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Biomedical subjects

I Ghosh

Publications and source records attributed to I Ghosh.

At least 37 records · Page 2Linked to original sources
PubMed1995

Nucleoside diphosphate kinase from the parasitic nematode Brugia malayi.

Using a reverse transcription-polymerase chain reaction (RT-PCR) procedure that exploited the presence of a conserved 22-nucleotide spliced leader (SL) sequence that is trans-spliced to the 5' end of nematode transcripts, a novel Brugia malayi (Bm) infective-stage SL cDNA expression library was constructed and characterized. The library was immunoscreened with rabbit anti-infective-stage antibodies (Ab) and an immunodominant clone, BmG4-7, was identified and characterized. BmG4-7 contained a full-length cDNA that had significant sequence similarity to nucleoside diphosphate kinase (NDK)-encoding sequences reported from a number of species, including Drosophila melanogaster and humans. BmNDK was found to be constitutively transcribed during all stages of parasite development. An anti-BmNDK Ab was used to immunostain a Western blot of extracts from adult and larval parasites. The Ab specifically recognized a 17.5-kDa molecule in all of the parasite extracts. Molecular modeling of the BmNDK showed several regions surrounding the conserved catalytic site that may be important in the design of drugs specific for the disruption of NTP synthesis in filarial parasites.

Amino Acid Sequence↗
PubMed1995

Synthesis of the basic-helix-loop-helix region of the immunoglobulin enhancer binding protein E47 and evaluation of its structural and DNA binding properties.

The basic-helix-loop-helix (bHLH) region of the immunoglobulin enhancer binding protein E47 (IEB E47) was prepared in high yield by a solid-phase peptide synthesis methodology. Size-exclusion chromatography, sedimentation equilibrium and cross-linking data showed that the synthetic bHLH protein, 1, was dimeric, and higher-order aggregates of trimer and tetramer were also observed. The circular dichroism spectrum of 1 showed a high helical content, which increased upon addition of DNA containing the kappa E2 sequence. Gel mobility shift experiments showed that protein 1 bound sequence specifically to the kappa E2 sequence with a binding constant of 10(-10) M2, and had an affinity for other E box sequences as well. Comparisons between the co-crystal structure of IEB E47 with DNA and structural studies in solution showed lower helical contents in solution as would have been predicted from the crystal structure.

Amino Acid Sequence↗
PubMed1994

Analysis of E.coli promoter structures using neural networks.

Backpropagation neural network is trained to identify E.coli promoters of all spacing classes (15 to 21). A three module approach is employed wherein the first neural net module predicts the consensus boxes, the second module aligns the promoters to a length of 65 bases and the third neural net module predicts the entire sequence of 65 bases taking care of the possible interdependencies between the bases in the promoters. The networks were trained with 106 promoters and random sequences which were 60% AT rich and tested on 126 promoters (Bacterial, Mutant and Phage promoters). The network was 98% successful in promoter recognition and 90.2% successful in non-promoter recognition when tested on 5000 randomly generated sequences. The network was further trained with 11 mutated non-promoters and 8 mutated promoters of the p22ant promoter. The testing set with 7 mutated promoters and 13 mutated non-promoters of p22ant were identified. The network was upgraded using total 1665 data of promoters and non-promoters to identify any promoter sequences in the gene sequences. The network identified the locations of P1, P2 and P3 promoters in the pBR322 plasmid. A search for the start codon, Ribosomal Binding Site and the stop codon by a string search procedure has also been added to find the possible promoters that can yield protein products. The network was also successfully tested on a synthetic plasmid pWM528.

Base Sequence↗
PubMed1994

Molecular dynamics study of the binding of phenylalanine stereoisomers to thermolysin.

The stereospecificity in binding of phenylalanine as inhibitor in the active site of the thermolysin, has been investigated by means of molecular dynamics simulations using free energy integration techniques. The difference in the free energy of binding was found to be 2.0 +/- 1.8 kJ/mol in favour of the D-form. This agrees with the experimental value, 2.8 kJ/mol. The result was obtained using a standard empirical force field (that of GROMOS). A different force field with 30% bigger charges (more like ab initio charges) was also tried. This resulted in less fluctuations and a more precise binding, but in a free energy difference that was clearly larger than the experimental one. The phenylalanine backbone is located close to the zinc atom and the ring stays in the hydrophobic pocket in both the cases. The two stereoisomers differ mainly in the orientation of the backbone plane with respect to the active site and the rotational state of the dihedral around the C alpha-C beta bond.

Binding Sites↗
PubMed1987

Structure and expression of dog apolipoprotein C-II and C-III mRNAs. Implications for the evolution and functional constraints of apolipoprotein structure.

