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Biomedical subjects

D Ghosh

Publications and source records attributed to D Ghosh.

At least 19 recordsLinked to original sources
PubMed2000

Familial hypertrophic cardiomyopathy mutations in the regulatory light chains of myosin affect their structure, Ca2+ binding, and phosphorylation.

The effect of the familial hypertrophic cardiomyopathy mutations, A13T, F18L, E22K, R58Q, and P95A, found in the regulatory light chains of human cardiac myosin has been investigated. The results demonstrate that E22K and R58Q, located in the immediate extension of the helices flanking the regulatory light chain Ca(2+) binding site, had dramatically altered Ca(2+) binding properties. The K(Ca) value for E22K was decreased by approximately 17-fold compared with the wild-type light chain, and the R58Q mutant did not bind Ca(2+). Interestingly, Ca(2+) binding to the R58Q mutant was restored upon phosphorylation, whereas the E22K mutant could not be phosphorylated. In addition, the alpha-helical content of phosphorylated R58Q greatly increased with Ca(2+) binding. The A13T mutation, located near the phosphorylation site (Ser-15) of the human cardiac regulatory light chain, had 3-fold lower K(Ca) than wild-type light chain, whereas phosphorylation of this mutant increased the Ca(2+) affinity 6-fold. Whereas phosphorylation of wild-type light chain decreased its Ca(2+) affinity, the opposite was true for A13T. The alpha-helical content of the A13T mutant returned to the level of wild-type light chain upon phosphorylation. The phosphorylation and Ca(2+) binding properties of the regulatory light chain of human cardiac myosin are important for physiological function, and alteration any of these could contribute to the development of hypertrophic cardiomyopathy.

Amino Acid Sequence↗
PubMed2000

Object-oriented transcription factors database (ooTFD).

ooTFD (object-oriented Transcription Factors Database) is an object-oriented successor to TFD. This database is aimed at capturing information regarding the polypeptide interactions which comprise and define the properties of transcription factors. ooTFD contains information about transcription factor binding sites, as well as composite relationships within transcription factors, which frequently occur as multisubunit proteins that form a complex interface to cellular processes outside the transcription machinery through protein-protein interactions. In the past year, a few additions and changes were made to this database and associated tools, which are accessible through the IFTI-MIRAGE web site at http://www.ifti.org/

Databases, Factual↗
PubMed2000

Anti-nidatory effect of vaginally administered (Ala8,13, 18)-magainin II amide in the rhesus monkey.

The hypothesis that timed application of a potent anti-microbial, anti-tumor agent like magainin peptides can inhibit blastocyst implantation was examined in the present study using the rhesus monkey as the primate model. Incidence of pregnancy, vaginal bleeding patterns, serum levels of progesterone, estrogen and monkey chorionic gonadotropin were examined following vaginal administration of (Ala8,13,18)-magainin II amide, a synthetic analogue of magainin 2, via tampon during days 20 to 26 of mated cycles. Implantation occurred in two out of three animals following administration of 0.25 mg magainin, while administration of 0.5 mg (Ala8,13,18)-magainin II amide resulted in inhibition of implantation in all females with no change in lengths of treatment cycles, and subsequent cycles. It appears from the present study that, besides being a local microbicidal agent, intravaginal administration of (Ala(8,13,18))-magainin II amide is a potential anti-implantation strategy for intercepting pregnancy.

Administration, Intravaginal↗
PubMed2000

Steroid dehydrogenase structures, mechanism of action, and disease.

