Backbone and side chain assignment strategies for multiply labeled membrane peptides and proteins in the solid state

We demonstrate that the SPECIFIC CP technique can be used to obtain heteronuclear correlation (HETCOR) spectra of peptide backbones with greater efficiency than conventional HETCOR methods. We show that similar design principles can be employed to achieve selective homonuclear polarization transfer mediated through dipolar or scalar couplings. Both approaches are demonstrated in a tripeptide with uniform 15N and 13C labeling, and with uniform 15N labeling and natural abundance 13C. In other applications, the high efficiency of the heteronuclear SPECIFIC CP transfer allows discrimination of single amide signals in the 248-residue membrane protein bacteriorhodopsin (bR). In particular, variations are detected in the ordering of the Ala81-Arg82 peptide bond among the photocycle intermediates of bR and SPECIFIC CP is used to correlate 15N and 13C signals from the three Val-Pro peptide bonds.     

Ipertrofan Revisited—The Proposal of the Complete Stereochemistry of Mepartricin A and B

Being a methyl ester of partricin, the mepartricin complex is the active substance of a drug called Ipertrofan (Tricandil), which was proven to be useful in treatment of benign prostatic hyperplasia and chronic nonbacterial prostatitis/chronic pelvic pain syndrome. Nevertheless, no direct structural evidence on the stereochemistry of its components has been presented to date. In this contribution, we have conducted detailed, NMR-driven stereochemical studies on mepartricins A and B, aided by molecular dynamics simulations. The absolute configuration of all the stereogenic centers of mepartricin A and B was defined as 3R, 7R, 9R, 11S, 13S, 15R, 17S, 18R, 19S, 21R, 36S, 37R, and 38S, and proposed as 41R. The geometry of the heptaenic chromophore of both compounds has been established as 22E, 24E, 26E, 28Z, 30Z, 32E, and 34E. Our studies on mepartricin ultimately proved that partricins A and B are structurally identical to the previously described main components of the aureofacin complex: gedamycin and vacidin, respectively. The knowledge of the stereochemistry of this drug is a fundamental matter not only in terms of studies on its molecular mode of action, but also for potential derivatization, aiming at improvement of its pharmacological properties.     

Cocrystals “Divorce and Marriage”: When a Binary System Meets an Active Multifunctional Synthon in a Ball Mill

A well-defined and stable “AB” binary system in the presence of “C” a crystalline synthon ground in a ball mill undergoes selective transformation in the solid state according to the equation AB+C→AC+B. When the amount of C is increased two times then the equation AB+2C→AC+BC is valid. The other variants are more complex. The pathway BC+A is allowed and leads to the AC and B products. The pathway AC+B is not preferred, and no transformation is observed. These non-obvious correlations were observed for cocrystal of barbituric acid (BA):thiobarbituric acid (TBA) recently reported by Shemchuk et al. (Chem. Commun. 2016 , 52, 11815–11818) in the presence of 1-hydroxy-4,5-dimethyl-imidazole 3-oxide (HIMO). This synthon shows high affinity for the BA_0.5TBA_0.5 cocrystal as well for its individual components, BA and TBA. Single-quantum, double-quantum (SQ-DQ) 2D ¹H very fast MAS NMR with a spinning rate of 60 kHz was employed as a basic and most diagnostic tool for the study of cocrystals transformations. Analysis of the experimental data was supported by theoretical calculations, including computation of the stabilization energy, E^stab, defined as the energy difference between the energy of a co-crystal and the sum of the energies of particular components in the respective stoichiometric ratios. Two mechanisms of synthon replacement have been proposed. Pathway 1 assumes a concerted mechanism of substitution. In this approach, synthon attack is synchronized in time with the departure of one of the components of the binary system. Pathway 2 implies a non-concerted process, with an intermediate stage in which three separate components are present. Evidence suggesting a preference for Pathway 2 is shown.     

Correlations of NBO energies of individual hydrogen bonds in nucleic acid base pairs with some QTAIM parameters

Structural Chemistry - DNA and RNA base-pairs are the most important systems containing multiple hydrogen bonds. Characterizing the energy of individual intermolecular interactions in such systems...     

