Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor

Prediction of 3D structures of membrane proteins, and of G-protein coupled receptors (GPCRs) in particular, is motivated by their importance in biological systems and the difficulties associated with experimental structure determination. In the present study, a novel method for the prediction of 3D structures of the membrane-embedded region of helical membrane proteins is presented. A large pool of candidate models are produced by repacking of the helices of a homology model using Monte Carlo sampling in torsion space, followed by ranking based on their geometric and ligand-binding properties. The trajectory is directed by weak initial restraints to orient helices towards the original model to improve computation efficiency, and by a ligand to guide the receptor towards a chosen conformational state. The method was validated by construction of the β₁ adrenergic receptor model in complex with (S)-cyanopindolol using bovine rhodopsin as template. In addition, models of the dopamine D₂ receptor were produced with the selective and rigid agonist (R)-N-propylapomorphine ((R)-NPA) present. A second quality assessment was implemented by evaluating the results from docking of a library of 29 ligands with known activity, which further discriminated between receptor models. Agonist binding and recognition by the dopamine D₂ receptor is interpreted using the 3D structure model resulting from the approach. This method has a potential for modeling of all types of helical transmembrane proteins for which a structural template with sequence homology sufficient for homology modeling is not available or is in an incorrect conformational state, but for which sufficient empirical information is accessible.     

Discovery and validation of urinary exposure markers for different plant foods by untargeted metabolomics

While metabolomics is increasingly used to investigate the food metabolome and identify new markers of food exposure, limited attention has been given to the validation of such markers. The main objectives of the present study were to (1) discover potential food exposure markers (PEMs) for a range of plant foods in a study setting with a mixed dietary background and (2) validate PEMs found in a previous meal study. Three-day weighed dietary records and 24-h urine samples were collected three times during a 6-month parallel intervention study from 107 subjects randomized to two distinct dietary patterns. An untargeted UPLC-qTOF-MS metabolomics analysis was performed on the urine samples, and all features detected underwent strict data analyses, including an iterative paired t test and sensitivity and specificity analyses for foods. A total of 22 unique PEMs were identified that covered 7 out of 40 investigated food groups (strawberry, cabbages, beetroot, walnut, citrus, green beans and chocolate). The PEMs reflected foods with a distinct composition rather than foods eaten more frequently or in larger amounts. We found that 23 % of the PEMs found in a previous meal study were also valid in the present intervention study. The study demonstrates that it is possible to discover and validate PEMs for several foods and food classes in an intervention study with a mixed dietary background, despite the large variability in such a dataset. Final validation of PEMs for intake of foods should be performed by quantitative analysis.

The Vibrational Behavior of Coupled Bladed Disks with Variable Rotational Speed

Low pressure steam turbine blades are subjected to high static and dynamic loads during operation. These loads strongly depend on the turbine's rotational speed, leading to entirely new load conditions. To avoid high dynamic stresses due to the forced vibrations, a coupling of the blades, such as shrouds or snubber coupling, is applied to reinforce the structure. In this work the influence of the rotational speed on the vibration behavior of shrouded blades is investigated. Two fundamental phenomena are considered: the stress stiffening and the spin softening effect. Both effects are caused by centrifugal forces and affect the structural mechanical properties, i.e. the stiffness matrix K , of the rotating system. Since the rotational speed Ω appears quadratically, it is possible to derive the stiffness matrix as a second order matrix polynomial in Ω² [3]. In the case of shrouded blades, contact forces between neighboring blades must be taken into account. The contact status and the pressure distribution in particular is strongly influenced by the rotational speed, respectively, centrifugal forces, caused by the untwisting and radial deformation of the blades. For the calculation, a three dimensional structural mechanical model including a spatial contact model is considered. The solution of the nonlinear equations of motion is based on the well known Multiharmonic Balance Method [2]. Here, the nonlinear forces are computed in the time domain and transferred in the frequency domain by the use of the Fast Fourier Transformation (FFT), also known as the Alternating Frequency Time method (AFT) [1]. (© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Comprehensive Characterization of Shredded Lithium-Ion Battery Recycling Material

Herein we report on an analytical study of dry-shredded lithium-ion battery (LIB) materials with unknown composition. Samples from an industrial recycling process were analyzed concerning the elemental composition and (organic) compound speciation. Deep understanding of the base material for LIB recycling was obtained by identification and analysis of transition metal stoichiometry, current collector metals, base electrolyte and electrolyte additive residues, aging marker molecules and polymer binder fingerprints. For reversed engineering purposes, the main electrode and electrolyte chemistries were traced back to pristine materials. Furthermore, possible lifetime application and accompanied aging was evaluated based on target analysis on characteristic molecules described in literature. With this, the reported analytics provided precious information for value estimation of the undefined spent batteries and enabled tailored recycling process deliberations. The comprehensive feedstock characterization shown in this work paves the way for targeted process control in LIB recycling processes.     

