bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental resolution of the free energies of aqueous solvation contributions to ligand-protein binding: quinone-QA site interactions in the photosynthetic reaction center protein.
Authors: Warncke K , Dutton P L
Published: May 2006

Equilibrium binding free energies of 14 benzo-, naphtho-, and anthraquinone cofactors have been determined at the QA redox catalytic site of the purified photosynthetic reaction center protein from Rhodobacter sphaeroides solubilized in water (delta G degrees B,w), in hexane solution containing 30 mM water (delta G degrees B,hh), and after partial dehydration (delta G degrees B,dh) with magnesium sulfate. Our aim is to resolve the contributions of aqueous bulk phase solvation and protein hydration contributions to binding in order to characterize in detail the direct interactions between the ligands and protein at the QA site. This is accomplished by comparing the differences between delta G degrees B,w and delta G degrees B,hh (or delta G degrees B,dh) with the water to hexane solvent transfer free energies of the quinones (delta G degrees tr,Q). Values of delta G degrees tr,Q are determined separately in binary solution and range from 0.65 to -5.69 kcal/mol (1 cal = 4.184 J). The results are interpreted in terms of a thermodynamic cycle that links the species involved in the binding and solvent transfer equilibria. Values of delta G degrees B,hh -delta G degrees B,w are linearly correlated with -delta G degrees tr,Q (slope, 0.78 +/- 0.04; ordinate intercept, -0.13 +/- 0.12 kcal/mol). The deviation of the experimental slopes from the predicted value of unity is attributed in part to a systematic decrease of quinone thermodynamic activity in the aqueous binding medium relative to the aqueous phase in the binary partitioning solvent system. The difference between the quinone-QA site binding free energies measured in hydrated hexane and water is therefore related only to the difference in bulk phase quinone solvation, as given by 0.78 delta G degrees tr,Q. The linear relation obtained using delta G degrees B,dh -delta G degrees B,w has the same slope, but the intercept is decreased to -1.48 +/- 0.19 kcal/mol, indicating that quinone binding strengths in the hexane system are uniformly enhanced after partial dehydration. This suggests that the quinones encounter a common opposition to interaction with the site in the hydrated, relative to the partially dehydrated, state. The further utility of the method to directly assess ligand-site binding free energies is demonstrated with examples that address the contributions of molecular size and dipolar or hydrogen bond interactions to the binding of quinones at the QA site.
Localization of a retroviral element within the rd gene coding for the beta subunit of cGMP phosphodiesterase.
Authors: Bowes C , Li T , Frankel W N , Danciger M , Coffin J M , Applebury M L , Farber D B
Published: May 2006

Retinal degeneration in the rd mouse is inherited as an autosomal recessive trait and is caused by a defect in the gene encoding the beta subunit of cGMP phosphodiesterase. Recently, a close genetic association of the rd gene with an endogenous xenotropic murine leukemia virus (Xmv-28) was established by linkage analysis using recombinant inbred strains of mice. In this study, genomic DNA mapping and sequence analyses clarify the position of the proviral sequences in relation to the rd gene. We find that the Xmv-28 provirus is integrated into intron I of the rd gene 1511 bp downstream of the exon-intron boundary. The transcriptional orientation of the provirus is opposite to that of the gene for the beta subunit of cGMP phosphodiesterase. Reverse transcription-PCR demonstrates that the integrated Xmv-28 sequences are transcribed in the retina. The provirus is present in every strain of rd mouse tested.
Chemical and molecular regulation of enzymes that detoxify carcinogens.
Authors: Prestera T , Holtzclaw W D , Zhang Y , Talalay P
Published: May 2006

