Binding structure of elastase inhibitor scyptolin A

Natural bioactive compounds are of general interest to pharmaceutical research because they may be used as leads in drug development campaigns. Among them, scyptolin A and B from Scytonema hofmanni PCC 7110 are known to inhibit porcine pancreatic elastase, which in turn resembles the attractive drug target neutrophil elastase. The crystal structure of scyptolin A as bound to pancreatic elastase was solved at 2.8 A resolution. The inhibitor occupies the most prominent subsites S1 through S4 of the elastase and prevents a hydrolytic attack by covering the active center with its rigid ring structure. The observed binding structure may help to design potent elastase inhibitors.     

Deuterium-labelled N-acyl-L-homoserine lactones (AHLs)--inter-kingdom signalling molecules--synthesis, structural studies, and interactions with model lipid membranes

N-Acyl-l-homoserine lactones (AHLs) are synthesized by Gram-negative bacteria. These quorum-sensing molecules play an important role in the context of bacterial infection and biofilm formation. They also allow communication between microorganisms and eukaryotic cells (inter-kingdom signalling). However, very little is known about the entire mechanism of those interactions. Precise structural studies are required to analyse the different AHL isomers as only one form is biologically most active. Theoretical studies combined with experimental infrared and Raman spectroscopic data are therefore undertaken to characterise the obtained compounds. To mimic interactions between AHL and cell membranes, we studied the insertion of AHL in supported lipid bilayers, using vibrational sum-frequency-generation spectroscopy. Deuterium-labelled AHLs were thus synthesized. Starting from readily available deuterated fatty acids, a two-step procedure towards deuterated N-acyl-l-homoserine lactones with varying chain lengths is described. This included the acylation of Meldrum’s acid followed by amidation. Additionally, the detailed analytical evaluation of the products is presented herein.     

Probing the ATP hydrolysis cycle of the ABC multidrug transporter LmrA by pulsed EPR spectroscopy

Members of the ATP binding cassette (ABC) transporter superfamily translocate various types of molecules across the membrane at the expense of ATP. This requires cycling through a number of catalytic states. Here, we report conformational changes throughout the catalytic cycle of LmrA, a homodimeric multidrug ABC transporter from L. lactis. Using site-directed spin labeling and pulsed electron-electron double resonance (PELDOR/DEER) spectroscopy, we have probed the reorientation of the nucleotide binding domains and transmembrane helix 6 which is of particular relevance to drug binding and part of the dimerization interface. Our data show that LmrA samples a very large conformational space in its apo state, which is significantly reduced upon nucleotide binding. ATP binding but not hydrolysis is required to trigger this conformational change, which results in a relatively fixed orientation of both the nucleotide binding domains and transmembrane helices 6. This orientation is maintained throughout the ATP hydrolysis cycle until the protein cycles back to its apo state. Our data present strong evidence that switching between two dynamically and structurally distinct states is required for substrate translocation.     

Tetrachlorinated Tetraazaperopyrenes (TAPPs): Highly Fluorescent Dyes and Semiconductors for Air‐Stable Organic n‐Channel Transistors and Complementary Circuits

A range of 2,9‐perfluoroalkyl‐substituted tetraazaperopyrene (TAPP) derivatives ( 1 – 5 ) was synthesised by reacting 4,9‐diamino‐3,10‐perylenequinone diimine (DPDI) with the corresponding carboxylic acid chloride or anhydride in the presence of a base. The reaction of compounds 1 – 4 with dichloroisocyanuric acid (DIC) in concentrated sulphuric acid resulted in the fourfold substitution of the tetraazaperopyrene core, yielding the 2,9‐bisperfluoroalkyl‐4,7,11,14‐tetrachloro‐1,3,8,10‐tetraazaperopyrenes 6 – 9 , respectively. The optical and electrochemical data demonstrate the drastic influence of the core substitution on the properties. All compounds are highly luminescent (fluorescence quantum yields of up to Φ=0.8). The LUMO energies of the tetrachlorinated TAPP derivatives (determined by cyclic voltammetry and computed by DFT calulations) were found to be below ?4 eV. In the course of this work the performance of TAPP derivatives in organic thin‐film transistors (TFTs) was investigated, and their n‐channel characteristics with field‐effect mobilities of up to 0.14 cm² V^?1 s^?1 and an on/off current ratio of >10⁶ were confirmed. Long‐term stabilities of 3–4 months under ambient conditions of the devices were established. Complementary inverters and ring oscillators with n‐channel TFTs based on compound 8 and p‐channel TFTs based on dinaphtho‐[2,3‐b:2′,3′‐f]thieno[3,2‐b]thiophene (DNTT) were fabricated on a glass substrate.     