Direct observation of the substitution effects on the hydrogen bridge dynamics in selected Schiff bases--a comparative molecular dynamics study

We have studied substituent effects on the properties of the intramolecular hydrogen bond of some ortho-hydroxy Schiff bases using density functional theory (DFT) based first-principle molecular dynamics (FPMD) and path integral molecular dynamics. The studied compounds possess a strong intramolecular hydrogen bond (r((O???N)) ≤ 2.6 A?), which can be tuned by substitution to either (i) enhance the basicity of the acceptor moiety by induction effects or (ii) decrease the hydrogen bond length through steric repulsion. DFT calculations and FPMD were employed to investigate structural and dynamical properties of the selected molecules, while quantum effects on the structural properties were assessed using path integral FPMD. The simulations were performed in vacuo and in the solid state to study the influence of the environment on the hydrogen bond and spectroscopic properties. We give computational support to the suggestion that induction effects are less effective to tune the intramolecular hydrogen bond properties of the discussed ortho-hydroxy Schiff bases than the steric or the environmental effects.     

The MM2QM tool for combining docking,molecular dynamics,molecular mechanics,and quantum mechanics†

The use of the MM2QM tool in a combined docking + molecular dynamics (MD) + molecular mechanics (MM) + quantum mechanical (QM) binding affinity prediction study is presented, and the tool itself is discussed. The system of interest is Mycobacterium tuberculosis (MTB) pantothenate synthetase in complexes with three highly similar sulfonamide inhibitors, for which crystal structures are available. Starting from the structure of MTB pantothenate synthetase in the “open” conformation and following the combined docking + MD + MM + QM procedure, we were able to capture the closing of the enzyme binding pocket and to reproduce the position of the ligands with an average root mean square deviation of 1.6 Å. Protein–ligand interaction energies were reproduced with an average error lower than 10%. The discussion on the MD part and a protein flexibility importance is carried out. The presented approach may be useful especially for finding analog inhibitors or improving drug candidates. © 2012 Wiley Periodicals, Inc.     

The Equilibria of Phosphatidylethanolamine-Cholesterol and Phosphatidylcholine–Phosphatidylethanolamine in Monolayers at the Air/Water Interface

Monolayers of phosphatidylethanolamine (PE), cholesterol (Ch), phosphatidylcholine (PC), and binary mixtures (PC-PE or PE-Ch) were investigated at the air/water interface. The surface tension values of pure and mixed monolayers were used to calculate π -A isotherms. The surface tension measurements were carried out at 20°C using an improved Teflon trough and a Nima 9000 tensiometer. The Teflon trough was filled with a subphase of triple-distilled water. Known amounts of lipid dissolved in 1-chloropropane were placed at the surface using a syringe. The interactions between phosphatidylethanolamine and cholesterol as well as phosphatidylcholine and phosphatidylethanolamine result in significant deviations from the additivity rule. An equilibrium theory to describe the behavior of monolayer components at the air/water interface was developed in order to obtain the stability constants of PC-PE and PE-Ch complexes. We considered the equilibrium between the individual components and the complex and established that phosphatidylethanolamine and cholesterol as well as phosphatidylcholine and phosphatidylethanolamine formed highly stable 1:1 complexes.     

The Effect of Filtration on Physical and Chemical Properties of Osmo-Dehydrated Material

Osmotic dehydration (OD) performed in concentrated fruit juices used as osmotic solution (OS) comes with some limitations resulting from the material cell structure and is not entirely recognized at the moment. Filtration of the juice could provide some insight into the phenomena occurring throughout the OD. Therefore, the main aim of the study was to recognize the mechanism of selective penetration during OD and evaluate the effect of filtration on physical and chemical properties of osmo-dehydrated material. For this purpose, OD of pumpkin in non-filtrated and filtrated (filters 0.2, 0.45, 0.8, 1.2, 3, 5 and 8 μm) concentrated chokeberry juice was carried out in the study. Moreover, scanning electron microscope (SEM) images were provided. Total phenolic content (TPC) and antioxidant capacity measured by Ferric Reducing Antioxidant Potential (FRAP) and Trolox Equivalent Antioxidant Capacity (TEAC ABTS) of OS and the material were determined. It was found that even though filtration of osmotic solution had a moderate influence on the mass transfer, it greatly affected the chemical composition of dehydrated material. The best option, considering both chemical and physical properties of the dehydrated material, is the use of non-filtrated solution. However, when shorter time of OD is considered, much better results are obtained for filtrated solutions.     

