How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP,TP2 and ONEG?

Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) ¹H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.

A protocol for simulating intrinsically disordered peptides in aqueous and hydrophobic solvents is proposed. Results from four force fields are compared with experiment. CHARMM36m performs the best for the simulated IDPs in all environments.     

Monthly Increase in Vitamin D Levels upon Supplementation with 2000 IU/Day in Healthy Volunteers: Result from “Integriamoci”, a Pilot Pharmacokinetic Study

Vitamin D (VD) is a calcium- and phosphate-controlling hormone used to treat bone disorders; yet, several other effects are progressively emerging. VD deficiency is highly prevalent worldwide, with suboptimal exposure to sunlight listed among the leading causes: oral supplementation with either cholecalciferol or calcitriol is used. However, there is a scarcity of clinical studies investigating how quickly VD concentrations can increase after supplementation. In this pilot study, the commercial supplement ImmuD3 (by Erboristeria Magentina^®) was chosen as the source of VD and 2000 IU/day was administered for one month to 21 healthy volunteers that had not taken any other VD supplements in the previous 30 days. Plasma VD levels were measured through liquid chromatography coupled to tandem mass spectrometry after 7, 14, and 28 days of supplementation. We found that 95% of the participants had insufficient VD levels at baseline (<30 ng/mL; median 23.72 ng/mL; IQR 18.10–26.15), but after 28 days of supplementation, this percentage dropped to 62% (median 28.35 ng/mL; IQR 25.78–35.20). The median increase in VD level was 3.09 ng/mL (IQR 1.60–5.68) after 7 days and 8.85 ng/mL (IQR 2.85–13.97F) after 28 days. This study suggests the need for continuing VD supplementation and for measuring target level attainment.     

Development and Validation of a Reliable UHPLC-MS/MS Method for Simultaneous Quantification of Macrocyclic Lactones in Bovine Plasma

A fast, accurate and reliable ultra-high performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) method was developed for simultaneous quantification of ivermectin (IVER), doramectin (DORA), and moxidectin (MOXI) in bovine plasma. A priority for sample preparation was the eradication of possible infectious diseases to avoid travel restrictions. The sample preparation was based on protein precipitation using 1% formic acid in acetonitrile, followed by Ostro^® 96-well plate pass-through sample clean-up. The simple and straightforward procedure, along with the short analysis time, makes the current method unique and suitable for a large set of sample analyses per day for PK studies. Chromatographic separation was performed using an Acquity UPLC HSS-T3 column, with 0.01% acetic acid in water and methanol, on an Acquity H-Class ultra-high performance liquid chromatograph (UHPLC) system. The MS/MS instrument was a Xevo TQ-S^® mass spectrometer, operating in the positive electrospray ionization mode and two multiple reaction monitoring (MRM) transitions were monitored per component. The MRM transitions of m/z 897.50 > 753.4 for IVER, m/z 921.70 > 777.40 for DORA and m/z 640.40 > 123.10 for MOXI were used for quantification. The method validation was performed using matrix-matched calibration curves in a concentration range of 1 to 500 ng/mL. Calibration curves fitted a quadratic regression model with 1/x2 weighting (r ≥ 0.998 and GoF ≤ 4.85%). Limits of quantification (LOQ) values of 1 ng/mL were obtained for all the analytes, while the limits of detection (LOD) were 0.02 ng/mL for IVER, 0.03 ng/mL for DORA, and 0.58 ng/mL for MOXI. The results of within-day (RSD < 6.50%) and between-day (RSD < 8.10%) precision and accuracies fell within acceptance ranges. No carry-over and no peak were detected in the UHPLC-MS/MS chromatogram of blank samples showing good specificity of the method. The applicability of the developed method was proved by an analysis of the field PK samples.     

SuFEx-enabled,chemoselective synthesis of triflates,triflamides and triflimidates

Sulfur(vi) Fluoride Exchange (SuFEx) chemistry has emerged as a next-generation click reaction, designed to assemble functional molecules quickly and modularly. Here, we report the ex situ generation of trifluoromethanesulfonyl fluoride (CF₃SO₂F) gas in a two chamber system, and its use as a new SuFEx handle to efficiently synthesize triflates and triflamides. This broadly tolerated protocol lends itself to peptide modification or to telescoping into coupling reactions. Moreover, redesigning the S^VI–F connector with a S O → S NR replacement furnished the analogous triflimidoyl fluorides as SuFEx electrophiles, which were engaged in the synthesis of rarely reported triflimidate esters. Notably, experiments showed H₂O to be the key towards achieving chemoselective trifluoromethanesulfonation of phenols vs. amine groups, a phenomenon best explained—using ab initio metadynamics simulations—by a hydrogen bonded termolecular transition state for the CF₃SO₂F triflylation of amines.

