Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: UNIPROT:P51532 (transcriptional activator)
 6,546 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A novel approach for the modeling of coiled coils through molecular dynamics is described and applied to the dimerization region of the yeast transcriptional activator GCN4. Initially, a model is created consisting of C alpha atoms only, representing an idealized coiled coil with infinite pitch. Human bias in the placing of the other atoms is reduced by an automatic building procedure using simulated annealing with simple geometric restraints. The resulting all-atom model is then allowed to relax during a short molecular dynamics run using an empirical energy function and weak restraints which reflect the coiled coil assumption. These models are then further refined using unrestrained molecular dynamics in water. In this report we test the model-building procedure on the known dimerization region of catabolyte gene activator protein (CAP), part of which forms a coiled coil, and we predict the structure of the coiled coil dimerization region (the 'leucine zipper' domain) of GCN4. Several models are built, starting from different arrangements of the C alpha atoms in the initial structures. The final structures show similar crossing angles of the coiled coil, although this was not used as a restraint in the calculation. The leucines adopt a ladder-like conformation around the 2-fold axis of the coiled coil. A number of electrostatic interactions could be identified which may contribute to the stability of the helical structure of the monomers and of the dimer.
 ...
PMID:Automated modeling of coiled coils: application to the GCN4 dimerization region. 194 22

Two molecular dynamics (MD) simulations were performed in order to increase the understanding of the dependence of protein conformation on solvent environment. The protein used for these simulations is the transcriptional activator of the equine infectious anemia virus (EIAV-Tat). The structure of this protein has been determined by nuclear magnetic resonance (NMR) in aqueous solution (Willbold et al., Science 264, 1584 (1994)) and in 40% (v/v) trifluoroethanol (TFE) (Sticht et al., Eur. J. Biochem., submitted) showing considerable differences in the stability of the secondary structure elements. In order to investigate the influence of the solvent MD simulations (300 K: 200 ps) were carried out in water and in a solvent containing 40% (v/v) TFE. In both simulations the structure as determined in 40% TFE by NMR showing three-helices and a tight type II turn, was used as the initial structure. The MD simulations clearly indicate a decreased stability of the secondary structure elements in aqueous environment as made obvious by larger atomic motions and stronger fluctuations in the length of the hydrogen bonds. Complete unfolding of the helices was not observed on a 200 ps timescale. The root mean square deviation (RMSD) values of the backbone atoms after 200 ps simulation compared to the starting structure underline the strong influence of the solvent on the protein stability. This RMSD value is 1.95 A for the simulation in water and 1.29 A for the simulation in TFE/water. This result supports the notion that TFE acts as a secondary structure inducing and stabilizing solvent. The differences apparent from the MD simulations are in good agreement with the data derived from NMR measurements, showing the relevance of MD as a method for estimating conformational and dynamical properties of proteins.
 ...
PMID:Molecular dynamics simulation of equine infectious anemia virus Tat protein in water and in 40% trifluoroethanol. 784 58

Pseudomonas sp. strain CF600 can degrade phenol and some of its methylated derivatives via a plasmid (pVI150)-encoded pathway. The metabolic route involves hydroxylation by a multi-component phenol hydroxylase and a subsequent meta-cleavage pathway. All 15 structural genes involved are clustered in an operon that is regulated by a divergently transcribed transcriptional activator. The multi-component nature of the phenol hydroxylase is unusual since reactions of this type are usually accomplished by single component flavoproteins. We have isolated and analysed a number of marine bacterial isolates capable of degrading phenol and a range of other aromatic compounds as sole carbon and energy sources. Southern hybridization and enzyme assays were used to compare the catabolic pathways of these strains and of the archetypal phenol-degrader Pseudomonas U, with respect to known catabolic genes encoded by Pseudomonas CF600. All the strains tested that degraded phenol via a meta-cleavage pathway were found to have DNA highly homologous to each of the components of the multicomponent phenol hydroxylase. Moreover, DNA of the same strains also strongly hybridized to probes specific for pVI150-encoded meta-pathway genes and the specific regulator of its catabolic operon. These results demonstrate conservation of structural and regulatory genes involved in aromatic catabolism within strains isolated from diverse geographical locations (UK, Norway and USA) and a range of habitats that include activated sludge, sea water and fresh-water mud.
 ...
PMID:Conservation of regulatory and structural genes for a multi-component phenol hydroxylase within phenol-catabolizing bacteria that utilize a meta-cleavage pathway. 827 53

