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T Dandekar

Publications and source records attributed to T Dandekar.

46 records · Page 3Linked to original sources
PubMed1992

Potential of genetic algorithms in protein folding and protein engineering simulations.

Genetic algorithms are very efficient search mechanisms which mutate, recombine and select amongst tentative solutions to a problem until a near optimal one is achieved. We introduce them as a new tool to study proteins. The identification and motivation for different fitness functions is discussed. The evolution of the zinc finger sequence motif from a random start is modelled. User specified changes of the lambda repressor structure were simulated and critical sites and exchanges for mutagenesis identified. Vast conformational spaces are efficiently searched as illustrated by the ab initio folding of a model protein of a four beta strand bundle. The genetic algorithm simulation which mimicked important folding constraints as overall hydrophobic packaging and a propensity of the betaphilic residues for trans positions achieved a unique fold. Cooperativity in the beta strand regions and a length of 3-5 for the interconnecting loops was critical. Specific interaction sites were considerably less effective in driving the fold.

Algorithms↗
PubMed1991

Identification of a novel iron-responsive element in murine and human erythroid delta-aminolevulinic acid synthase mRNA.

Iron-responsive elements (IREs) are regulatory RNA elements which are characterized by a phylogenetically defined sequence-structure motif. Their biological function is to provide a specific binding site for the IRE-binding protein (IRE-BP). Iron starvation of cells induces high affinity binding of the cytoplasmic IRE-BP to an IRE which has at least two different known biological consequences, repression of ferritin mRNA translation and stabilization of the transferrin receptor transcript. We report the identification of a novel, evolutionarily conserved IRE motif in the 5' UTR of murine and human erythroid-specific delta-aminolevulinic acid synthase (eALAS) mRNA which encodes the first, and possibly rate limiting, enzyme of the heme biosynthetic pathway. We demonstrate the function of the eALAS IRE as a specific binding site for the IRE-BP by gel retardation analyses and by in vitro translation experiments. In addition, we show that the 5' UTR of eALAS mRNA is sufficient to mediate iron-dependent translational regulation in vivo. These findings strongly suggest involvement of the IRE-IRE-BP system in the control of heme biosynthesis during erythroid differentiation.

5-Aminolevulinate Synthetase↗
PubMed1991

Thirty-three nucleotides of 5' flanking sequence including the 'TATA' box are necessary and sufficient for efficient U2 snRNA transcription in Schizosaccharomyces pombe.

We have sequenced the 5' flanking region of the U2 gene and compared this with the 5' flanking sequences of other snRNA genes from Schizosaccharomyces pombe. This revealed no regions of clear homology 5' to a region surrounding the 'TATA' box at -32 to -29. Deletion analysis shows that a 5' flanking region extending to only -33 is sufficient for accurate and efficient transcription of U2 in Schizosaccharomyces pombe.

Base Sequence↗
PubMed1990

Trans-splicing of pre-mRNA is predicted to occur in a wide range of organisms including vertebrates.

Several known trans-splicing RNA structures were used to define a canonical trans-splicing structure which was then used to perform a computer search of the EMBL nucleotide database. In addition to most known trans-splicing structures, many putative new trans-splicing sites were detected. These were found in a broad range of organisms including the vertebrates. Control experiments indicate that the search predicts known false positives at a rate of only 20%. Trans-splicing may therefore be a very wide-spread phenomenon.

Animals↗
PubMed1989

Cloning of Schizosaccharomyces pombe genes encoding the U1, U2, U3 and U4 snRNAs.

Schizosaccharomyces pombe contains a group of five relatively abundant small nuclear RNAs (snRNAs) which are immunoprecipitated by human autoimmune antibodies of Sm serotype. The S. pombe RNAs hybridise to probes specific for human U1, U2, U4, U5 and U6 and in each case are similar in size to the human species. A further group of snRNAs from S. pombe are precipitated by antibodies against U3 containing ribonucleoprotein; the most abundant of these species hybridises to a probe specific for human U3. We have cloned the genes encoding U1, U2, U3 and U4 from S. pombe, together with that encoding another abundant snRNA, previously designated SPU43. U2 and U4 are encoded by single-copy genes, while two genes encode U3. The latter are not clustered, since a chromosomal Southern transfer shows them to lie on different chromosomes.

Cell Fractionation↗
PubMed1989

Schizosaccharomyces pombe U4 small nuclear RNA closely resembles vertebrate U4 and is required for growth.

