Department of Biophysics: Recent submissions
Now showing items 21-40 of 64
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Structural features of a cold-adapted Alaskan bacterial lipase
(ADENINE, 2007-04)The three dimensional model of cold-adapted Alaskan psychrotroph Pseudomonas species (Strain B11-1) lipase has been constructed by homology modeling based on the crystal structure of acetyl esterase from Rhodococcus species ... -
Paramagnetic viral nanoparticles as potential high-relaxivity magnetic resonance contrast agents
(JOHN WILEY, 2005-10)In order to compensate for the inherent high threshold of detectability of MR contrast agents, there has been an active interest in the development of paramagnetic nanoparticles incorporating high payloads of Gd3+ with ... -
Cloning, expression, purification, and characterization of Vibrio cholerae transcriptional activator, HlyU
(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2006-07)The HlyU from Vibrio cholerae, involved in the transcriptional regulation of haemolysin genes, plays an important role in the regulation of virulence gene expression. We have cloned, over-expressed and purified HlyU from ... -
An insight into the molecular basis of salt tolerance of L-myo-inositol 1-P synthase (PcINO1) from Porteresia coarctata (Roxb.) Tateoka, a halophytic wild rice
(AMER SOC PLANT BIOLOGISTS, 2006-04)The molecular basis of salt tolerance of L myo-inositol 1-P synthase (MIPS; EC 5.5.1.4) from Porteresia coarctata (Roxb.) Tateoka (PcINO1, AF412340) earlier reported from this laboratory, has been analyzed by in vitro ... -
Homology modeling of a transcriptional regulator SoxR of the lithotrophic sulfur oxidation (sox) operon in α-proteobacteria
(ADENINE PRESS, 2005-04)Microbial oxidation of reduced inorganic sulfur compounds in the environment is one of the major reactions of the global sulfur cycle mediated by phylogenetically diverse prokaryotes. The sulfur oxidizing gene cluster (sox) ... -
Biphasic kinetics of the colchicine-tubulin interaction: Role of amino acids surrounding the a ring of bound colchicine molecule
(AMER CHEMICAL SOC, 2005-08-02)Isotypes of vertebrate tubulin have variable amino acid sequences, which are clustered at their C-terminal ends. Isotypes bind colchicine at different on-rates and affinity constants. The kinetics of colchicine binding to ... -
Structural considerations for designing adenosine analogs as selective inhibitors of Trichomonas sp. glyceraldehyde-3- phosphate dehydrogenase.
(IOS Press, 2007)Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of pathogenic protozoa Trichomonas vaginalis (TvGAPDH) is an attractive drug target since this parasite lacks functional citric acid cycle and is dependent solely on glycolysis ... -
Differential colchicine-binding across eukaryotic families: The role of highly conserved Pro268 beta and Ala248 beta residues in animal tubulin
(ELSEVIER, 2007-10-30)Colchicine-tubulin interaction, responsible for the disruption of microtubule formation, has immense pharmacological importance but is poorly understood in terms of its biological significance. The interaction is characterized ... -
Computational study of glyceraldehyde-3-phosphate dehydrogenase of Entamoeba histolytica: Implications for structure-based drug design
(ADENINE, 2007-08)Glyceraldehyde-3 -phosphate dehydrogenase (GAPDH) of the pathogenic protozoa Entamoeba histolytica (Eh) is a major glycolytic enzyme and an attractive drug target since this parasite lacks a functional citric acid cycle ... -
A chimaeric glutamyl:glutaminyl-tRNA synthetase: implications for evolution
(PORTLAND, 2009-01-15)aaRSs (aminoacyl-tRNA synthetases) are multi-domain proteins that have evolved by domain acquisition. The anti-codon binding domain was added to the more ancient catalytic domain during aaRS evolution. Unlike in eukaryotes, ... -
Temperature-induced unfolding pathway of a type III antifreeze protein: Insight from molecular dynamics simulation
(ELSEVIER, 2008-08)Molecular dynamics simulations of the temperature-induced unfolding reaction of a cold-adapted type III antifreeze protein (AFPIII) from the Antarctic eelpout Lycodichthys dearborni have been carried out for 10 ns each at ... -
The role of the catalytic domain of E. coli GluRS in tRNA(Gln) discrimination
(ELSEVIER SCIENCE, 2009-06-18)Discrimination of tRNAGln is an integral function of several bacterial glutamyl-tRNA synthetases (GluRS). The origin of the discrimination is thought to arise from unfavorable interactions between tRNAGln and the ... -
Coulomb energies of protein-protein complexes with monopole-free charge distributions
(ELSEVIER SCIENCE, 2009-04)From an analysis of Coulomb energy distributions of a large set of protein-protein complexes we show that the positive tail in the energy distribution disappears when the monopole-monopole term, the only energy term ... -
Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature
(WILEY-BLACKWELL, 2009-07)The amino acid Aib predisposes a peptide to be helical with context-dependent preference for either 3(10)- or alpha- or a mixed helical conformation. Short peptides also show an inherent tendency to be unfolded. To ... -
Structural study of biologically significant ligands with major birch pollen allergen Betv1 by docking and molecular dynamics simulation.
(Biomedical Informatics, 2010-01-24)The major birch pollen allergen, Betv1 of Betula verrucosa is the main causative agent of birch pollen allergy in humans. Betv1 is capable of binding several physiological ligands including fatty acids, flavones, cytokinins ... -
Comparative structural studies of psychrophilic and mesophilic protein homologues by molecular dynamics simulation
(ELSEVIER, 2009-06)Comparative molecular dynamics simulations of psychrophilic type III antifreeze protein from the North-Atlantic ocean-pout Macrozoarces americanus and its corresponding mesophilic counterpart, the antifreeze-like domain ... -
Codon usage and gene expression pattern of Stenotrophomonas maltophilia R551-3 for pathogenic mode of living
(ACADEMIC PRESS, 2009-12-11)Stenotrophomonas maltophilia strain R551-3 is a multiple-antibiotic-resistant opportunistic human pathogen involved in nosocomial infections. It has a widely distributed GC-rich (>66%) genome. Analysis of differential ... -
Structural study of carboxylesterase from hyperthermophilic bacteria Geobacillus stearothermophilus by molecular dynamics simulation
(ELSEVIER SCIENCE, 2010-06)Carboxylesterases are ubiquitous enzymes with important physiological, industrial and medical applications such as synthesis and hydrolysis of stereo specific compounds, including the metabolic processing of drugs, and ... -
Human telomere d[(TTAGGG)(4)] undergoes a conformational transition to the Na+-form upon binding with sanguinarine in presence of K+
(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2011-01-07)Guanine-rich telomeric sequences fold into G-quadruplex conformation and are known to bind a variety of ligands including potential drug candidates. By means of CD spectroscopy and fluorescence lifetime measurements we ... -
Faculty Publication List : Dept. of Biophysics , 2001-02
(Bose Institute, 2002)