Triflyl fluoride gas (CF₃SO₂F) and its aza analogues are reported as new SuFEx activators. These S^VI–F reagents react efficiently with a variety of nucleophiles, yet the presence of water grants complete chemoselectivity to phenols.     

Cationic ≠3-allylmetal complexes, 13a) electrical properties of new poly(phenylacetylene) obtained from nickel catalysts

Monometallic complexes of Nickel have been successfully, tested in reaction with olefinic and acetylenic compounds. This paper is devoted to one of the resulting products, a polyphenylacetylene which presents interesting properties. It is readily obtained avoiding the step of a polymer precursor; it is soluble in several solvents, stable in air up to 200° C and may possess a rather high conductivity, depending on polymerization conditions. This is a noticeable difference versus previously reported polyphenylacetylenes which were insulating materials.     

The blossoming of quantum mechanics in Italy: the roots,the context and the first spreading in Italian universities (1900–1947)

The European Physical Journal H - The widespread positivist approach of physics research in Italy at the turn of the XIX and XX centuries did not provide a fertile ground for the scientific debate...     

Single and double electron capture associated with target K-shell ionization for F7 + ,8 + ,9++Ar

Ratios for target Ar K-shell ionization associated with single and double electron capture, as well as the ratios corresponding to total capture and the projectile K x rays, were determined for 1.8- to 2.2-MeV/u F^{7 + ,8 + ,9+} projectiles. This work was performed at Western Michigan University with the tandem Van de Graaff accelerator. Coincidences between emitted K-shell X-rays (both target and projectile) and the corresponding charge-changed particles were observed. The F⁹⁺ Ar K X-ray coincidence ratios for double to single capture are found to well exceed unity over the limited energy range of the measurements. Possible explanations for this anomalous behavior are discussed.     

Rapid and high-performance analysis of thyreostatic drug residues in urine using gas chromatography-mass spectrometry

A more sensitive method was developed using the hyphenated technique of gas chromatography-mass spectrometry (GC-MS) supplementary to the official high-performance thin-layer chromatography (HPTLC) method. Even combined with less efficient extraction and clean-up methods, GC-MS is able to lower the detection limit to less than 50 ppb. The powerful technique of GC-MS-MS is tried out to reduce the detection limit even more, in combination with simplified extraction methods. This time-saving approach combined with the increase in sensitivity is of great importance for a routine technique.     

Determination of biogenic amines in alcoholic beverages by ion chromatography with suppressed conductivity detection and integrated pulsed amperometric detection

The determination of biogenic amines in alcoholic beverages is important to assess the potential risks associated with the consumption of high concentrations of these compounds. In addition, product storage conditions and the length of storage can cause the formation of biogenic amines that reduce product quality. We report a new method using cation-exchange chromatography with either suppressed conductivity, integrated pulsed amperometry, UV, or a combination of these detection techniques to determine biogenic amines in alcoholic beverages. The main objective was to provide a direct comparison between IPAD and suppressed conductivity detection for determining biogenic amines in alcoholic beverages. Suppressed conductivity is the simplest detection approach for determining putrescine, cadaverine, histamine, agmatine, phenylethylamine, spermidine, and spermine with good sensitivity (0.004-0.08 mg/l) and was used to evaluate the influence of storage time and conditions on the evolution of biogenic amines in alcoholic beverages. Integrated pulsed amperometric detection (IPAD) detects more biogenic amines than suppressed conductivity detection, enabling the detection of dopamine, tyramine, and serotonin. Tyramine was simultaneously determined by UV detection and IPAD to provide confirmation and ensure the accuracy of the analytical results. The linearity of biogenic amine responses was within 0.1-20 mg/l and peak area precisions were 0.24-4.97% for IPAD, suppressed conductivity-IPAD, and UV detection. The sensitivity for the 10 biogenic amines using the 3 detection techniques varied considerably from 0.004-1.1 mg/l and recoveries were within 85-122%.     

Theoretical study of the interaction between sodium ion and a cyclopeptidic tubular structure

DFT calculations have been carried out to describe the pathway of a sodium ion along the stacking direction of a tubular structure set up by five cyclopeptidic units, which can be considered a suitable model of a hollow tubular structure of indefinite length. A lattice of points inside the tubular structure is defined and the DFT interaction energy values with a sodium ion are obtained. The data allow predicting a zigzag path of the ion inside the hosting structure.