Inductions of detoxication (phase 2) enzymes, such as glutathione transferases and NAD(P)H:(quinone-acceptor) oxidoreductase, are a major mechanism for protecting animals and their cells against the toxic and neoplastic effects of carcinogens. These inductions result from enhanced transcription, and they are evoked by diverse chemical agents: oxidizable diphenols and phenylenediamines; Michael reaction acceptors; organic isothiocyanates; other electrophiles--e.g., alkyl and aryl halides; metal ions--e.g., HgCl2 and CdCl2; trivalent arsenic derivatives; vicinal dimercaptans; organic hydroperoxides and hydrogen peroxide; and 1,2-dithiole-3-thiones. The molecular mechanisms of these inductions were analyzed with the help of a construct containing a 41-bp enhancer element derived from the 5' upstream region of the mouse liver glutathione transferase Ya subunit gene ligated to the 5' end of the isolated promoter region of this gene, and inserted into a plasmid containing a human growth hormone reporter gene. When this construct was transfected into Hep G2 human hepatoma cells, the concentrations of 28 compounds (from the above classes) required to double growth hormone production, and the concentrations required to double quinone reductase specific activities in Hepa 1c1c7 cells, spanned a range of four orders of magnitude but were closely linearly correlated. Six compounds tested were inactive in both systems. A 26-bp subregion of the above enhancer oligonucleotide (containing the two tandem "AP-1-like" sites but lacking the preceding ETS protein binding sequence) was considerably less responsive to the same inducers. We conclude that the 41-bp enhancer element mediates most, if not all, of the phase 2 enzyme inducer activity of all of these widely different classes of compounds.
Functional inhibition of retinoic acid response by dominant negative retinoic acid receptor mutants.
Authors: Damm K , Heyman R A , Umesono K , Evans R M
Published: May 2006

The diverse effects of retinoids on the development, growth, and homeostasis of vertebrate organisms are mediated in part by three distinct isoforms of retinoic acid receptors (RARs). These proteins, which are structurally and functionally closely related to thyroid hormone receptors and the oncogene product v-ErbA, regulate patterns of gene expression in target tissues. One approach to study the distinct effects of retinoic acid in cells is to subvert this activity of endogenous receptors by expression of dominant negative receptor derivatives. We demonstrate here that RAR alpha, RAR beta, and RAR gamma can be converted into potent negative transcriptional regulators that block wild-type RAR function. Furthermore, these mutant RARs, but not the wild-type receptors, actively repress the basal transcription level of target promoters. When expressed in transgenic mice, the most potent of these inhibitory receptor mutants is apparently able to disturb developmental processes by inducing a cleft palate in transgenic offspring.
Association of GAD-65, but not of GAD-67, with the Golgi complex of transfected Chinese hamster ovary cells mediated by the N-terminal region.
Authors: Solimena M , Aggujaro D , Muntzel C , Dirkx R , Butler M , De Camilli P , Hayday A
Published: May 2006

Glutamic acid decarboxylase (GAD) is the enzyme responsible for synthesis of the neurotransmitter gamma-aminobutyric acid in neurons and pancreatic beta cells. It is represented by two isoforms, GAD-65 and GAD-67, which are the products of two different genes and differ substantially only at their N-terminal regions. GAD-65 is a dominant autoantigen in stiff-man syndrome and insulin-dependent diabetes mellitus. In neurons and beta cells, GAD is concentrated around synaptic vesicles and synaptic-like microvesicles, respectively, as well as in the area of the Golgi complex. The mechanisms responsible for specific targeting of GAD to these organelles are not yet understood. The elucidation of the mechanism of subcellular targeting of GAD may be relevant to understanding its role as an autoantigen. In this study, the cloned genes for GAD-65 and GAD-67 were expressed separately in Chinese hamster ovary (CHO) cells and COS cells. While GAD-67 had a diffuse cytoplasmic localization, GAD-65 had a punctate distribution, with most of the immunoreactivity being concentrated in the area of the Golgi complex. A chimeric protein in which the 88 N-terminal amino acids of GAD-67 were replaced by the 83 N-terminal amino acids of GAD-65 was targeted to the Golgi complex, indicating that the N-terminal region of GAD-65 contains a targeting signal sufficient for directing the remaining portion of the molecule, highly similar in GAD-65 and GAD-67, to the Golgi complex-associated structures.
Identification and characterization of a nuclease activity specific for G4 tetrastranded DNA.
Authors: Liu Z , Frantz J D , Gilbert W , Tye B K
Published: May 2006