Steroid dehydrogenase enzymes influence mammalian reproduction, hypertension, neoplasia, and digestion. The three-dimensional structures of steroid dehydrogenase enzymes reveal the position of the catalytic triad, a possible mechanism of keto-hydroxyl interconversion, a molecular mechanism of inhibition, and the basis for selectivity. Glycyrrhizic acid, the active ingredient in licorice, and its metabolite carbenoxolone are potent inhibitors of human 11 beta-hydroxysteroid dehydrogenase and bacterial 3 alpha, 20 beta-hydroxysteroid dehydrogenase (3 alpha, 20 beta-HSD). The three-dimensional structure of the 3 alpha, 20 beta-HSD carbenoxolone complex unequivocally verifies the postulated active site of the enzyme, shows that inhibition is a result of direct competition with the substrate for binding, and provides a plausible model for the mechanism of inhibition of 11 beta-hydroxysteroid dehydrogenase by carbenoxolone. The structure of the ternary complex of human 17 beta-hydroxysteroid dehydrogenase type 1 (17 beta-HSD) with the cofactor NADP+ and the antiestrogen equilin reveals the details of binding of an inhibitor in the active site of the enzyme and the possible roles of various amino acids in the catalytic cleft. The short-chain dehydrogenase reductase (SDR) family includes these steroid dehydrogenase enzymes and more than 60 other proteins from human, mammalian, insect, and bacterial sources. Most members of the family contain the tyrosine and lysine of the catalytic triad in a YxxxK sequence. X-ray crystal structures of 13 members of the family have been completed. When the alpha-carbon backbone of the cofactor binding domains of the structures are superimposed, the conserved residues are at the core of the structure and in the cofactor binding domain, but not in the substrate binding pocket.

17-Hydroxysteroid Dehydrogenases↗
PubMed2000

Methods for analysis of multiple events in the presence of death.

The use of multiple events data in the design and analysis of clinical trials is becoming quite common. Several methods for analyzing such data have been proposed in the literature. However, they do not account for deaths in the analysis. In this article, an overview of available methods for modeling recurrent events and death is given. These methods are illustrated using data from an HIV clinical trial.

Clinical Trials as Topic↗
PubMed2000

Preimplantation embryo morphology following early luteal phase anti-nidatory treatment with mifepristone (RU486) in the rhesus monkey.

The ultrastructural characteristics of peri-implantation stage embryos recovered on day 6 after ovulation from rhesus monkeys with or without mifepristone (RU486) treatment during the early luteal phase were examined in the present study. Monkeys were randomly allocated to two groups; group 1 animals were injected s.c. with 2 ml vehicle (1:4, benzyl benzoate: olive oil, v/v, n = 21) and group 2 animals received a single dose of mifepristone (2 mg/kg body weight, w/v, n = 30) in the same volume of vehicle on day 2 after ovulation in mated cycles. On day 6 after ovulation, female monkeys of both groups were laparotomized and their reproductive tracts were flushed to retrieve preimplantation stage embryos. Embryos that showed frank degeneration or desynchrony on gross microscopical examination were not included in the present study. Preimplantation embryo growth on day 6 after ovulation was significantly (P < 0.05) affected in the morula-blastocyst transition stage in mifepristone-treated monkeys compared with that in the control group of monkeys. Ultrastructurally, administration of mifepristone on day 2 after ovulation depressed preimplantation stage embryo development, characterized by loss of cell polarity, lack of mitochondrial maturity, and lack of differentiation in trophoblast cells. Furthermore, preimplantation embryos from mifepristone-treated animals displayed a higher occurrence of inter-blastomere space, intra-cytoplasmic vacuoles, myelinoid bodies, accumulation of lipid droplets, lysosomes, lipofuscins, autophagosomes and multivesicular bodies. Collectively, it appears that the developmental potential of preimplantation embryos was significantly compromised in mifepristone-treated cycles.

Animals↗
PubMed2000

Expression of vascular endothelial growth factor (VEGF) and placental growth factor (PlGF) in conceptus and endometrium during implantation in the rhesus monkey.

