Division of Bioinformatics (DIC): Recent submissions
Now showing items 41-60 of 83
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Structural insight into the functionality of the transcriptional regulator SoxR from Paracoccus pantotrophus in sulfur oxidation operon
(Academic Journals, 2007)The redox reactions involving inorganic sulfur compounds in the environment are one of the major reactions of the global sulfur cycle mediated by prokaryotes of different phylogenetic groups. The Sulfur oxidizing gene ... -
Homology modeling and molecular dynamics study of the interactions of SoxY and SoxZ: The central player of biochemical oxidation of sulfur anions in Pseudaminobacter salicylatoxidans
(Academic Journals, 2007)Microbial redox reactions of inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically diverse ... -
On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes
(ELSEVIER, 2007-12-22)Synonymous codon usage analysis between thermophilic and mesophilic prokaryotes has gained wide attention in recent years. Although it is known that thermophilic and mesophilic prokaryotes use different subset of synonymous ... -
Different functional classes of genes are characterized by different compositional properties
(ELSEVIER, 2007-12-22)A compositional analysis on a set of human genes classified in several functional classes was performed. We found out that the GC3, i.e. the GC level at the third codon positions, of the genes involved in cellular metabolism ... -
Structural studies on Vibrio cholerae ToxR periplasmic and cytoplasmic domains
(ELSEVIER, 2007-10)The transcription activator ToxR controls the expression of cholera toxin, pilus colonization factor and outer membrane protein in Vibrio cholerae. It binds to the 5'-TTTTGAT-3' tandernly repeated DNA sequence in the cholera ... -
Demethylation of (Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic pathways of cancer development
(SPRINGER, 2008-06)Cancer cells and tissues exhibit genome wide hypomethylation and regional hypermethylation. CpG-methylation of DNA ((Me)CpG-DNA) is defined as the formation of a C-C covalent bond between the 5'-C of cytosine and the -CH(3) ... -
Differential Selective Constraints Shaping Codon Usage Pattern of Housekeeping and Tissue-specific Homologous Genes of Rice and Arabidopsis
(OXFORD UNIV, 2008-12)Intra-genomic variation between housekeeping and tissue-specific genes has always been a study of interest in higher eukaryotes. To-date, however, no such investigation has been done in plants. Availability of whole genome ... -
Nucleotide Triplet Based Molecular Phylogeny of Class I and Class II Aminoacyl t-RNA Synthetase in Three Domain of Life Process: Bacteria, Archaea, and Eukarya
(ADENINE, 2008-12)The amoniacyl-tRNA synthetases are one of the major protein components in the translation machinery. These essential proteins are found in all forms of life and are responsible for charging their cognate tRNAs with the ... -
Delving deeper into the unexpected correlation between gene expressivity and codon usage bias of Escherichia coli genome
(ADENINE, 2008-06)Biased usage of synonymous codons has been elucidated under the perspective of cellular tRNA abundance and more recently by the mRNA secondary structure folding stability of the corresponding genes. Taking advantage of ... -
Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network
(ELSEVIER, 2009-01-15)Evolutionary rates of party hub and date hub proteins of Saccharomyces cerevisiae are analyzed under the perspective of ordered/disordered ness of proteins and the three dimensional structural context such as the solvent ... -
Structural interaction between DsrE-DsrF-DsrH proteins involved in the transport of electrons in the dsr operon.
(PubMed, 2008-04)Biological redox reactions of inorganic sulfur compounds are important for the proper maintenance of environmental sulfur balance. These reactions are mediated by phylogeneticaly diverse set of microorganisms. The protein ... -
Genomic adaptation of prokaryotic organisms at high temperature.
(Biomedical Informatics, 2010-02-28)One of the central issues of evolutionary genomics is to find out the adaptive strategies of microorganisms to stabilize nucleic acid molecules under high temperature. Thermal adaptation hypothesis gives a link between G+C ... -
Evolutionary constraints on hub and non-hub proteins in human protein interaction network: Insight from protein connectivity and intrinsic disorder
(ELSEVIER SCIENCE, 2009-04-01)It has been claimed that proteins with more interacting partners (hubs) are structurally more disordered and have a slow evolutionary rate. Here, in this paper we analyzed the evolutionary rate and structural disorderness ... -
Relationship between Gene Compactness and Base Composition in Rice and Human Genome
(ADENINE, 2010-02)In human, highly expressed genes contain shorter and fewer introns and these have been attributed to selection for economy in transcription and translation. On the other hand, in plants, it has been shown that highly ... -
Multifunctionality dominantly determines the rate of human housekeeping and tissue specific interacting protein evolution
(ELSEVIER SCIENCE, 2009-06-15)Elucidation of the determinants of the rate of protein sequence evolution is one of the great challenges in evolutionary biology. It has been proposed that housekeeping genes are evolutionarily slower than tissue specific ... -
Investigation of the molecular evolution of nitrogen fixation using nucleotide triplet based condensed matrix method
(IJIB, 2010)Evolutionary history of nitrogen fixation has been retraced by analyzing nif H, D and K genes, and whole genomes from cyanobacteria, proteobacteria, clostridia, actinobacteria, green sulfur bacteria and archaea using ... -
Role of Protein Flexibility in the Discovery of New Drugs
(WILEY-BLACKWELL, 2011-02)Proteins have inherent flexibility, and this plays a critical role in a vast array of biological functions, including ligand binding. Structure-based drug design (SBDD) strategies incorporate biomolecular structures with ... -
Moleculardynamicssimulations of Aβfibrilinteractions with β-sheetbreakerpeptides
(ELSEVIER SCIENCE, 2010-11)Accumulation and aggregation of the 42-residue amyloid-β (Aβ) protein fragment, which originates from the cleavage of amyloid precursor protein by β and γ secretase, correlates with the pathology of Alzheimer's disease ... -
Functional Characterization and Expression Profiling of Human Induced Pluripotent Stem Cell- and Embryonic Stem Cell-Derived Endothelial Cells
(MARY ANN LIEBERT, 2011-10)With regard to human induced pluripotent stem cells (hiPSCs), in which adult cells are reprogrammed into embryonic-like cells using defined factors, their functional and transcriptional expression pattern during endothelial ... -
Prediction of Active Site Cleft Using Support Vector Machines
(AMER CHEMICAL SOC, 2010-12)Computational tools are available today for the detection and delineation of the clefts and cavities in protein 3D structure and ranking them on the basis of probable binding site clefts. There is a need to improve the ...