Spectroscopic and photophysical properties of dUTP and internally DNA bound fluorophores for optimized signal detection in biological formats

Efficient signal generation in DNA-based assays requires understanding of the influence of fluorophore's interactions on the spectroscopic properties. The resulting changes in fluorescence intensity, quantum yield, emission anisotropy, and fluorescence lifetime provide straightforward tools for the study of molecular dynamics and interaction between labels and nucleic acids. Searching for bright fluorescent reporters for rolling circle amplification (RCA) as efficient signal enhancement strategy for biological formats, we investigated the spectroscopic properties of seven dyes: cyanines, rhodamines, and BODIPYs. They spectrally resemble Cy3, the most frequently used fluorophore in biodetection formats, and are measured in six samples (free dye, dye-dUTP, internally labeled ssDNA and dsDNA-single- and triple-labeled) using steady-state and time-resolved fluorometry. Special emphasis was dedicated to characterizing the nature of the interaction of these fluorophores differing in dye class, charge, and rigidity. Our results suggest dye charge and structure as main factors governing the dye's interactions, with DY-555 and Cy3B presenting the best candidates for our envisaged signal amplification strategy. This label comparison underlines the importance of a proper understanding of structure-property relations and dye-biomolecule interactions for reporter choice and presents a road map towards the design and interpretation of experiments using these labels on DNA of known sequence.     

Cyclodysidins A–D,cyclic lipopeptides from the marine sponge-derived Streptomyces strain RV15

Four new cyclic lipopeptides, cyclo-(AFA-Ser-Gln-Asn-Tyr-Asn-Ser-Thr), named cyclodysidins A–D, were isolated from the broth culture of Streptomyces strain RV15 associated with the marine sponge Dysidea tupha. The sequences of the amino acid building blocks in the compounds and their structures were determined by 1D- and 2D-NMR techniques and CID-MS/MS experiments. The absolute configurations of all α-amino acids were determined by HPLC analysis after derivatization with Marfey’s reagent and comparison with commercially available reference samples, while those two of the β-amino fatty acids were determined by using racemic and enantiopure reference samples synthetically prepared.     

Quantifying diffusion for an ultrasonic wire bonding process by applying the theory of material forces

Ultrasonic wire bonding is a method applied in electronic packaging to fabricate interconnections between two devices at ambient temperature. In order to investigate the material diffusion during this process, the occurring thermal and mechanical mechanisms at and around the interface of the formed bond were studied by means of coupled thermo-mechanical FE simulations. Within the framework of material forces the local jump of the Eshelby tensor was compared with the thickness of the formed intermetallic phase for various bonding parameters. This allows us to predict an effective diffusion constant which takes temperature and mechanical driving forces into account. After this relation has been established a subsequent objective of our investigations is to optimize the growth of the Au8Al3 intermetallic phase in terms of bonding parameters. (© 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Synthesis and structure of the scandium‐rich indides Sc5Ni2In4 and Sc5Rh2In4

The ternary indides Sc₅ Ni₂ In₄ and Sc₅ Rh₂ In₄ were synthesized by arc‐melting of the elements and subsequent annealing. A structural investigation by X‐ray powder and single crystal diffraction revealed: Lu₅ Ni₂ In₄ type, Pbam, a = 1716.3(2), b = 755.1(1), c = 335.22(5) pm, wR2 = 0.0721, 844 F² values for Sc₅ Ni₂ In₄, and a = 1754.3(3), b = 765.0(1), c = 332.97(6) pm, wR2 = 0.0363, 1107 F² values for Sc₅ Rh₂ In₄ with 36 variables per refinement. Both structures can be described as intergrowths of distorted AlB₂‐ and CsCl‐related slabs, where the transition metal (T) atoms have a trigonal prismatic and the indium atoms a distorted square prismatic coordination. The shortest interatomic distances occur for Sc T and T In. The crystal chemistry and chemical bonding in these intermetallics are briefly discussed. © 2005 Wiley Periodicals, Inc. Heteroatom Chem 16:364–368, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20106     

Tailor-made derivatizing agents for carbonyl compounds using liquid chromatography

A new approach for the synthesis and application of tailor-made derivatizing agents for liquid chromatography is presented. The s-triazine ring serves as the backbone for these substances. Synthesis is performed in three steps based on substitution reactions of cyanuric chloride. A chromophor or fluorophor, a reactive group and a third moiety intended to modify the polarity of the derivatizing agent are coupled to cyanuric chloride. The three groups may be selected freely from molecules which carry functional groups which might be linked to cyanuric chloride. As an example, the synthesis and application of a respective reagent for the determination of aldehydes and ketones using HPLC with fluorescence detection is carried out. Baseline separation of the derivatives and low limits of detection (1.5×10⁻⁹ mol/l for formaldehyde, 2.0×10⁻⁹ mol/l for acetaldehyde and 3.0×10⁻⁹ mol/l for p-tolualdehyde) are obtained with the new versatile reagent.