OB-fold: growing bigger with functional consistency

It was predicted that the folding space for various protein sequences is restricted and a maximum of 1000 protein folds could be expected. Although, there were about 648 folds identified, general functional features of individual folds is not thoroughly studied. We selected OB-fold, which is supposed to be an oligonucleotide and oligosaccharide binding fold to study the general functional features. OB-fold is a small beta-barrel fold formed from 5 strands connected by modulating loops. We observed consistently 2 or 3 loops on the same face of barrel acting as clamps to bind to their ligands. Depending on the ligand, which could be a single or double stranded DNA/RNA or an oligosaccharide, and their conformational properties the loops change in length and sequence to accommodate various ligands. Different classes of OB-folded proteins were analyzed and found that the functional features are retained in spite of negligible sequence homology among various proteins studied.     

Efficient primer strand extension beyond oxadiazole carboxamide nucleobases

Two oxadiazole carboxamide deoxyribonucleoside analogues are described that can be incorporated and efficiently extended by Taq DNA polymerase. The primer strand extension beyond oxadiazole nucleoside analogues occurs at rates similar to the values observed for the canonical Watson-Crick base pairs irrespective of the template nucleobase. These distinctive chemical effects in DNA polymerase extensions are attributed to the smaller size and unique electronic properties of the oxadiazole nucleobase.     

Strategies for locating disulfide bonds in a monoclonal antibody via mass spectrometry

The location of the disulfide bonds in a recombinant monoclonal antibody was confirmed by matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry (MS). A non-reduced Endoproteinase Lys-C (Endo Lys-C) digest of the antibody was analyzed directly by MALDI-TOFMS. The sample was then reduced on-plate by depositing dithiothreitol (DTT) on the sample spot and re-analyzed by MALDI-TOFMS. The disulfide bonds were assigned based on the disappearance of certain mass ions in the non-reduced digest and the appearance of product ions in the reduced digest. A rapid LC/ESI-MS protocol was also developed to determine the location of the disulfide bonds. The peptides generated from the Endo Lys-C digest of the antibody were partially separated on a high performance liquid chromatography (HPLC) column by utilizing a steep gradient and analyzed by ESI-MS. The masses of the partially resolved peptides were determined by deconvoluting the mass spectra.     

Characterization of proteins separated by displacement chromatography using low angle laser light scattering photometry

Summary -Lactoglobulin A and B (-LACT) were separated by displacement chromatography (DSC) on an ionexchange column using dextran sulfate as the displacer. A LALLS photometer and a UV detector, in series, were used to determine the molecular weight (MW) of the proteins, on-line. The results indicate that both, -LACT A and B, were present as dimers in the buffer used for the mobile phase. The MWs of the proteins were about 6–8% higher than the theoretical MW of a dimer (37,000). Additional control studies have shown the presence of a high molecular weight species in both the proteins, which could possibly be an aggregate. This species was observed in the LALLS signal but was nearly absent in the UV signal. Our work has demonstrated the feasibility of interfacing LALLS with displacement chromatography for detecting impurities or aggregates which may be difficult to detect by conventional detectors used for chromatography.     

Molecular dynamics simulation of titanium dioxide nanoparticle sintering

Nanoparticles have been an area of active research in recent years due to their properties, which can be greatly different from the bulk. In this work, we study the sintering of TiO2 nanoparticles using molecular dynamics simulations. Such sintering occurs in flame reactors where nanotitania is prepared via the chloride process. Decrease in free energy due to reduction in surface area is the main driving force for sintering of particles. Simulations, at various starting temperatures and orientations, indicate that the process of sintering is strongly affected by temperature and initial orientation. Extremely high diffusion of ions in the neck region of sintering nanoparticles supports the idea that solid-state diffusion is significant in metal-oxide nanoparticle sintering. It is found that the dipole-dipole interaction between sintering nanoparticles plays a very important role at temperatures away from the melting point. The duration of the simulation is not enough to observe the complete sintering process, but important initial stages are well studied.     

A single amino acid Gly-tag enables metal-free protein purification

Analytically pure proteins are indispensable for diverse applications, including therapeutics. Here, we report a methodology where a single amino acid, glycine, enables metal-free protein purification. This robust platform is enabled by a Gly-tag resin for site-specific capture, enrichment, and release through chemically triggered C–C bond dissociation by resonance-assisted electron density polarization.

Gly-tag resin precisely captures and releases a protein with one glycine at the N-terminus. The user-friendly protocol delivers analytically pure protein free of metal contaminants.     

Magnetic nanoparticle‐tethered Schiff base–palladium(II): Highly active and reusable heterogeneous catalyst for Suzuki–Miyaura cross‐coupling and reduction of nitroarenes in aqueous medium at room temperature

As a continuation of our efforts to develop new heterogeneous nanomagnetic catalysts for greener reactions, we identified a Schiff base–palladium(II) complex anchored on magnetic nanoparticles (SB‐Pd@MNPs) as a highly active nanomagnetic catalyst for Suzuki–Miyaura cross‐coupling reactions between phenylboronic acid and aryl halides and for the reduction of nitroarenes using sodium borohydride in an aqueous medium at room temperature. The SB‐Pd@MNPs nanomagnetic catalyst shows notable advantages such as simplicity of operation, excellent yields, short reaction times, heterogeneous nature, easy magnetic work up and recyclability. Characterization of the synthesized SB‐Pd@MNPs nanomagnetic catalyst was performed with various physicochemical methods such as attenuated total reflectance infrared spectroscopy, UV–visible spectroscopy, inductively coupled plasma atomic emission spectroscopy, energy‐dispersive X‐ray spectroscopy, field‐emission scanning electron microscopy, transmission electron microscopy, powder X‐ray powder diffraction, thermogravimetric analysis and Brunauer–Emmett–Teller surface area analysis.     

Lanthanum Trifluoromethane-sulfonate‐Catalyzed Facile Synthesis of Per‐O‐acetylated Sugars and Their One‐Pot Conversion to S‐Aryl and O‐Alkyl/Aryl Glycosides†

Lanthanum trifluoromethanesulfonate‐catalyzed solvent‐free per‐O‐acetylation with stoichiometric acetic anhydride proceeds in high yield (95%–99%) to afford exclusively pyranose products as anomeric mixtures. Subsequent anomeric substitution employing borontrifluoride etherate and thiols or alcohols furnished the corresponding 1,2‐trans‐linked thioglycosides and O‐glycosides, respectively, in good to excellent overall yield (75%–85%). Alternatively, reaction of free sugars in neat alcohol employing the same catalyst at elevated temperature gives the corresponding 1,2‐cis‐linked O‐glycosides (along with 1,2‐trans‐linked glycosides as minor product) in good yield (73%–80%). Anomeric mixtures of compounds thus produced were characterized as their per‐O‐acetylated derivatives.