International Journal of Bioinformatics Research

7-11

Authors: Vinobha C.S., Rajasekaran E., Rajadurai M.

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.

17-32

Authors: Anushree Chaphalkar, Nivedita Salunkhe

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.

42-60

Authors: Ajmal Ali M., Karuppusamy S., Fahad M. Al-Hemaid

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.

67-87

Authors: Desai N.S., Agarwal A.A. , Uplap S.S.

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.

96-102

Authors: Raja Chakraborty, Sayak Ganguli, Hirak Jyoti Chakraborty , Abhijit Datta

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.