We have identified a nuclease activity that is specific for G4 tetrastranded DNA. This activity, found in a partially purified fraction for a yeast telomere-binding protein, binds to DNA molecules with G4 tetrastranded structure, regardless of their nucleotide sequences, and cleaves the DNA in a neighboring single-stranded region 5' to the G4 structure. Competition with various G4-DNA molecules inhibits the cleavage reaction, suggesting that this nuclease activity is specific for G4 tetrastranded DNA. The existence of this enzymatic activity that reacts with G4 DNAs but not with single-stranded or Watson-Crick duplex DNAs suggests that tetrastranded DNA may have a distinct biological function in vivo.
Transactivation of gene expression by Myc is inhibited by mutation at the phosphorylation sites Thr-58 and Ser-62.
Authors: Gupta S , Seth A , Davis R J
Published: May 2006

The product of the human c-myc protooncogene (Myc) is a sequence-specific DNA binding protein. Here, we demonstrate that the placement of the specific Myc DNA binding site CACGTG upstream of a luciferase reporter gene conferred Myc-stimulated expression that was inhibited by the overexpression of the basic-helix-loop-helix/leucine zipper protein Max. It was observed that Myc was phosphorylated in vivo within the NH2-terminal domain at Thr-58 and Ser-62. Replacement of these phosphorylation sites with Ala residues caused a marked decrease in Myc-stimulated reporter gene expression. In contrast, the replacement of Thr-58 or Ser-62 with an acidic residue (Glu) caused only a small inhibition of transactivation. Together, these data demonstrate that the NH2-terminal phosphorylation sites Thr-58 and Ser-62 are required for high levels of transactivation of gene expression by Myc.
Two members of a distinct subfamily of 5-hydroxytryptamine receptors differentially expressed in rat brain.
Authors: Erlander M G , Lovenberg T W , Baron B M , de Lecea L , Danielson P E , Racke M , Slone A L , Siegel B W , Foye P E , Cannon K
Published: May 2006

We report two serotonin (5-hydroxytryptamine, 5-HT) receptors, MR22 and REC17, that belong to the G-protein-associated receptor superfamily. MR22 and REC17 are 371 and 357 amino acids long, respectively, as deduced from nucleotide sequence and share 68% mutual amino acid identity and 30-35% identity with known catecholamine and 5-HT receptors. Saturable binding of 125I-labeled (+)-lysergic acid diethylamide to transiently expressed MR22 in COS-M6 cells was inhibited by ergotamine > methiothepin > 5-carboxamidotryptamine > 5-HT. For REC17, the rank of potency was ergotamine > 5-carboxamidotryptamine > methiothepin > methysergide > 5-HT. Both were insensitive to 5-HT1A, 5-HT1D or 5-HT2 serotonergic ligands [8-hydroxy-2-(di-n-propylamino)tetralin, sumatriptan, and 1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane]. The mRNAs encoding MR22 were detected in the CA1 region of hippocampus, the medial habenula, and raphe nuclei. In contrast, mRNAs encoding REC17 were found throughout the rat central nervous system. We propose that REC17 and MR22, designated as 5-HT5 alpha and 5-HT5 beta, represent a distinct subfamily of 5-HT receptors.
Targeted delivery of peptide epitopes to class I major histocompatibility molecules by a modified Pseudomonas exotoxin.
Authors: Donnelly J J , Ulmer J B , Hawe L A , Friedman A , Shi X P , Leander K R , Shiver J W , Oliff A I , Martinez D , Montgomery D
Published: May 2006