HNF1 is a transcriptional activator of many hepatic genes including albumin, alpha1-antitrypsin, and alpha- and beta-fibrinogen. It is related to the homeobox gene family and is predominantly expressed in liver and kidney. Mice lacking HNF1 fail to thrive and die around weaning after a progressive wasting syndrome with a marked liver enlargement. The transcription rate of genes like albumin and alpha1-antitrypsin is reduced, while the gene coding for phenylalanine hydroxylase is totally silent, giving rise to phenylketonuria. Mutant mice also suffer from severe Fanconi syndrome caused by renal proximal tubular dysfunction. The resulting massive urinary glucose loss leads to energy and water wasting. HNF1-deficient mice may provide a model for human renal Fanconi syndrome.
 ...
PMID:Hepatocyte nuclear factor 1 inactivation results in hepatic dysfunction, phenylketonuria, and renal Fanconi syndrome. 859 44

The PHO84 gene in Saccharomyces cerevisiae encodes the P(i) transporter Pho84p. The other three genes, GTR1, PHO86 and PHO87, are also suggested to be involved in the P(i) uptake system. We cloned and sequenced PHO86 and found that it encodes a 34-kDa protein consisting of 311 amino acid residues with two strongly hydrophobic segments in its N-terminal half. Western blotting analysis of cell extracts revealed that Pho86p, tagged with c-Myc, was fractionated into a water-insoluble fraction. Disruption of PHO86 did not affect cell viability even in combination with the pho84 and/or pho87 disruptions. The triple disruptants showed high levels of constitutive rAPase synthesis and arsenate resistance similar to the pho84 mutant, but showed slower cell growth than the pho84 mutant. PHO86 has two putative binding sites for the transcriptional activator, Pho4p, at nucleotide positions -191 and -497 relative to the ATG start codon, and showed substantial levels of transcription under high-P(i) conditions and more enhanced levels in low-P(i) medium.
 ...
PMID:A putative new membrane protein, Pho86p, in the inorganic phosphate uptake system of Saccharomyces cerevisiae. 867 28

In the photosynthetic bacterium Rhodospirillum rubrum, the presence of carbon monoxide (CO) induces expression of several proteins. These include carbon monoxide dehydrogenase (CODH) and a CO-tolerant hydrogenase. Together these enzymes catalyze the following conversion: CO + H2O --> CO2 + H2. This system enables R. rubrum to grow in the dark on CO as the sole energy source. Expression of this system has been shown previously to be regulated at the transcriptional level by CO. We have now identified the remainder of the CO-regulated genes encoded in a contiguous region of the R. rubrum genome. These genes, cooMKLXU, apparently encode proteins related to the function of the CO-induced hydrogenase. As seen before with the gene for the large subunit of the CO-induced hydrogenase (cooH), most of the proteins predicted by these additional genes show significant sequence similarity to subunits of Escherichia coli hydrogenase 3. In addition, all of the newly identified coo gene products show similarity to subunits of NADH-quinone oxidoreductase (energy-conserving NADH dehydrogenase I) from various eukaryotic and prokaryotic organisms. We have found that dicyclohexylcarbodiimide, an inhibitor of mitochondrial NADH dehydrogenase I (also called complex I), inhibits the CO-induced hydrogenase as well. We also show that expression of the cooMKLXUH operon is regulated by CO and the transcriptional activator CooA in a manner similar to that of the cooFSCTJ operon that encodes the subunits of CODH and related proteins.
 ...
PMID:Characterization of the region encoding the CO-induced hydrogenase of Rhodospirillum rubrum. 889 19

Recent efforts have defined a cis-acting DNA regulatory element in plants, the C-repeat/dehydration responsive element (DRE), that stimulates transcription in response to low temperature and water deficit. Here we report the isolation of an Arabidopsis thaliana cDNA that encodes a C-repeat/DRE binding factor, CBF1 (C-repeat/DRE Binding Factor 1). Analysis of the deduced CBF1 amino acid sequence indicates that the protein has a molecular mass of 24 kDa, a potential nuclear localization sequence, and a possible acidic activation domain. CBF1 also has an AP2 domain, which is a DNA-binding motif of about 60 aa present in the Arabidopsis proteins APETALA2, AINTEGUMENTA, and TINY; the tobacco ethylene response element binding proteins; and numerous other plant proteins of unknown function. The transcript levels for CBF1, which appears to be a single or low copy number gene, did not change appreciably in plants exposed to low temperature or in detached leaves subjected to water deficit. Binding of CBF1 to the C-repeat/DRE was demonstrated in gel shift assays using recombinant CBF1 protein expressed in Escherichia coli. Moreover, expression of CBF1 in yeast was found to activate transcription of reporter genes containing the C-repeat/DRE as an upstream activator sequence but not mutant versions of the DNA element. We conclude that CBF1 can function as a transcriptional activator that binds to the C-repeat/DRE DNA regulatory element and, thus, is likely to have a role in cold- and dehydration-regulated gene expression in Arabidopsis.
 ...
PMID:Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. 902 78

