Some estimates on entropy numbers

First we show that the Carl-Maurey inequality for entropy numbers

A new approach for the detection of carbon-centered radicals in enzymatic processes using prefluorescent probes

In this communication we propose a novel application for prefluorescent probes in the detection of free carbon-centered radicals in enzymatic processes. Prefluorescent probes combine a fluorescent moiety tethered to a paramagnetic nitroxide that acts as a fluorescence quencher. Trapping of a radical by the nitroxide group restores the fluorescence properties. The increase in fluorescence intensity with time reflects the formation and quenching of carbon-centered radicals and can be used for the quantitative evaluation of yields and kinetics. As a test system we used horseradish peroxidase, an oxidoreductase that is widely accepted to operate by a radical-mediated mechanism. We used the prefluorescent probe (quinoline-TEMPO), where a quinoline moiety has been tethered to 2,2,6,6-tetramethylpiperidin-1-oxyl.     

Kinetic studies of dicopper complexes in catechol oxidase model reaction by using an approximationless evaluating method

The oxidation of 3,5-di-tert-butylcatechol to 3,5-di-tert-butyl-o-benzoquinone catalyzed by dinuclear copper(II) complexes {[Cu₂(L¹)(CF₃SO₃)₂(H₂O)₄]-(CF₃SO₃)₂ (1) and [Cu₂(L²O)](CF₃SO₃)₂ (2)| has been investigated in methanol saturated with O₂ at ambient temperature. Detailed kinetic studies were carried out and for the treatment the fitting software ZiTa was applied. On the basis of the results in the kinetic studies a possible mechanism of the catalytic reaction is proposed.This revised version was published online in December 2005 with corrections to the Cover Date.     

Synthesis, structures, and strain energies of dispirophosphiranes. Comparisons with dispirocyclopropanes

Six novel dispirophosphirane complexes have been synthesized from the reaction of bicycloalkylidenes with the electrophilic phosphinidene complex PhPW(CO)(5). They contain a central phosphirane ring, which is spirofused on one side to a cyclopropane or cyclobutane ring and on the other side with a three-, four-, five-, or six-membered ring. Their crystal structures and MP2/6-31G-computed geometries for simplified parent systems suggest that spirofusion with small rings results in a tightening of the central three-membered phosphaheterocycle, while spirofusion with larger rings results in a relaxation of the phosphirane geometry. Similar theoretical predictions are made for the corresponding annulated hydrocarbons. Strain energies for both the hydrocarbon and phosphorus series of structures have been calculated at G3(MP2). Whereas the [3]triangulane hydrocarbon and phospha[3]triangulane have a significant excess strain of 8.1 and 5.2 kcal/mol per spiroatom, respectively, the excess strain for systems spirofused with larger rings are negligible for the hydrocarbons and even negative for the phosphorus-containing species because of hyperconjugative stabilization.     

Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments

The major rate-limiting step in high-throughput NMR protein structure determination involves the calculation of a reliable initial fold, the elimination of incorrect nuclear Overhauser enhancement (NOE) assignments, and the resolution of NOE assignment ambiguities. We present a robust approach to automatically calculate structures with a backbone coordinate accuracy of 1.0-1.5 A from datasets in which as much as 80% of the long-range NOE information (i.e., between residues separated by more than five positions in the sequence) is incorrect. The current algorithm differs from previously published methods in that it has been expressly designed to ensure that the results from successive cycles are not biased by the global fold of structures generated in preceding cycles. Consequently, the method is highly error tolerant and is not easily funnelled down an incorrect path in either three-dimensional structure or NOE assignment space. The algorithm incorporates three main features: a linear energy function representation of the NOE restraints to allow maximization of the number of simultaneously satisfied restraints during the course of simulated annealing; a method for handling the presence of multiple possible assignments for each NOE cross-peak which avoids local minima by treating each possible assignment as if it were an independent restraint; and a probabilistic method to permit both inactivation and reactivation of all NOE restraints on the fly during the course of simulated annealing. NOE restraints are never removed permanently, thereby significantly reducing the likelihood of becoming trapped in a false minimum of NOE assignment space. The effectiveness of the algorithm is demonstrated using completely automatically peak-picked experimental NOE data from two proteins: interleukin-4 (136 residues) and cyanovirin-N (101 residues). The limits of the method are explored using simulated data on the 56-residue B1 domain of Streptococcal protein G.     