Cytotoxic T lymphocytes (CTLs) expressing the CD8 surface marker recognize peptides in association with major histocompatibility complex (MHC) class I molecules. Although most peptides expressed on MHC class I molecules are derived from self- or virally encoded proteins, delivery of exogenous proteins to the cytosol can result in their being processed for presentation to CTLs on MHC class I molecules. We describe two fusion proteins (PEMa and PENP), consisting of the binding and translocating domains of Pseudomonas exotoxin A (PE), fused to peptide epitopes from influenza A matrix protein and nucleoprotein, respectively. These fusion proteins were internalized and processed by MHC class I-positive target cells, resulting in sensitization of target cells for lysis by peptide-specific CTLs. A point mutation known to interfere with intoxication by wild-type PE also reduced the ability of PEMa to sensitize target cells. Fusion of peptide or polypeptide epitopes with PE provides a potential means of eliciting CTLs without the use of self-replicating agents, as well as a useful probe for studying MHC class I-restricted antigen processing.
Chirality of DNA supercoiling assigned by scanning force microscopy.
Authors: Samorí B , Siligardi G , Quagliariello C , Weisenhorn A L , Vesenka J , Bustamante C J
Published: May 2006

Reproducible images of pBR322 plasmid molecules have been recorded by scanning force microscopy under 1-propanol. Most of the plasmids were found in a coiled state. The supercoiled molecules of our samples look like branched or unbranched interwound superhelixes. This is consistent with available electron microscopy data on circular DNA molecules. By applying a stratigraphic analysis which takes advantage of the height information contained in the scanning force microscopy images, it is possible to assign the chirality of the local supercoiling of the individual molecules.
Thy-1 glycoprotein and src-like protein-tyrosine kinase p53/p56lyn are associated in large detergent-resistant complexes in rat basophilic leukemia cells.
Authors: Dráberová L , Dráber P
Published: May 2006

Thy-1 is a surface glycoprotein that is attached to the plasma membrane by a glycosyl-phosphatidyl-inositol anchor. Crosslinking of Thy-1 in rat mast cells and basophilic leukemia cells (RBL-2H3) induces cell activation including histamine release and tyrosine phosphorylation of several proteins. Here we show that glycosyl-phosphatidylinositol-linked Thy-1 forms noncovalent complexes with src-related protein-tyrosine kinase p53/p56lyn and other protein-tyrosine kinases and/or their substrates. These complexes are resistant to solubilization by a nonionic detergent, sedimentable at 200,000 x g, and very large ( > 10 MDa) as determined by gel chromatography. Activation of RBL-2H3 cells by crosslinking of the high-affinity IgE receptors resulted in decreased recovery of the complexes. The combined data indicate the existence of large detergent-resistant domains in the surface membrane of mast cells that may play an important role in their activation.
Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution.
Authors: Macaya R F , Schultze P , Smith F W , Roe J A , Feigon J
Published: May 2006

We have used two-dimensional 1H NMR spectroscopy to study the conformation of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG) in solution. This is one of a series of thrombin-binding DNA aptamers with a consensus 15-base sequence that was recently isolated and shown to inhibit thrombin-catalyzed fibrin clot formation in vitro [Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H. & Toole, J. J. (1992) Nature (London) 355, 564-566]. The oligonucleotide forms a unimolecular DNA quadruplex consisting of two G-quartets connected by two TT loops and one TGT loop. A potential T.T bp is formed between the two TT loops across the diagonal of the top G-quartet. Thus, all of the invariant bases in the consensus sequence are base-paired. This aptamer structure was determined by NMR and illustrates that this molecule forms a specific folded structure. Knowledge of this structure may be used in the further development of oligonucleotide-based thrombin inhibitors.
External GTP alters the motility and elicits an oscillating membrane depolarization in Paramecium tetraurelia.
Authors: Clark K D , Hennessey T M , Nelson D L
Published: May 2006

