Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies

Förster resonance energy transfer (FRET) measurements are widely used to investigate (bio)molecular interactions or/and association. FRET efficiencies, the primary data obtained from this method, give, in combination with the common assumption of isotropic chromophore orientation, detailed insight into the lengthscale of molecular phenomena. This study illustrates the application of a FRET efficiency restraint during classical atomistic molecular dynamics simulations of a mutant mastoparan X peptide in either water or 7 M aqueous urea. The restraint forces acting on the donor and acceptor chromophores ensure that the sampled peptide configurational ensemble satisfies the experimental primary data by modifying interchromophore separation and chromophore transition dipole moment orientations. By means of a conformational cluster analysis, it is seen that indeed different configurational ensembles may be sampled without and with application of the restraint. In particular, while the FRET efficiency and interchromophore distances monitored in an unrestrained simulation may differ from the experimentally‐determined values, they can be brought in agreement with experimental data through usage of the FRET efficiency restraining potential. Furthermore, the present results suggest that the assumption of isotropic chromophore orientation is not always justified. The FRET efficiency restraint allows the generation of configurational ensembles that may not be accessible with unrestrained simulations, and thereby supports a meaningful interpretation of experimental FRET results in terms of the underlying molecular degrees of freedom. Thus, it offers an additional tool to connect the realms of computer and wet‐lab experimentation. © 2014 Wiley Periodicals, Inc.     

A Diverse Assemblage of Indole-3-Acetic Acid Producing Bacteria Associate with Unicellular Green Algae

Microalgae have tremendous potential as a renewable feedstock for the production of liquid transportation fuels. In natural waters, the importance of physical associations and biochemical interactions between microalgae and bacteria is generally well appreciated, but the significance of these interactions to algal biofuels production have not been investigated. Here, we provide a preliminary report on the frequency of co-occurrence between indole-3-acetic acid (IAA)-producing bacteria and green algae in natural and engineered ecosystems. Growth experiments with unicellular algae, Chlorella and Scenedesmus, revealed IAA concentration-dependent responses in chlorophyll content and dry weight. Importantly, discrete concentrations of IAA resulted in cell culture synchronization, suggesting that biochemical priming of cellular metabolism could vastly improve the reliability of high density cultivation. Bacterial interactions may have an important influence on algal growth and development; thus, the preservation or engineered construction of the algal–bacterial assembly could serve as a control point for achieving low input, reliable production of algal biofuels.     

Facile Synthesis of Phosphaamidines and Phosphaamidinates using Nitrilium Ions as an Imine Synthon

Readily accessible nitrilium triflates are convenient imine building blocks for the expedient synthesis of a novel class of 1,3‐P,N ligands as demonstrated for the reaction with primary phosphanes. This procedure allows variation of all substituents. X‐ray crystal structures are reported for nitrilium ions, phosphaamidines, and three phosphaamidinate complexes. The lithium phosphaamidinate is N coordinated and its reaction with [AuCl(tht)] (tht=tetrahydrothiophene) gives a unique P‐bridged gold trimer, while a P,N‐bidentate complex results from [{RhCl(cod)}₂]. The nitrilium ion methodology allows extension of the 1,3‐P,N motive to bis(imino)phosphanes, which are the neutral phosphorus analogues of the valuable β‐diketiminate ligand.     

Mapping of the Photoinduced Electron Traps in TiO2 by Picosecond X‐ray Absorption Spectroscopy

Titanium dioxide (TiO₂) is the most popular material for applications in solar‐energy conversion and photocatalysis, both of which rely on the creation, transport, and trapping of charges (holes and electrons). The nature and lifetime of electron traps at room temperature have so far not been elucidated. Herein, we use picosecond X‐ray absorption spectroscopy at the Ti K‐edge and the Ru L₃‐edge to address this issue for photoexcited bare and N719‐dye‐sensitized anatase and amorphous TiO₂ nanoparticles. Our results show that 100 ps after photoexcitation, the electrons are trapped deep in the defect‐rich surface shell in the case of anatase TiO₂, whereas they are inside the bulk in the case of amorphous TiO₂. In the case of dye‐sensitized anatase or amorphous TiO₂, the electrons are trapped at the outer surface. Only two traps were identified in all cases, with lifetimes in the range of nanoseconds to tens of nanoseconds.     