The single-copy gene snu4, which encodes the small nuclear RNA (snRNA) U4, has been cloned and sequenced. Schizosaccharomyces pombe U4 is 128 nucleotides in length, similar in size to vertebrate U4 and shows substantial primary and secondary structure homology. The gene lacks sequences closely resembling vertebrate snRNA transcription signals, but has a TATA box at -33 to -30; TATA sequences flanked by several additional conserved nucleotides are found in the same position in the 5' regions of other snRNA genes from Schiz. pombe. The cloned snu4 gene was disrupted by transposon mutagenesis and used to replace one chromosomal copy of snu4 in a diploid strain. On sporulation snu4- haploid strains could not be recovered, demonstrating that U4 is required, at least for spore germination. Haploid snu4- strains are viable if they also carry snu4+ on a replicating plasmid but are unable to loose the plasmid under non-selective growth, demonstrating a continuous requirement for U4 for viability.

Animals↗
PubMed1987

Evidence for the expression of peptides derived from three opioid precursors in NG 108CC15 hybrid cells.

Five opioid peptides (immunoreactivity) derived from their respective opioid precursors were measured in neuroblastoma-glioma hybrid cells (NG 108CC15; pmol/g protein): heptapeptide (Tyr-Gly-Gly-Phe-Met-Arg-Phe), 13.0 +/- 2.6; alpha-neoendorphin, 6.6 +/- 0.8; dynorphin A, 4.4 +/- 1.5; dynorphin A 1-8, 1.3 +/- 0.29; beta-endorphin, 0.3 +/- 0.13. These peptides originate from preproenkephalin A (heptapeptide), prodynorphin (alpha-neonedorphin, dynorphin A, dynorphin A 1-8) and proopiomelanocortin (beta-endorphin). The data suggest the expression of all three known opioid precursors in a single hybrid cell line, permitting a simultaneous investigation of the processing of different opioid peptides under identical experimental conditions.

Animals↗
PubMed1986

Opiates induce long-term increases in prodynorphin-derived peptide levels in the guinea-pig myenteric plexus.

The subcutaneous administration of a single dose of an opiate agonist (levorphanol) or antagonist (naloxone) to guinea pigs results in an at least 3-fold elevation of dynorphin and alpha-neoendorphin-immunoreactivity in the longitudinal muscle myenteric plexus preparation. The effects are time- and dose-dependent, significant elevations first being observed 6 h after treatment and lasting for up to 24 h. Pretreatment levels of opioid peptides were observed after 8 days. Combined injection of the narcotic agonist and antagonist, at sufficiently high doses, resulted in an additive effect of the individual drugs. The respective stereoisomers dextrorphan and (+)-naloxone did not affect prodynorphin-derived peptide concentrations. An increase of endogenous opioids was also observed after administration of the nonopiate clonidine, a compound which, like opiates, alters the activity of the myenteric plexus. It is suggested that feedback mechanisms in the myenteric plexus are responsible for the elevation of endogenous opioid peptides following exposure to exogenous opiates. Using a monoclonal antibody (3-E7), which recognizes virtually all endogenous opioid peptides, it was found that levels of higher molecular material were also increased upon opiate challenge. This suggests that a single dose of an exogenous opiate results in an increase in peptide synthesis.

Animals↗
PubMedDate not supplied

Fine mapping of the antigen-antibody interaction of scFv215, a recombinant antibody inhibiting RNA polymerase II from Drosophila melanogaster.

A bacterially expressed single chain antibody (scFv215) directed against the largest subunit of drosophila RNA polymerase II was analysed. Structure and function of the antigen binding site in scFv215 were probed by chain shuffling and by site-specific mutagenesis. The entire variable region of either the heavy or light chain was replaced by an unrelated heavy or light chain. Both replacements resulted in a total loss of binding activity suggesting that the antigen binding site is contributed by both chains. The functional contributions of each complementarity determining region (CDR) were investigated by site specific mutagenesis of each CDR separately. Mutations in two of the CDRs, CDR1 of light chain and CDR2 of heavy chain, reduced the binding activity significantly. Each of the amino acids in these two CDRs was replaced individually by alanine (alanine walking). Seven amino acid substitutions in the two CDRs were found to reduce the binding activity by more than 50%. The data support a computer model of scFv215 which fits an epitope model based on a mutational analysis of the epitope suggesting an alpha-helical structure for the main contact area.

Alanine↗