The aim of this study was to analyse the expression of transcripts and proteins for vascular endothelial growth factor (VEGF) and placenta growth factor (PlGF) in different compartments of the early conceptus at primary implantation sites during lacunar (n = 6), early villous (n = 9) and villous placenta (n = 6) stages of gestation in the rhesus monkey. During the lacunar stage, VEGF expression was observed in the cytotrophoblast cells lining the extraembryonic cavity, but these cells did not express PlGF. With further development, cytotrophoblast cells lining villi, forming columns, and constituting anchoring villi, expressed both VEGF and PlGF during early villous and villous placenta stages. In addition, chorion, amnion and villous stromal cells expressed both VEGF and PlGF proteins and mRNA. During the lacunar stage, all epithelial cells in maternal endometrium generally expressed VEGF, while PlGF expression was observed in the plaque epithelium only. As gestation advanced, the expression of VEGF and PlGF from plaque cells decreased, and in surface and glandular epithelium the expression of VEGF increased, while the expression of PlGF remained unaltered. Decidual stromal cells expressed VEGF and PlGF only at low levels during the lacunar stage, while the expression of both increased during the early villous and the villous placenta stages of implantation. It appears from the present study that the expression of VEGF and PlGF are regulated in a temporal and spatial manner during early stages of implantation and that their concerted actions in placental and maternal compartments play a critical role in the evolving pregnancy in the rhesus monkey.

Animals↗
PubMed2000

Macrophage protein kinase C: its role in modulating membrane microviscosity and superoxide in leishmanial infection.

Pretreatment of macrophages with, an agonist of PKC, showed diverse effects on degradation and survival of two virulent strains of Leishmania donovani promastigotes. Treatment of macrophages with PMA for 45 min at 37 degrees C generated significant amounts of superoxide anions and reduced the parasite burden of macrophages by up to 48 and 43% when AG83 and GE-1 strains were used for infection. Staurosporine, an inhibitor of PKC, inhibited PMA-dependent killing of the parasites, while tyrphostin AG 126, an inhibitor of protein tyrosine kinase, showed very little effect. Depletion of PKC by prolonged incubation with PMA drastically reduced the superoxide anion generation and increased the uptake and multiplication of the parasites. Finally, to understand the mechanism of higher uptake of the parasites by PKC-depleted macrophages, membrane microviscosity was measured by fluorescence depolarization. Membrane microviscosity was found to be approximately 40% lower in PKC-depleted macrophages than in normal macrophages, indicating the role of membrane fluidity in the infection process. Together, these data suggest PKC activation, superoxide generation, and membrane fluidity are essential factors in the efficient regulation of leishmanial infection.

Animals↗
PubMed2000

Nonparametric analysis of recurrent events and death.

This article is concerned with the analysis of recurrent events in the presence of a terminal event such as death. We consider the mean frequency function, defined as the marginal mean of the cumulative number of recurrent events over time. A simple nonparametric estimator for this quantity is presented. It is shown that the estimator, properly normalized, converges weakly to a zero-mean Gaussian process with an easily estimable covariance function. Nonparametric statistics for comparing two mean frequency functions and for combining data on recurrent events and death are also developed. The asymptotic null distributions of these statistics, together with consistent variance estimators, are derived. The small-sample properties of the proposed estimators and test statistics are examined through simulation studies. An application to a cancer clinical trial is provided.

Antineoplastic Agents, Alkylating↗
PubMed2000

High throughput and global approaches to gene expression.

In the past several years, a new set of technologies based on whole genome analysis have revolutionized the study of gene expression. These microarray or "gene chip" technologies, which arose out of the development of large-scale sequencing approaches, are now coming into increasing use, generating a far greater volume of data than the data representing the sequences themselves. This review focuses on the current state of development of these technologies, and the available approaches to manage and analyze the information they generate. The applicability of this technology to general problems in biomedicine is also discussed.

Electronic Data Processing↗
PubMed1999

Co-occupancy of the interferon regulatory element of the class II transactivator (CIITA) type IV promoter by interferon regulatory factors 1 and 2.

Class II transactivator (CIITA) activates the expression of major histocompatibility class II genes, which encode antigen-presenting molecules recognized by the T-cell receptor of CD4+ T cells. IFN-gamma induced CIITA transcription in many cell types is directed by the CIITA Type IV promoter. Here we report that the human CIITA Type IV promoter IRF-E binds IRF-1 and can be activated by exogenous expression of IRF-1. Surprisingly, the CIITA Type IV promoter IRF-E is also activated by IRF-2, another member of the IRF family that generally acts as a transcriptional repressor. In addition, we found that IRF-1 and IRF-2 synergistically activate the CIITA Type IV promoter. Electrophoretic mobility shift assays revealed that IRF-1 and IRF-2 can simultaneously occupy the IRF-E of the CIITA Type IV promoter, suggesting a novel mechanism for the role of these two proteins in promoter activation. Our results also indicate that IRF-1 and IRF-2 can cooperatively activate and co-occupy the IRF-E of the guanylate binding protein (GBP) promoter. Finally, CIITA induction by IFN-gamma does not occur in a pancreatic tumor cell line that expresses a mutated IRF-2, representing the first IRF-2 mutation identified in a human tumor cell line.

