Methyl groups as probes for proteins and complexes in in-cell NMR experiments

Studying protein components of large intracellular complexes by in-cell NMR has so far been impossible because the backbone resonances are unobservable due to their slow tumbling rates. We describe a methodology that overcomes this difficulty through selective labeling of methyl groups, which possess more favorable relaxation behavior. Comparison of different in-cell labeling schemes with three different proteins, calmodulin, NmerA, and FKBP, shows that selective labeling with [(13)C]methyl groups on methionine and alanine provides excellent sensitivity with low background levels at very low costs.     

Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

Continuous sample deposition from reversed-phase liquid chromatography to tracks on a matrix-assisted laser desorption/ionization precoated target for the analysis of protein digests

Peptide mass fingerprinting by matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry (MS) is one of the standard high-throughput methods for protein identification today. Traditionally this method has been based on spotting peptide mixtures onto MALDI targets. While this method works well for more abundant proteins, low-abundance proteins mixed with high-abundance proteins tend to go undetected due to ion suppression effects, instrumental dynamic range limitations and chemical noise interference. We present an alternative approach where liquid chromatography (LC) effluent is continuously collected as linear tracks on a MALDI target. In this manner the chromatographic separation is spatially preserved on the target, which enables generation of off-line LC-MS and LC-MS/MS data by MALDI. LC-MALDI sample collection provides improved sensitivity and dynamic range, spatial resolution of peptides along the sample track, and permits peptide mass mapping of low-abundance proteins in mixtures containing high-abundance proteins. In this work, standard and ribosomal protein digests are resolved and captured using LC-MALDI sample collection and analyzed by MALDI-TOF-MS.     

On the swelling behavior of poly(N-Isopropylacrylamide) hydrogels exposed to perfluoroalkyl acids

Per- and polyfluoroalkyl substances (PFAS) have rapidly accumulated in the environment due to their widespread use prior to commercial discussion in the early 21st century, and their slow degradation has magnified concerns of their potential toxicity. Monitoring their distribution is, therefore, necessary to evaluate and control their impact on the health of exposed populations. This investigation evaluates the capability of a simple polymeric detection scheme for PFAS based on crosslinked, thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) hydrogels. Surveying swelling perturbations induced by several hydrotropes and comparable hydrocarbon analogs, tetraethylammonium perfluorooctane sulfonate (TPFOS) showed a significantly higher swelling ratio on a mass basis (65.5 ± 8.8 at 15°C) than any of the other analytes tested. Combining swelling with the fluorimetric response of a solvachromatic dye, nile red, revealed the fluorosurfactant to initiate observable aggregation (i.e., its critical aggregation concentration) at 0.05 mM and reach saturation (i.e., its charge neutralization concentration) at 0.5 mM. The fluorosurfactant was found to homogeneously distribute throughout the polymer matrix with energy dispersive X-ray spectroscopy, marking the swelling response as a peculiar nexus of fluorinated interfacial positioning and delocalized electrostatic repulsion. Results from the current study hold promise for exploiting the physiochemical response of PNIPAM to assess TPFOS's concentration.     

Optimizing the monomer structure of polyhedral oligomeric silsesquioxane for ion transport in hybrid organic–inorganic block copolymers

Poly(ethylene oxide)-b-polyhedral oligomeric silsesquioxane (PEO–POSS) mixed with lithium bis(trifluoromethanesulfonyl)imide salt is a nanostructured hybrid organic–inorganic block copolymer electrolyte that may enable lithium metal batteries. The synthesis and characteristics of three PEO–POSS block copolymer electrolytes which only differ by their POSS silica cage substituents (ethyl, isobutyl, and isooctyl) is reported. Changing the POSS monomer structure results in differences in both thermodynamics and ion transport. All three neat polymers exhibit lamellar morphologies. Adding salt results in the formation of a disordered window which closes and gives way to lamellae at higher salt concentrations. The width of disordered window decreases with increasing length of the POSS alkyl chain substituent from ethyl to isobutyl and is absent in the isooctyl sample. Rheological measurements demonstrate good mechanical rigidity when compared with similar all-organic block copolymers. While salt diffusion coefficient and current ratio are unaffected by substituent length, ionic conductivity increases as the length of the alkyl chain substituent decreases: the ethyl substituent is optimal for ion transport. This is surprising because conventional wisdom suggests that ion transport occurs primarily in the PEO-rich domains, that is, ion transport should be unaffected by substituent length after accounting for the minor change in conducting phase volume fraction. © 2020 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2020 © 2020 Wiley Periodicals, Inc. J. Polym. Sci. 2020 , 58, 363–371     

Thermochemistry of fluorine compounds: IV. Rubidium tetrafluoroiodate

From measurement of the heat of hydrolysis, at 25°C , the enthalpy of formation of rubidium tetrafluoroiodate is derived: ΔH°_f [RbIF₄, cryst.]₂₉₈= ?191.12±4.43 kJ mol^?1. Heat capacity measurements for RbIF₄ over the range 273–303 K are also reported.     

The phase behavior of a polymer‐fullerene bulk heterojunction system that contains bimolecular crystals

Polymer:fullerene blends have been widely studied as an inexpensive alternative to traditional silicon solar cells. Some polymer:fullerene blends, such as blends of poly(2,5‐bis(3‐tetradecylthiophen‐2‐yl)thieno[3,2‐b]thiophene (pBTTT) with phenyl‐c71‐butyric acid methyl ester (PC₇₁BM), form bimolecular crystals due to fullerene intercalation between the polymer side chains. Here we present the determination of the eutectic pBTTT:PC₇₁BM phase diagram using differential scanning calorimetry (DSC) and two‐dimensional grazing incidence X‐ray scattering (2D GIXS) with in‐situ thermal annealing. The phase diagram explains why the most efficient pBTTT:PC₇₁BM solar cells have 75–80 wt % PC₇₁BM since these blends lie in the center of the only room‐temperature phase region containing both electron‐conducting (PC₇₁BM) and hole‐conducting (bimolecular crystal) phases. We show that intercalation can be suppressed in 50:50 pBTTT:PC₇₁BM blends by using rapid thermal annealing to heat the blends above the eutectic temperature, which forces PC₇₁BM out of the bimolecular crystal, followed by quick cooling to kinetically trap the pure PC₇₁BM phase. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011