Quorum sensing relies upon the interaction of a diffusible signal molecule with a transcriptional activator protein to couple gene expression with cell population density. In Gram-negative bacteria, such signal molecules are usually N-acylhomoserine lactones (AHLs) which differ in the structure of their N-acyl side chains. Chromobacterium violaceum, a Gram-negative bacterium commonly found in soil and water, produces the characteristic purple pigment violacein. Previously the authors described a violacein-negative, mini-Tn5 mutant of C. violaceum (CV026) in which pigment production can be restored by incubation with supernatants from the wild-type strain. To develop this mutant as a general biosensor for AHLs, the natural C. violaceum AHL molecule was first chemically characterized. By using solvent extraction, HPLC and mass spectrometry, a single AHL, N-hexanoyl-L-homoserine lactone (HHL), was identified in wild-type C. violaceum culture supernatants which was absent from CV026. Since the production of violacein constitutes a simple assay for the detection of AHLs, we explored the ability of CV026 to respond to a series of synthetic AHL and N-acylhomocysteine thiolactone (AHT) analogues. In CV026, violacein is inducible by all the AHL and AHT compounds evaluated with N-acyl side chains from C4 to C8 in length, with varying degrees of sensitivity. Although AHL compounds with N-acyl side chains from C10 to C14 are unable to induce violacein production, if an activating AHL (e.g. HHL) is incorporated into the agar, these long-chain AHLs can be detected by their ability to inhibit violacein production. The versatility of CV026 in facilitating detection of AHL mixtures extracted from culture supernatants and separated by thin-layer chromatography is also demonstrated. These simple bioassays employing CV026 thus greatly extend the ability to detect a wide spectrum of AHL signal molecules.
 ...
PMID:Quorum sensing and Chromobacterium violaceum: exploitation of violacein production and inhibition for the detection of N-acylhomoserine lactones. 942 96

A bacterial biosensor for benzene, toluene, and similar compounds has been constructed, characterized, and field tested on contaminated water and soil. The biosensor is based on a plasmid incorporating the transcriptional activator xylR from the TOL plasmid of Pseudomonas putida mt-2. The XylR protein binds a subset of toluene-like compounds and activates transcription at its promoter, Pu. A reporter plasmid was constructed by placing the luc gene for firefly luciferase under the control of XylR and Pu. When Escherichia coli cells were transformed with this plasmid vector, luminescence from the cells was induced in the presence of benzene, toluene, xylenes, and similar molecules. Accurate concentration dependencies of luminescence were obtained and exhibited K1/2 values ranging from 39.0 +/- 3.8 microM for 3-xylene to 2,690 +/- 160 microM for 3-methylbenzylalcohol (means +/- standard deviations). The luminescence response was specific for only toluene-like molecules that bind to and activate XylR. The biosensor cells were field tested on deep aquifer water, for which contaminant levels were known, and were able to accurately detect toluene derivative contamination in this water. The biosensor cells were also shown to detect BETX (benzene, toluene, and xylene) contamination in soil samples. These results demonstrate the capability of such a bacterial biosensor to accurately measure environmental contaminants and suggest a potential for its inexpensive application in field-ready assays.
 ...
PMID:Development and testing of a bacterial biosensor for toluene-based environmental contaminants. 950 40

We measure the effects of low concentrations of helix-stabilizing cosolvents, including 2,2,2-trifluoroethanol (TFE), on the thermodynamics and kinetics of folding of the dimeric alpha-helical coiled coil derived from the leucine zipper region of bZIP transcriptional activator GCN4. The change in kinetic behavior upon addition of 5% (v/v) TFE indicates that it stabilizes the transition state to the same degree as the fully helical native state. However, folding rates are largely insensitive to alanine to glycine mutagenesis, indicating that the majority of helical structure is formed after the transition state. Equilibrium hydrogen isotope partitioning measurements indicate that intramolecular hydrogen bonds are not strengthened by TFE and that amide hydrogen bonds in the transition state are nearly the same strength as those in the unfolded state. Thus, the mechanism by which TFE exerts its helix-stabilizing effects can be divorced from helix formation and does not depend on the strengthening of intrahelical hydrogen bonds. Rather, TFE increases the structure of the binary alcohol/water solvent, thereby increasing the energetic cost associated with solvation of the polypeptide backbone. At low concentrations, TFE destabilizes the unfolded species and thereby indirectly enhances the kinetics and thermodynamics of folding of the coiled coil. A high degree of polypeptide backbone desolvation, and not the formation of regular helical structure and native strength hydrogen bonds, is the critical feature of the transition state for folding of this small dimeric protein.
 ...
PMID:Trifluoroethanol promotes helix formation by destabilizing backbone exposure: desolvation rather than native hydrogen bonding defines the kinetic pathway of dimeric coiled coil folding. 977 90


1 2 3 4 5 6 Next >>