Predicting metal-binding site residues in low-resolution structural models

The accurate prediction of the biochemical function of a protein is becoming increasingly important, given the unprecedented growth of both structural and sequence databanks. Consequently, computational methods are required to analyse such data in an automated manner to ensure genomes are annotated accurately. Protein structure prediction methods, for example, are capable of generating approximate structural models on a genome-wide scale. However, the detection of functionally important regions in such crude models, as well as structural genomics targets, remains an extremely important problem. The method described in the current study, MetSite, represents a fully automatic approach for the detection of metal-binding residue clusters applicable to protein models of moderate quality. The method involves using sequence profile information in combination with approximate structural data. Several neural network classifiers are shown to be able to distinguish metal sites from non-sites with a mean accuracy of 94.5%. The method was demonstrated to identify metal-binding sites correctly in LiveBench targets where no obvious metal-binding sequence motifs were detectable using InterPro. Accurate detection of metal sites was shown to be feasible for low-resolution predicted structures generated using mGenTHREADER where no side-chain information was available. High-scoring predictions were observed for a recently solved hypothetical protein from Haemophilus influenzae, indicating a putative metal-binding site.     

Whole genome sequence of the rifamycin B-producing strain Amycolatopsis mediterranei S699

Amycolatopsis mediterranei S699 is an actinomycete that produces an important antibiotic, rifamycin B. Semisynthetic derivatives of rifamycin B are used for the treatment of tuberculosis, leprosy, and AIDS-related mycobacterial infections. Here, we report the complete genome sequence (10.2 Mb) of A. mediterranei S699, with 9,575 predicted coding sequences.     

A liquid culture system for shoot proliferation and analysis of pharmaceutically active constituents of Catharanthus roseus (L.) G. Don

An efficient and cost effective micropropagation protocol using liquid medium was developed for Catharanthus roseus, a commercially important medicinal plant. Comparative analysis of shoot growth and proliferation in liquid Murashige and Skoog (MS) medium supplemented with different concentrations of cytokinins [6-Benzyladenine (BA), Kinetin (KN) and Thidiazuron (TDZ)] was conducted. Better response in terms of shoot proliferation, shoot diameter, number of leaves/shoot, number of branches/shoot, fresh weight and dry weight was observed in a liquid medium vis-à-vis solid medium. A sample of 20 ml of liquid medium supplemented with 5 ??M of BA was optimized for propagation of C. roseus by a liquid culture system. Among various concentrations of auxins tried, 1-Naphthaleneacetic acid (NAA) 5 ??M was found to be the best for root induction. Quantification of pharmaceutically important constituents (vincristine and vinblastine) and total alkaloid content of microshoots grown in solid and liquid medium as well as in vitro raised plants and mother plant was also conducted, hitherto unreported in this high-value medicinal plant. This work further lays the foundations for the shifting of plant production from small to commercial scale.     

Characterization of oat lipase for lipolysis of rice bran oil

Summary Lipases from plant and microbial sources were screened for lipolysis of rice bran oil (RBO). Oat lipase was found to give reproducibly 60% lipolysis. Factors affecting the efficiency of lipolysis such as oil:emulsifier ratio, duration of homogenization for the substrate preparation, substrate:enzyme ratio, substrate pH, kinetics of lipolysis and efficiency of lipase as a function of pH, oat particle size, its quality and reuseability were studied to assess the feasibility of using of oat lipase for splitting RBO commercially. The efficiency of lipolysis was optimal at (a) RBO:emulsifier (0.5:1) ratio, homogenized for 2.5 min, (b) pH 7.5 and (c) substrate:enzyme ratio of 5 ml: 2 g.     

A modified Western blot protocol for enhanced sensitivity in the detection of a membrane protein

Membrane proteins, owing to their highly hydrophobic nature, have always posed a daunting challenge to biochemists and structural biologists working on the characterization of these “naughty” proteins. Here we describe a problem that we encountered in the immunodetection of a hemagglutinin (HA) epitope-tagged membrane protein, Hgt1p (high-affinity glutathione transporter from the yeast Saccharomyces cerevisiae), for which little or no signal was observed on the blots with monoclonal antibody, on following the standard Western blot protocol. The introduction of a single step that involved posttransfer incubation of the blots with sodium dodecyl sulfate (SDS)/β-mercaptoethanol solution at 55 °C for 15 min enabled us to detect a strong, stable, and reproducible signal for the membrane protein.