Asymmetric Organocatalytic Homologation: Access to Diverse Chiral Trifluoromethyl Organoboron Species

A broad range of aliphatic, aromatic, and heterocyclic boronic acids were successfully homologated using trifluorodiazoethane in the presence of BINOL derivatives to provide the corresponding chiral trifluoromethyl containing boronic acid derivatives in high yields and excellent enantioselectivity. The in situ conversion of the chiral transient boronic acids to the corresponding alcohols or β-CF3 carboxylates are also demonstrated.     

Germaborenes: Borylene Transfer Agents for the Synthesis of Iminoboranes

Halide and phenyl substituted germaborenes were shown to react with azides at room temperature and transfer a borylene moiety to give iminoboranes. This iminoborane synthesis based on a borylene transfer route was investigated computationally in the case of the phenyl substituted germaborene.     

Phosphine-Stabilized Pnictinidenes

The reaction of the intramolecular germylene-phosphine Lewis pair (o-PPh₂)C₆H₄GeAr* ( 1 ) with Group 15 element trichlorides ECl₃ (E=P, As, Sb) was investigated. After oxidative addition, the resulting compounds (o-PPh₂)C₆H₄(Ar*)Ge(Cl)ECl₂ ( 2 : E=P, 3 : E=As, 4 : E=Sb) were reduced by using sodium metal or LiHBEt₃. The molecular structures of the phosphine-stabilized phosphinidene (o-PPh₂)C₆H₄(Ar*)Ge(Cl)P ( 5 ), arsinidene (o-PPh₂)C₆H₄(Ar*)Ge(Cl)As ( 6 ) and stibinidene (o-PPh₂)C₆H₄(Ar*)Ge(Cl)Sb ( 7 ) are presented; they feature a two-coordinate low-valent Group 15 element. After chloride abstraction, a cyclic germaphosphene [(o-PPh₂)C₆H₄(Ar*)GeP] [B(C₆H₃(CF₃)₂)₄] ( 8 ) was isolated. The ³¹P NMR data of the germaphosphene were compared with literature examples and analyzed by quantum chemical calculations. The phosphinidene was treated with [iBu₂AlH]₂, and the product of an Al−H addition to the low-valent phosphorus atom (o-PPh₂)C₆H₄(Ar*)Ge(H)P(H)Al(C₄H₉)₂ ( 9 ) was characterized.     

Cation-Induced Stabilization of Protein Complexes in the Gas Phase: Mechanistic Insights From Hemoglobin Dissociation Studies

Collision-induced dissociation (CID) of electrosprayed protein complexes usually involves asymmetric charge partitioning, where a single unfolded chain gets ejected that carries a disproportionately large fraction of charge. Using hemoglobin (Hb) tetramers as model system, we confirm earlier reports that bound metal ions can stabilize protein complexes under CID conditions. We examine the mechanism underlying this effect. Nonvolatile salts cause extensive adduct formation. Significant stabilization was observed for Mg²⁺ and Ca²⁺, whereas K⁺, Rb⁺, and Cs⁺ had no effect. Precursor ion selection was used to examine Hb subpopulations with well-defined metal binding levels. K⁺, Rb⁺, and Cs⁺-adducted tetramers eject monomers that carry roughly one-quarter of the metal ions that were bound to the precursor. This demonstrates that charge migration during CID is exclusively due to proton transfer, not metal ion transfer. Also, replacement of highly mobile charge carriers (protons) with less mobile species (metal ions) does not exert a stabilizing influence under the conditions used here. Interestingly, Hb carrying stabilizing ions (Mg²⁺ and Ca²⁺) generates monomeric CID products that are metal depleted. This effect is attributed to a combination of two factors: (1) Me²⁺ binding stabilizes Hb via formation of chelation bridges (e.g., R-COO^– Me^{2+ –}OOC-R); the more Me²⁺ a subunit contains the more stable it is. (2) More than ~90 % of the tetramers contain at least one subunit with a below-average number of Me²⁺. The prevalence of monomeric CID products with depleted Me²⁺ levels is caused by the tendency of these low metal-containing subunits to undergo preferential unfolding/ejection.