Azasugar inhibitors as pharmacological chaperones for Krabbe disease

Krabbe disease is a devastating neurodegenerative disorder characterized by rapid demyelination of nerve fibers. This disease is caused by defects in the lysosomal enzyme β-galactocerebrosidase (GALC), which hydrolyzes the terminal galactose from glycosphingolipids. These lipids are essential components of eukaryotic cell membranes: substrates of GALC include galactocerebroside, the primary lipid component of myelin, and psychosine, a cytotoxic metabolite. Mutations of GALC that cause misfolding of the protein may be responsive to pharmacological chaperone therapy (PCT), whereby small molecules are used to stabilize these mutant proteins, thus correcting trafficking defects and increasing residual catabolic activity in cells. Here we describe a new approach for the synthesis of galacto-configured azasugars and the characterization of their interaction with GALC using biophysical, biochemical and crystallographic methods. We identify that the global stabilization of GALC conferred by azasugar derivatives, measured by fluorescence-based thermal shift assays, is directly related to their binding affinity, measured by enzyme inhibition. X-ray crystal structures of these molecules bound in the GALC active site reveal which residues participate in stabilizing interactions, show how potency is achieved and illustrate the penalties of aza/iminosugar ring distortion. The structure–activity relationships described here identify the key physical properties required of pharmacological chaperones for Krabbe disease and highlight the potential of azasugars as stabilizing agents for future enzyme replacement therapies. This work lays the foundation for new drug-based treatments of Krabbe disease.     

Cover Picture: Turning Spiroketals Inside Out: A Rearrangement Triggered by an Enol Ether Epoxidation (ChemistryOpen 5/2015)

Invited for this month''s cover picture is the group of Professor Mark Peczuh at the University of Connecticut. The cover picture compares the rearrangement of a small molecule to the process of turning a stuffed animal inside out. The recycled, inside-out stuffed animals are both artistic and philosophically provocative. They capture the essence of the rearrangement reaction because the compounds themselves turn inside out over the course of the reaction, extending the diversity of products that can arise from simple starting materials. Small molecules often have functional groups with latent reactivity; under the appropriate conditions, those groups can react with other compounds (e.g., reagents) and also with other groups in the same molecule in an intramolecular reaction. The research team found that the epoxidation of some highly functionalized spiroketal compounds promoted rearrangements of their structures that turned them inside out. Some of the features of the products led them to use X-ray crystallography or a combination of computer-assisted structure elucidation, computation, and a new version of the 1,1-ADEQUATE NMR experiment to determine their structures. For more details, see the Communication on p. 577 ff.     

Supramolecular hydrogel microcapsules via cucurbit[8]uril host–guest interactions with triggered and UV-controlled molecular permeability

Host–guest assembly in droplet-based microfluidics opens a new avenue for fabricating supramolecular hydrogel microcapsules with high monodispersity and controlled functionality. In this paper, we demonstrate a single emulsion microdroplet platform to prepare microcapsules with supramolecular hydrogel skins from host molecule cucurbit[8]uril and guest polymer anthracene-functionalized hydroxyethyl cellulose. In contrast to construction of microcapsules from a droplet-in-droplet double emulsion, here the electrostatic attraction between charged polymer and surfactant facilitates formation of defined supramolecular hydrogel skins in a single emulsion. Furthermore, by taking advantage of dynamic interactions and the tunable cross-linked supramolecular hydrogel network, it is possible to prepare microcapsules with triggered and UV-controlled molecular permeability. These could be potentially used in a delivery system for e.g. agrochemicals, nutraceuticals or cosmetics.