VinaLigGen: a method to generate LigPlots and retrieval of hydrogen and hydrophobic interactions from protein-ligand complexes.

Developments in the field of computational structural biology and with increasing computing speeds have encouraged researchers in studying large compound libraries during the virtual screening. After performing molecular docking, the consideration of vina score in filtering the compounds without collecting the hydrogen bond or hydrophobic interaction between protein and ligand complex leads to missing multiple good lead molecules. The tools used for virtual screening in drug design and discovery studies were previously designed and developed for small datasets.

The TOC159 null mutant of Arabidopsis thaliana is impaired in the accumulation of plastid lipids and phosphatidylcholine.

We used electrospray ionization tandem mass spectrometry to profile glycerolipids in the TOC159 null mutant of Arabidopsis, which is referred to as plastid protein import 2, or ppi2. The goal was to evaluate the impact of a defective atToc159 receptor in the accumulation of plastid lipids. The ppi2 mutant is severely impaired in the accumulation of monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG) and phosphatidylglycerol (PG), which are major components of the thylakoid membranes.

A simple method of drying polyacrylamide slab gels that eliminates cracking.

The polyacrylamide slab gel is the most common gel format for analyzing protein samples by electrophoresis. Drying these gels is useful in many biological applications; for example, autoradiography, in which radiolabeled proteins are separated to enable their detection and identification. Dried protein gels can also serve as an ideal method of preserving the gel itself for permanent record-keeping and allowing densitometry at a convenient time.

Optimization of western blotting for the detection of proteins of different molecular weight.

Protein samples electroblotted onto nitrocellulose membranes and quenched with a mixture of blocking agents produced a strong signal for cystic fibrosis transmembrane-conductance regulator (CFTR), a high-molecular-weight protein, in western blotting. Optimized conditions for CFTR were then extended to medium- and low-molecular-weight proteins (LAMP1 and Rab11a, respectively) to determine the effects of methanol concentration (0-20%) in Towbin's transfer buffer (TTB). Methanol in TTB appears to have little to no effect on CFTR signal.

Effects of Reusing Gel Electrophoresis and Electrotransfer Buffers on Western Blotting.

SDS-PAGE and Western blotting are 2 of the most commonly used biochemical methods for protein analysis. Proteins are electrophoretically separated based on their MWs by SDS-PAGE and then electrotransferred to a solid membrane surface for subsequent protein-specific analysis by immunoblotting, a procedure commonly known as Western blotting. Both of these procedures use a salt-based buffer, with the latter procedure consisting of methanol as an additive known for its toxicity.