DNA-Binding Proteins↗
PubMed1999

Structure of Ustilago maydis killer toxin KP6 alpha-subunit. A multimeric assembly with a central pore.

Ustilago maydis is a fungal pathogen of maize, some strains of which secrete killer toxins. The toxins are encoded by double-stranded RNA viruses in the cell cytoplasm. The U. maydis killer toxin KP6 contains two polypeptide chains, alpha and beta, having 79 and 81 amino acids, respectively, both of which are necessary for its killer activity. The crystal structure of the alpha-subunit of KP6 (KP6alpha) has been determined at 1.80-A resolution. KP6alpha forms a single domain structure that has an overall shape of an ellipsoid with dimensions 40 A x 26 A x 21 A and belongs to the alpha/beta-sandwich family. The tertiary structure consists of a four-stranded antiparallel beta-sheet, a pair of antiparallel alpha-helices, a short strand along one edge of the sheet, and a short N-terminal helix. Although the fold is reminiscent of toxins of similar size, the topology of KP6alpha is distinctly different in that the alpha/beta-sandwich motif has two right-handed betaalphabeta split crossovers. Monomers of KP6alpha assemble through crystallographic symmetries, forming a hexamer with a central pore lined by hydrophobic N-terminal helices. The central pore could play an important role in the mechanism of the killing action of the toxin.

Hydrogen Bonding↗
PubMed1999

Equilin.

3-Hydroxyestra-1,3,5(10),7-tetraen-17-one, C18H20O2, crystallizes in space group P2(1)2(1)2(1) from ethyl acetate. The planarity of the B ring, and the difference in puckering of the C and D rings from that of estrone, are due to the presence of the C7 = C8 double bond, which may explain its function as an inhibitor of human type 1 17 beta-hydroxysteroid dehydrogenase, instead of being its substrate.

Crystallography, X-Ray↗
PubMed1999

Structure of the ternary complex of human 17beta-hydroxysteroid dehydrogenase type 1 with 3-hydroxyestra-1,3,5,7-tetraen-17-one (equilin) and NADP+.

Excess 17beta-estradiol (E2), the most potent of human estrogens, is known to act as a stimulus for the growth of breast tumors. Human estrogenic 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1), which catalyzes the reduction of inactive estrone (E1) to the active 17beta-estradiol in breast tissues, is a key enzyme responsible for elevated levels of E2 in breast tumor tissues. We present here the structure of the ternary complex of 17beta-HSD1 with the cofactor NADP+ and 3-hydroxyestra-1,3,5,7-tetraen-17-one (equilin), an equine estrogen used in estrogen replacement therapy. The ternary complex has been crystallized with a homodimer, the active form of the enzyme, in the asymmetric unit. Structural and kinetic data presented here show that the 17beta-HSD1-catalyzed reduction of E1 to E2 in vitro is specifically inhibited by equilin. The crystal structure determined at 3.0-A resolution reveals that the equilin molecule is bound at the active site in a mode similar to the binding of substrate. The orientation of the 17-keto group with respect to the nicotinamide ring of NADP+ and catalytic residues Tyr-155 and Ser-142 is different from that of E2 in the 17beta-HSD1-E2 complex. The ligand and substrate-entry loop densities are well defined in one subunit. The substrate-entry loop adopts a closed conformation in this subunit. The result demonstrates that binding of equilin at the active site of 17beta-HSD1 is the basis for inhibition of E1-to-E2 reduction by this equine estrogen in vitro. One possible outcome of estrogen replacement therapy in vivo could be reduction of E2 levels in breast tissues and hence the reduced risk of estrogen-dependent breast cancer.