Electrocatalytic properties of platinum nanocenters electrogenerated at ultra-trace levels within zeolitic phosphododecatungstate cesium salt matrices

A unique preparation method of obtaining stable composite film (with ultra-low platinum content) highly active towards oxygen reduction and hydrogen oxidation is presented here. The matrix for platinum centers consists of high-surface-area zeolite-type acidic salt of cesium phosphododecatungstate (Cs_2.5H_0.5PW₁₂O₄₀) admixed with carbon (Vulcan XC-72) carriers. Platinum nanoparticles were deposited on the working electrode modified with matrix via corrosion of platinum counter electrode during cyclic voltammetry experiment conducted in acid electrolyte containing chloride ions. The results obtained from rotating disk voltammetry revealed that the composite film containing Pt nanoparticles at very low loadings (on the level of 2–5 μg cm^?2) demonstrated remarkable electrocatalytic activity towards both oxygen reduction and hydrogen oxidation, particularly, when compared to the performance of the Cs_2.5H_0.5PW₁₂O₄₀-free system (i.e., containing only Vulcan support) prepared and examined under analogous conditions. The phenomenon should be primarily ascribed to the mesoporous nature of the matrix enabling immobilization and stabilization of small catalytic nanoparticles (1–2 nm diameters) inside the pores as well as to high surface acidity of the polyoxometalate-based salt providing proton-rich environment at the electrocatalytic interface.     

Simultaneous monitoring of monoamines,amino acids,nucleotides and neuropeptides by liquid chromatography‐tandem mass spectrometry and its application to neurosecretion in bovine chromaffin cells

The primary functions of adrenal medullary chromaffin cells are the synthesis and storage in their chromaffin vesicles of the catecholamines noradrenaline (NA) and adrenaline (AD), and their subsequent release into the bloodstream by Ca²⁺‐dependent exocytosis under conditions of fear or stress (fight or flight response). Several monoamines, nucleotides and opiates, such as leucine‐enkephalin (LENK) and methionine‐enkephalin (MENK), are also co‐stored and co‐released with the catecholamines. However, other neurotransmitters have not been studied in depth. Here, we present a novel high‐resolution liquid chromatography‐tandem mass spectrometry approach for the simultaneous monitoring of 14 compounds stored and released in bovine chromaffin cells (BCCs). We validated the analytical method according to the recommendations of the EMA and FDA by testing matrix effect, selectivity, sensitivity, precision, accuracy, stability and carry‐over. After testing on six batches of BCCs from different cultures, the method enabled simultaneous quantitative determination of monoamines (AD, NA, dopamine, serotonin, 5‐hydroxyindoleacetic acid, histamine and metanephrine), amino acids (L‐glutamic acid, γ‐aminobutyric acid), nucleotides (adenosine 5′‐diphosphate, adenosine 5′‐monophosphate, cyclic adenosine 5′‐monophosphate) and neuropeptides (LENK and MENK) in the intracellular content, basal secretion and acetylcholine induced secretion of BBCs. The high‐resolution approach used here enabled us to determine the levels of 14 compounds in the same BCC batch in only 16 min. This novel approach will make it possible to study the regulatory mechanisms of Ca²⁺ signaling, exocytosis and endocytosis using different neurotrophic factors and/or secretagogues as stimuli in primary BCC cultures. Our method is actually being applied to human plasma samples of different therapeutic areas where sympathoadrenal axis is involved in stress situations such as Alzheimer's disease, migraine or cirrhosis, to improve diagnosis and clinical practice. Copyright © 2016 John Wiley & Sons, Ltd.