The complete cDNAs for canine apolipoprotein (apo) C-II and C-III have been cloned in the plasmid vector, pUC-18, and the phage vector, lambda gt11. With 32P-labeled nick-translated cDNAs as hybridization probes, apoC-II and apoC-III mRNAs were found to be expressed in canine liver, jejunum, ileum, colon, pancreas, spleen, ovary, and bladder at the following relative concentrations: 100, 35, 30, 10, 15, 5, 30, and 2% for apoC-II, and 100, 35, 15, 2, 20, 5, 30, and 5% for apoC-III. Neither mRNA was detected in canine brain, kidney, lung, muscle, oviduct, uterus, or testis. Both mRNAs are approximately 700 nucleotides in length. Complete sequence analysis revealed that apoC-II mRNA codes for a protein of 101 amino acid residues including 22 residues in the signal peptide and 79 residues in the mature peptide region. ApoC-III mRNA codes for a protein of 100 amino acid residues, including 20 in the signal peptide and 80 residues in the mature peptide region. It contains a single cysteine residue in position 54. Secondary structural analysis shows the presence of two regions each of amphipathic helix for apoC-II (residues 14-33 and 44-63) and apoC-III (residues 16-33 and 50-69). Computer analysis of the amphipathic helical regions demonstrates the importance of variation in the dihedral angles of the side chains in the charge microenvironment of the helices. Statistical analysis of sequence similarities between human apoC-II, apoC-III, apoA-II, apoA-I, apoE, and apoA-IV, and dog apoC-II and apoC-III, and rat apoC-III, apoA-II, apoA-I, apoE, and apoA-IV indicates that all these proteins have evolved rapidly, especially in the rat in which apoC-III has evolved at three times the rate in man and dog. Further, the shorter apolipoproteins, apoA-II, apoC-II, and a-poC-III, have evolved more rapidly than the longer ones, apoA-I, apoE, and apoA-IV. Some regions in the individual apolipoproteins are better conserved than others. The rate of evolution of individual regions seems to be related to the stringency of their functional requirements.

Amino Acid Sequence↗
PubMed1987

Sidechain rotational isomerization in proteins. Dynamic simulation with solvent surroundings.

Molecular dynamics simulations are used to study the rotational isomerization of the tyrosine 35 ring in bovine pancreatic trypsin inhibitor immersed in liquid water. Inclusion of the solvent surroundings improves the agreement with experimental results significantly, although the theoretical free energy barrier (13 kcal/mol at 300K) is still approximately 3 kcal/mol below that found by nuclear magnetic resonance studies. This remaining discrepancy will probably be eliminated in future calculations by the use of a more accurate model for the hydrogen atoms on the tyrosine ring. An important finding in the present work is that frictional effects due to solvent damping appear to be small for the tyrosine 35 ring, which is largely but not completely buried in the protein surface.

Isomerism↗
PubMed1984

Effect of configuration of the inhibitors on the mode of binding to the enzyme, thermolysin.

Preferred conformations of the competitive inhibitors glycyl-L-phenylalanine and glycyl-D-phenylalanine and their mode of binding to thermolysin have been studied. The difference in configuration is shown to affect significantly the mode of binding to thermolysin. Gly-D-Phe prefers to enter the active site in the global minimum conformation whereas Gly-L-Phe may enter in a higher energy conformation. Moreover, D-enantiomer is shown to have a better fit than the L-counterpart in the active site.

Binding Sites↗
PubMed1978

Mitotic asynchrony of multinucleate cells in tissue culture.

A high degree of mitotic asynchrony is reported for spontaneously arising multinucleate cells of HeLa and Pt-K1, tissue culture cell lines. Neither nuclear number, nor nuclear size nor the presence or absence of nucleoli, could be directly related to the asynchronous behaviour of the cells. Suboptimal levels of nutrients led to a higher frequency of asynchrony. A partial compartmentation of the cytoplasm could be detected in some of the multinucleate cells. The compartmentation of the cytoplasm may lead to an uneven distribution of inducer and non-inducer metabolites. All these factors together may be responsible for the high degree of mitotic asynchrony.

Animals↗
PubMed1975

Variation of stemline karyotype in a HeLa cell line.

100 karyotypes of a HeLa cell line (modal number 69) were studied in details. It was observed that the stemline cells of this "triploid" somatic cell population showed high degree of chromosomal polymorphism. It has been discussed that the stemline cells have number of extra chromosomes (or parts of chromosomes) which are not essential for the genetic integrity of this cell population. A loss of some of these chromosomes (or their parts) does not induce any appreciable change in the genetic make-up of these cells. The broken chromosomes lose their identity and are grouped together with the non-homologues, when the Denver system of classification is followed. However, it has been argued that in absence of any other acceptable system for classification, the Denver system can still be employed for analyzing human chromosomes both at diploid and abnormal heteroploid level. It has been held in contrast to the pseudo-stemline concept that these cells in general, have the essential genes in common and are responsible for the genetic make-up of this cell line and constitute together the stemline of this somatic cell population.

Cell Line↗