Bacterial peptides of low molecular weight displaying antagonism towards other bacterial members are referred to as bacteriocins. Bacteriocins are an essential member of the broadly classified group of lantibiotics which finds several commercial uses. This work comprises of the determination of structure of the most important class of bacteriocins – the leucocin group. Structure elucidation was performed using homology modelling approach and the modeled structure was validated using their Ramachandran calculations. Ligand interaction pockets were identified by calculating the Delaunay triangulation number and structural properties of amino acids were documented. Structure elucidations of such lantibiotics are important for future endeavours towards analyses of protein - protein interactions.

We describe several protein sequence statistics designed to evaluate distinctive attributes of residue content and arrangement in primary structure. As per the global consideration, the compositional biases of clustering different residue types (charged residues, hydrophobic residues) of long runs of charged or uncharged residues, periodic patterns, counts and distribution of homooligopeptides, and unusual spacing between particular residue types. The computer program SEQUANA (statistical analysis of protein sequences) calculates all the statistics for any individual protein sequence input and is available for the WINDOWS environment through electronic mail on request to csvinobha@gmail.com.

The completion of genome sequences of pathogenic bacteria and the completion of human genome project has provided lot amount of data that can be utilized to design vaccines and drug targets. One of the recently adopting strategies for drug designing is based on comparative genomics approach, in which the subtraction dataset between the host and the pathogen genome provides information for a set of genes that are likely to be essential to the pathogen but absent in the host. This approach has been used to identify vaccine and drug targets of Pseudomonas aeruginosa and Helicobacter pylori. We have used the same approach to identify the vaccine and drug targets of Clostridium botulinum F strain. Our analysis has revealed that out of 3631 coding sequences of the pathogen, 446 represent essential genes that have no human homolog. We have further analyzed these 446 genes by the protein sequence database to list some 96 genes whose products are possibly exposed on the pathogen surface. This preliminary work reported here identifies a small subset of the Clostridium botulinum F strain proteome that might be investigated further for identifying potential drug and vaccine targets in this pathogen.

The present study involves phylogenetic analysis of distinguished bacterial population essentially grouped into functional attributes, namely nitrogen fixation and quorum sensing. The basis of this analysis are protein sequences of NifH (nitrogenase reductase), LuxA (Luciferase alpha subunit) and LuxS (Sribosyl homocysteine lyase) from 30, 17, 25 species of bacteria respectively. These bacteria show vast diversity in terms of habitat mode of survival pathogenicity. Phylogenetic analysis gives an insight into the evolution and interrelationships of these microbial species. GeneBee, ClustalW and Phylip softwares were found to be satisfactory for the chosen work. Phylogenetic trees were constructed in the form of Cladograms, Phylograms and Unrooted radial trees. According to the results obtained, the most highly evolved group of organisms with respect to their nitrogenase reductase protein is that of Desulfovibrio vulgaris and Chlorobium phaeobacteriodes. Bacillus thuringiensis and Bacillus subtilis hold the most highly evolved forms of LuxS protein. Also knowledge abtained from the motif pattern analysis between Bradyrhizobium japonicum and Rhizobium leguminosarum NifH protein sequence are conserved and further analysis may show that there may be quorum sensing mediated gene regulation in host bacterium interaction. Phylogenetic analyses, thus, on the basis of highly conserved protein domains, universal in their existence, can provide a preamble to the actual 16S-rRNA based phylogeny or genomic analyses of phylogeny carried out in the wet lab.

Optimization of protein extraction using silk cocoon was carried out by the design of experiment (DOE) to obtain the response surface methodology ( RSM ). Box-Behnken rotatable design was used to create an experimental program to provide data to model the effects of various factors on protein extraction efficiency. The variables chosen were sodium carbonate concentration ( 1 X ), Lithum bromide concentration ( 2 X ) and temperature ( 3 X ). The mathematical relationship between protein extraction efficiency and three significant independent variables can be approximated by a second order quadratic model. RSM was used to describe the individual and interactive effects of three variables at three levels, combined according to a Box-Behnken Design. The coefficient of determination (2 R ) for the model is 0.9761. Probability value ( P < 0.0001) demonstrates a very high significance for the regression model indicating that Box-Behnken Design can be applied to the protein extraction from silk cocoon, and it is an economical way of obtaining the maximum amount of information with the fewest experiments.