Amino Acid Sequence↗
PubMed1999

Object oriented Transcription Factors Database (ooTFD).

ooTFD is an object-oriented database for the representation of information pertaining to transcription factors, the proteins and biochemical entities which play a central role in the regulation of gene expression. Given the recent explosion of genome sequence information, and that a large percentage of proteins encoded by fully sequenced genomes fall into this category, information pertaining to this class of molecules may become an essential aspect of biology and of genomics in the 21st century. In the past year, there was a small increase in the size of this database, and a number of new tools to facilitate data access and analysis have been added at the MIRAGE (Molecular Informatics Resource for the Analysis of Gene Expression) web site. ooTFD and associated tools and resources can be accessed at http://www.ifti.org/

Databases, Factual↗
PubMed1999

Structure of rabbit liver fructose 1,6-bisphosphatase at 2.3 A resolution.

The three-dimensional structure of the R form of rabbit liver fructose 1,6-bisphosphatase (Fru-1,6-Pase; E.C. 3.1.3.11) has been determined by a combination of heavy-atom and molecular-replacement methods. A model, which includes 2394 protein atoms and 86 water molecules, has been refined at 2.3 A resolution to a crystallographic R factor of 0.177. The root-mean-square deviations of bond distances and angles from standard geometry are 0.012 A and 1.7 degrees, respectively. This structural result, in conjunction with recently redetermined amino-acid sequence data, unequivocally establishes that the rabbit liver enzyme is not an aberrant bisphosphatase as once believed, but is indeed homologous to other Fru-1,6-Pases. The root-mean-square deviation of the Calpha atoms in the rabbit liver structure from the homologous atoms in the pig kidney structure complexed with the product, fructose 6-phosphate, is 0.7 A. Fru-1,6-Pases are homotetramers, and the rabbit liver protein crystallizes in space group I222 with one monomer in the asymmetric unit. The structure contains a single endogenous Mg2+ ion coordinated by Glu97, Asp118, Asp121 and Glu280 at the site designated metal site 1 in pig kidney Fru-1,6-Pase R-form complexes. In addition, two sulfate ions, which are found at the positions normally occupied by the 6-phosphate group of the substrate, as well as the phosphate of the allosteric inhibitor AMP appear to provide stability. Met177, which has hydrophobic contacts with the adenine moiety of AMP in pig kidney T-form complexes, is replaced by glycine. Binding of a non-hydrolyzable substrate analog, beta-methyl-fructose 1,6-bisphosphate, at the catalytic site is also examined.

Allosteric Site↗
PubMed1999

Structure of an activity suppressing Fab fragment to cytochrome P450 aromatase: insights into the antibody-antigen interactions.

The crystal structure of a Fab fragment (Fab3-2C2) of a monoclonal antibody raised against aromatase cytochrome P450 P450arom) has been determined at 3.0 A resolution. P450arom is a membrane bound enzyme responsible for the catalysis of indrogens to estrogens, the process of aromatization, and hence has been implicated in hormone-dependent breast cancer. The Fab fragment of MAb3-2C2 IgG suppresses P450arom activity in a dose dependent manner. The Fab3-2C2 molecule crystallizes n the space group P2(1)2(1)2(1) with a unit cell of a= 154.89 A, b = 73.51 A, and c= 36.90 A. The crystal structure consists of a light and a heavy chain in the asymmetric unit, each characterized by the greek-key antiparallel beta barrel folding seen in all Fab structures. The average elbow angle between the two domains is 143 degrees. Modeling of the interactions between the variable domains of the antibody and a known model of P450arom maps the epitope to a region of the enzyme that is consistent with the available biochemical data and the activity-suppressing function of the antibody. The epitope mapping result is further supported by the inability of MAb3-2C2 IgG to suppress the activity of, or to interact with placental porcine P450arom, which is 81% identical (86% similar) to human P450arom but has a few key substitutions in the putative epitope region.

Amino Acid Sequence↗