A Polyclonal Selex Aptamer Library Directly Allows Specific Labelling of the Human Gut Bacterium Blautia producta without Isolating Individual Aptamers

Recent studies have demonstrated that changes in the abundance of the intestinal bacterium Blautia producta, a potential probiotic, are closely associated with the development of various diseases such as obesity, diabetes, some neurodegenerative diseases, and certain cancers. However, there is still a lack of an effective method to detect the abundance of B. producta in the gut rapidly. Especially, DNA aptamers are now widely used as biometric components for medical testing due to their unique characteristics, including high chemical stability, low production cost, ease of chemical modification, low immunogenicity, and fast reproducibility. We successfully obtained a high-affinity nucleic acid aptamer library (B.p-R14) after 14 SELEX rounds, which efficiently discriminates B. producta in different analysis techniques including fluorometric suspension assays or fluorescence microscopy from other major gut bacteria in complex mixtures and even in human stool samples. These preliminary findings will be the basis towards aptamer-based biosensing applications for the fast and reliable monitoring of B. producta in the human gut microbiome.     

Precise Quantification of Molybdate In Vitro by the FRET-Based Nanosensor ‘MolyProbe’

Molybdenum (Mo) is an essential trace element in all kingdoms of life. Mo is bioavailable as the oxyanion molybdate and gains biological activity in eukaryotes when bound to molybdopterin, forming the molybdenum cofactor. The imbalance of molybdate homeostasis results in growth deficiencies or toxic symptoms within plants, fungi and animals. Recently, fluorescence resonance energy transfer (FRET) methods have emerged, monitoring cellular and subcellular molybdate distribution dynamics using a genetically encoded molybdate-specific FRET nanosensor, named MolyProbe. Here, we show that the MolyProbe system is a fast and reliable in vitro assay for quantitative molybdate determination. We added a Strep-TagII affinity tag to the MolyProbe protein for quick and easy purification. This MolyProbe is highly stable, resistant to freezing and can be stored for several weeks at 4 °C. Furthermore, the molybdate sensitivity of the assay peaked at low nM levels. Additionally, The MolyProbe was applied in vitro for quantitative molybdate determination in cell extracts of the plant Arabidopsis thaliana, the fungus Neurospora crassa and the yeast Saccharomyces cerevisiae. Our results show the functionality of the Arabidopsis thaliana molybdate transporter MOT1.1 and indicate that FRET-based molybdate detection is an excellent tool for measuring bioavailable Mo.     

2,9-Diazadibenzoperylene and 2,9-Dimethyldibenzoperylene-1,3,8,10-tetratriflates: Key to Functionalized 2,9-Diazaperopyrenes

The synthesis of 2,9-diaza-1,3,8,10-tetratriflato-dibenzoperylene (DDP 3 a ) and corresponding 2,9-dimethyl-1,3,8,10-tetratriflato-dibenzoperylene (DBP 3 b ) has been developed at multigram scale via reduction of one of the industrially most important high-performance dyes, perylene-3,4,9,10-tetracarboxylic diimide (PTCDI), and of the corresponding dihydroxy peropyrenequinone precursor. The focus of this paper is on the reactivity pattern of 3 a as key intermediate towards highly functionalized 2,9-diazadibenzopyrelenes (DDPs) obtained via catalytic substitution of four triflate by aryl, heteroaryl, alkynyl, aminyl, and O-phosphanyl substituents. The influence of electron-donating substituents (OSiMe₃, OPt-Bu₂, N-piperidinyl), electron-withdrawing (OTf, 3,5-bis-trifluoromethyl-phenyl), and of electron-rich π-conjugated (2-thienyl, 4-tert-butylphenyl, trimethylsilyl-ethynyl) substituents on optoelectronic and structural properties of these functionalized DDPs has been investigated via XRD analyses, UV/Vis, PL spectroscopy, and by electroanalytical CV. These results were correlated to results of DFT and TD-DFT calculations. Thus, functionalized DPPs with easily tunable HOMO and LUMO energies and gap became available via a new and reliable synthetic strategy starting from readily available PTCDI.     

Chain rules for linear openness in metric spaces and applications

In this work we present a general theorem concerning chain rules for linear openness of set-valued mappings acting between metric spaces. As particular cases, we obtain classical and also some new results in this field of research, including the celebrated Lyusternik–Graves Theorem. The applications deal with the study of the well-posedness of the solution mappings associated to parametric systems. Sharp estimates for the involved regularity moduli are given.