DOT2: Macromolecular docking with improved biophysical models

Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome. © 2013 Wiley Periodicals, Inc.     

A feasibility study of X‐ray phase‐contrast mammographic tomography at the Imaging and Medical beamline of the Australian Synchrotron

Results are presented of a recent experiment at the Imaging and Medical beamline of the Australian Synchrotron intended to contribute to the implementation of low‐dose high‐sensitivity three‐dimensional mammographic phase‐contrast imaging, initially at synchrotrons and subsequently in hospitals and medical imaging clinics. The effect of such imaging parameters as X‐ray energy, source size, detector resolution, sample‐to‐detector distance, scanning and data processing strategies in the case of propagation‐based phase‐contrast computed tomography (CT) have been tested, quantified, evaluated and optimized using a plastic phantom simulating relevant breast‐tissue characteristics. Analysis of the data collected using a Hamamatsu CMOS Flat Panel Sensor, with a pixel size of 100 µm, revealed the presence of propagation‐based phase contrast and demonstrated significant improvement of the quality of phase‐contrast CT imaging compared with conventional (absorption‐based) CT, at medically acceptable radiation doses.     

Super‐Resolution Imaging of the Golgi in Live Cells with a Bioorthogonal Ceramide Probe

We report a lipid‐based strategy to visualize Golgi structure and dynamics at super‐resolution in live cells. The method is based on two novel reagents: a trans‐cyclooctene‐containing ceramide lipid (Cer‐TCO) and a highly reactive, tetrazine‐tagged near‐IR dye (SiR‐Tz). These reagents assemble via an extremely rapid “tetrazine‐click” reaction into Cer‐SiR, a highly photostable “vital dye” that enables prolonged live‐cell imaging of the Golgi apparatus by 3D confocal and STED microscopy. Cer‐SiR is nontoxic at concentrations as high as 2 μM and does not perturb the mobility of Golgi‐resident enzymes or the traffic of cargo from the endoplasmic reticulum through the Golgi and to the plasma membrane.     

Multi-species detection using multi-mode absorption spectroscopy (MUMAS)

The detection of multiple species using a single laser and single detector employing multi-mode absorption spectroscopy (MUMAS) is reported. An in-house constructed, diode-pumped, Er:Yb:glass micro-laser operating at 1,565 nm with 10 modes separated by 18 GHz was used to record MUMAS signals in a gas mixture containing C₂H₂, N₂O and CO. The components of the mixture were detected simultaneously by identifying multiple transitions in each of the species. By using temperature- and pressure-dependent modelled spectral fits to the data, partial pressures of each species in the mixture were determined with an uncertainty of ±2 %.     

Freezing the Dynamic Gap for Selectivity: Motion‐Based Design of Inhibitors of the Shikimate Kinase Enzyme

Shikimate kinase (SK), the fifth enzyme of the aromatic amino acid biosynthesis, is a recognized target for antibiotic drug discovery. The potential of the distinct dynamic apolar gap, which isolates the natural substrate from the solvent environment for catalysis, and the motion of Mycobacterium tuberculosis and Helicobacter pylori SK enzymes, which was observed by molecular dynamics simulations, was explored for inhibition selectivity. The results of the biochemical and computational studies reveal that the incorporation of bulky groups at position C5 of 5‐aminoshikimic acid and the natural substrate enhances the selectivity for the H. pylori enzyme due to key motion differences in the shikimic acid binding domain (mainly helix α5). These studies show that the less‐exploited motion‐based design approach not only is an alternative strategy for the development of competitive inhibitors, but could also be a way to achieve selectivity against a particular enzyme among its homologues.     

Analysis of diverse direct arylation polymerization (DArP) conditions toward the efficient synthesis of polymers converging with stille polymers in organic solar cells

Despite the emergence of direct arylation polymerization (DArP) as an alternative method to traditional cross‐coupling routes like Stille polymerization, the exploration of DArP polymers in practical applications like polymer solar cells (PSCs) is limited. DArP polymers tend to have a reputation for being marginally inferior to Stille counterparts due to the increased presence of defects that result from unwanted side reactions in direct arylation, such as unselective C‐H bond activation and homocoupling. We report ten DArP protocols across the three major classes of DArP to generate poly[(2,5‐bis(2‐hexyldecyloxy)phenylene)‐alt‐(4,7‐di(thiophen‐2‐yl)benzo[c][1,2,5]thiadiazole)] (PPDTBT). Through evaluation of the method and resulting photophysical and electronic properties, we show not all DArP methods are suitable for generating device‐quality alternating copolymers. When DArP PPDTBT was synthesized in superheated THF with Cs₂CO₃, neodecanoic acid, and P(o‐anisyl)₃, it generated polymers of exceptional quality that performed comparably to Stille counterparts in both roll coated ITO‐free and spin‐coated ITO devices. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2907–2918