The phylogenetic position of long been debatable species Luffa tuberosa was inferred in the present study using ITS sequence of nuclear ribosomal DNA data. The study sampled a total number of 16 accessions which include five accessions of Luffa (under four species i.e. Luffa acutangula, L. cylindrica, L. aegyptiaca and L. tuberosa), nine accessions of Momordica (under eight species i.e. M. angustisepala, M. balsamina, M. cabraei, M. charantia, M. charantia subsp. macroloba, M. cissoides, M. cochinchinensis, M. dioica and M. foetida) and two accessions of Trichosanthes under two species (i.e. T. lepiniana and T. tricuspidata). The sequence data analysis clearly reveals nesting of Luffa tuberosa within the clade of Momordica, thus, we herein support the inclusion of Luffa tuberosa into the genus Momordica as M. tuberosa (Roxb.) Cogn.

Small cell-permeant inhibitors of protein kinases have become valuable reagents to investigate the physiological roles of protein kinases, because they can be used simply and rapidly to block endogenous kinase activity in normal cells and tissues, as well as transformed cell lines. There are no potent inhibitors of MKP-1, which dephosphorylates p38, JNK, and this is unfortunate because MKP-1 has been associated with human neoplasia and is an attractive potential therapeutic target. The active sites of MKP-1 were predicted and screened with synthesized analogs and related structures are obtained from PUBCHEM. The best hits were the analogs NU-126, NU-154 and these compounds were docked with the protein using AUTODOCK. MKP-1 constitutes an exciting, novel potential therapeutic target for Rheumatoid Arthritis. There is perfect active site information about the protein and selective inhibitor, so this docking work provides insights to develop new drug for the disease, rheumatoid arthritis.

Heat shock proteins (HSPs) are the proteins which are present normally in the cell but their expression level increases under stress condition and are mainly divided into five groups, low molecular weight HSP (LMW HSP), HSP 60, HSP 70, HSP 90 and high molecular weight HSP (HMW HSP). All these classes of HSPs are highly conserved and ubiquitous in nature and hence serve as a good model for phylogenetic analysis. For the first time in this study,the sequence and structural analysis has been carried out to predict evolution of HSPs. The results obtained clearly show higher degree of sequence and structural conservation. HSP 60 and HSP 70 are highly conserved in terms of both sequence and structure alignment in comparison to HSP 90. The minimum amino acid identity that has been observed between all the homologous sequences is 32.46%, 38%, 23.60% for HSP 60, HSP 70 and HSP 90 respectively, indicating HSP 70 as the most conserved protein family followed by HSP 60 and HSP 90 family. The structural analysis of these proteins showed dominance of beta sheets in HSP70 and helices in HSP 90. The detailed analysis of all the HSP homologues revealed high conservation of glycine residues and ATP binding pockets. Thus this study has revealed that HSPs are highly structurally and functionally conserved proteins and warrants further detailed analysis at organism level.

Computational biology is a term coined from analogy to the role of physical sciences, is now coming into its own as a major element of contemporary biological and biomedical research. In the sharp in this pattern, over past few years, experiments in life sciences in the academic institutions have begun to recognize the value of bioinformatics and computational biology in the field of algology. Cyanobacteria (also known as blue–green algae) are a group of extraordinarily diverse Gram-negative prokaryotes that originated 3.5 billion years ago. After the advent of bioinformatics in the field of algology, complete genome sequences of Cyanobacteria have been reported in more than 30 species and strains including unicellular. The filamentous cyanobacterium Anabaena sp. PCC 7120 (further referred to as Anabaena sp.) is a model system to study nitrogen fixation, cell differentiation, cell pattern formation and evolution of plastids. It is a multicellular photosynthetic microorganism consisting of two cell types, vegetative cells and nitrogen fixing heterocysts. The nucleotide sequence of the entire genome of a filamentous Cyanobacterium, Anabaena sp. Strain PCC 7120, was determined. This study focuses on the function and dynamics of the proteome of the Gram-negative outer membrane in Anabaena sp.

Dopamine has been shown to play a key role in the Central Nervous System. Any imbalance in dopamine production and dopamine receptor activity has been implicated widely in the pharmacology, of a number of neurobehavioral disorders existing today. The dopamine receptors interact with G-proteins to transduce dopamine stimulation into intracellular responses. In this work a 3D structure of DRD5 based on the template of High resolution crystal structure of human ı-2 adrenergic receptor (PDB code 2RH1A) was generated. The model was assessed using MOLPROBITY. The results revealed that 94% of the residues were found in the favoured region of Ramachandran’s plot. Active site analysis showed that predicted binding sites included all the seven transmembrane helices. Our work demonstrates that in silico modeling of proteins has been shown to play an important role in determining protein structure and provides a promising area in possible drug discovery.