Analysis of disulphide bond connectivity patterns in protein tertiary structure

The analysis of disulphide bond containing proteins in the Protein Data Bank (PDB) revealed that out of 27,209 protein structures analyzed, 12,832 proteins contain at least one intra-chain disulphide bond and 811 proteins contain at least one inter-chain disulphide bond. The intra-chain disulphide bond containing proteins can be grouped into 256 categories based on the number of disulphide bonds and the disulphide bond connectivity patterns (DBCPs) that were generated according to the position of half-cystine residues along the protein chain. The PDB entries corresponding to these 256 categories represent 509 unique SCOP superfamilies. A simple web-based computational tool is made freely available at the website http://www.ccmb.res.in/bioinfo/dsbcp that allows flexible queries to be made on the database in order to retrieve useful information on the disulphide bond containing proteins in the PDB. The database is useful to identify the different SCOP superfamilies associated with a particular disulphide bond connectivity pattern or vice versa. It is possible to define a query based either on a single field or a combination of the following fields, i.e., PDB code, protein name, SCOP superfamily name, number of disulphide bonds, disulphide bond connectivity pattern and the number of amino acid residues in a protein chain and retrieve information that match the criterion. Thereby, the database may be useful to select suitable protein structural templates in order to model the more distantly related protein homologs/analogs using the comparative modeling methods.     

Anaerobic Processes as the Core Technology for Sustainable Domestic Wastewater Treatment: Consolidated Applications, New Trends, Perspectives, and Challenges

Anaerobic digesters have been responsible for the removal of large fraction of organic matter (mineralization of waste sludge) in conventional aerobic sewage treatment plants since the early years of domestic sewage treatment (DST). Attention on the anaerobic technology for improving the sustainability of sewage treatment has been paid mainly after the energy crisis in the 1970s. The successful use of anaerobic reactors (especially up-flow anaerobic sludge blanket (UASB) reactors) for the treatment of raw domestic sewage in tropical and sub-tropical regions (where ambient temperatures are not restrictive for anaerobic digestion) opened the opportunity to substitute the aerobic processes for the anaerobic technology in removal of the influent organic matter. Despite the success, effluents from anaerobic reactors treating domestic sewage require post-treatment in order to achieve the emission standards prevailing in most countries. Initially, the composition of this effluent rich in reduced compounds has required the adoption of post-treatment (mainly aerobic) systems able to remove the undesirable constituents. Currently, however, a wealth of information obtained on biological and physical-chemical processes related to the recovery or removal of nitrogen, phosphorus and sulfur compounds creates the opportunity for new treatment systems. The design of DST plant with the anaerobic reactor as core unit coupled to the pre- and post-treatment systems in order to promote the recovery of resources and the polishing of effluent quality can improve the sustainability of treatment systems. This paper presents a broader view on the possible applications of anaerobic treatment systems not only for organic matter removal but also for resources recovery aiming at the improvement of the sustainability of DST.     

Structural characterization of β-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites

The bacterial fatty acid pathway is essential for membrane synthesis and a range of other metabolic and cellular functions. The β-ketoacyl-ACP synthases carry out the initial elongation reaction of this pathway, utilizing acetyl-CoA as a primer to elongate malonyl-ACP by two carbons, and subsequent elongation of the fatty acyl-ACP substrate by two carbons. Here we describe the structures of the β-ketoacyl-ACP synthase I from Brucella melitensis in complex with platencin, 7-hydroxycoumarin, and (5-thiophen-2-ylisoxazol-3-yl)methanol. The enzyme is a dimer and based on structural and sequence conservation, harbors the same active site configuration as other β-ketoacyl-ACP synthases. The platencin binding site overlaps with the fatty acyl compound supplied by ACP, while 7-hydroxyl-coumarin and (5-thiophen-2-ylisoxazol-3-yl)methanol bind at the secondary fatty acyl binding site. These high-resolution structures, ranging between 1.25 and 1.70 å resolution, provide a basis for in silico inhibitor screening and optimization, and can aid in rational drug design by revealing the high-resolution binding interfaces of molecules at the malonyl-ACP and acyl-ACP active sites.     

Screening the Main Factors Affecting Extraction of the Antimicrobial Substance from Bacillus sp. fmbJ using the Plackett–Burman Method

Summary The Plackett–Burman screening method was utilized as a tool to evaluate the importance of the selected six factors, including methanol, ethanol, propanol, butanol, pH and time, which are relevant to the extraction of the antimicrobial substance produced by Bacillus sp. fmbJ. The main factors that affected the extraction of the antimicrobial substance were determined as methanol (P < 0.0001), ethanol (P < 0.0001), pH (P = 0.0032), and time (P < 0.0001) by using the JMP software. Within the test ranges, methanol, ethanol, and time showed a significant positive relativity to the total extracted amounts respectively; while pH had a significant negative effect. The maximum prediction profile indicated that the total extracted amounts for the antimicrobial substance would reach 50.21 mg/100 ml with 99.64% probability.