol complexes can be extracted from acidic aqueous solutions by organic solvents, if organic basic compounds are added. Results with tetraphenyl arsonium chloride were especially favourable.     

Direkte elektrometrische Bestimmung des Fluorid-Ions

Zusammenfassung Die Arbeitsweise einer Fluoridionen-empfindlichen Elektrode wurde geprüft und der Einfluß von Fremdsubstanzen auf die Potentiale untersucht. Die Störungen können durch Maskierung, Pufferung oder durch eine Auswertmethode vermindert werden.

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Summary The working characteristics of a fluoride-sensitive electrode and the influence of foreign substances on the fluoride potentials were tested. Changes in potential can be diminished by masking or buffering. Furthermore, a special addition technique can be applied.

     

Configuration interaction calculations for the ground and excited states of ozone and its positive ion: Energy locations and transition probabilities

Large-scale configuration interaction calculations (including energy extrapolation) are reported for the various states of ozone and its positive ion. The first four dipole-forbidden electronic transitions in the O₃ spectrum are calculated to occur at 1.20, 1.44, 1.59, and 1.72 eV, respectively, while the corresponding low-energy-allowed species known as the Chappuis, Huggins, and Hartley bands are predicted to possess vertical excitation energies of 1.95, 3.60, and 4.97 eV, respectively. These results all appear to fit in quite well with the observed location of the pertinent spectral features, with respect to both energy and intensity. The 5- to 8-eV region of the ozone spectrum is found to be characterized by a series of double-excitation transitions out of the highest three occupied orbitals to the lowest unoccupied 2b₁(π^*) species. The strong features observed at 9.3 and 10.2 eV are thereupon calculated to result primarily from transitions into the 7a₁ (σ^*) MO (calculated 9.29 and 10.05 eV) and in the former case also from the 3s members of the various O₃ Rydberg series (calculated 9.21 and 9.38 eV). Finally the order of the first three ip's is found to be 6a₁, 4b₂, and 1a₂, while the feature in the neighborhood of 16 eV is attributed to a shake-up state of ²B₁ symmetry.