Paramecium, a unicellular ciliated protist, alters its motility in response to various stimuli. Externally added GTP transiently induced alternating forward and backward swimming interspersed with whirling at a concentration as low as 0.1 microM. ATP was 1000-fold less active, whereas CTP and UTP produced essentially no response. The response to the nonhydrolyzable GTP analogs guanosine 5'-[gamma-thio]triphosphate and guanosine 5'-[beta, gamma-imido]triphosphate was indistinguishable from that to GTP. This behavioral response was correlated with an unusual transient and oscillating membrane depolarization in both wild-type cells and the mutant pawn B, which is defective in the voltage-dependent Ca2+ current required for action potentials. This is a specific effect of external GTP on the excitability of a eukaryotic cell and, to our knowledge, is the first purinergic effect to be discovered in a microorganism.
A 24-base-pair sequence 3' to the human erythropoietin gene contains a hypoxia-responsive transcriptional enhancer.
Authors: Madan A , Curtin P T
Published: May 2006

Erythropoietin (Epo) synthesis increases in response to hypoxia. The hepatoma cell line Hep 3B produces low basal levels of Epo mRNA which increase markedly with hypoxia. To define the sequences necessary for this response, we linked fragments of the human Epo gene to a luciferase vector, introduced these plasmids into Hep 3B cells and assayed for luciferase activity after growth in 1% or 21% oxygen. A 621-bp Epo promoter fragment resulted in a 2.4-fold increase in luciferase activity with hypoxia. We tested several Epo gene fragments upstream of this Epo promoter fragment and found that a 613-bp Bgl II-Pvu II 3' fragment had a 10-fold increase in activity with hypoxia regardless of orientation. This fragment had a similar level of activity when linked to a simian virus 40 promoter. Portions of this fragment retained activity, including a 38-bp Apa I-Taq I fragment that had a 17-fold increase in activity with hypoxia. Deletion of nt 4-13 or 19-28 from this 38-bp fragment resulted in a loss of activity. The 24-bp upstream portion of the 38-bp fragment showed an 8-fold increase in activity with hypoxia. However, deletion of nt 19-24 or mutagenesis of nt 21 or 22 in this 24-bp fragment resulted in loss of activity. Our studies indicate that the transcriptional response of the human Epo gene to hypoxia is mediated in part by promoter sequences and to a greater degree by an enhancer element located in a 24-bp portion of the 3' flanking sequence of the gene.
A polypeptide bound by the chaperonin groEL is localized within a central cavity.
Authors: Braig K , Simon M , Furuya F , Hainfeld J F , Horwich A L
Published: May 2006

Chaperonins are oligomeric protein complexes that play an essential role in the cell, mediating ATP-dependent polypeptide chain folding in a variety of cellular compartments. They appear to bind early folding intermediates, preventing their aggregation; in the presence of MgATP and a cochaperonin, bound polypeptides are released in a stepwise manner, associated with folding to the native state. Chaperonin complexes appear in the electron microscope as cylindrical structures, usually composed of two stacked rings, each containing, by negative staining, an electron dense central "hole" approximately 6.0 nm in diameter. We sought to identify the site on the Escherichia coli chaperonin groEL, where the "molten globule"-like intermediate of dihydrofolate reductase (DHFR) becomes bound, by examining in the scanning transmission electron microscope complexes formed between groEL and DHFR molecules bearing covalently crosslinked 1.4-nm gold clusters. In top views of the groEL complexes, gold densities were observed in the central region; in side views, the densities were seen at the end portions of the cylinders, corresponding to positions within the individual rings. In some cases, two gold densities were observed in the same groEL complex. We conclude that folding intermediates are bound inside central cavities within individual chaperonin rings. In this potentially sequestered location, folding intermediates with a compact conformation can be bound at multiple sites by surrounding monomeric members of the ring; localization of folding within the cavity could also facilitate rebinding of structures that initially fail to incorporate properly into the folding protein.
Missense mutations in the beta-myosin heavy-chain gene cause central core disease in hypertrophic cardiomyopathy.
Authors: Fananapazir L , Dalakas M C , Cyran F , Cohn G , Epstein N D
Published: May 2006

Hypertrophic cardiomyopathy (HCM) is an important cause of sudden death in apparently healthy young individuals. In less than half of kindreds with HCM, the disease is linked to the beta-myosin heavy-chain gene locus (MYH7). We have recently described two missense MYH7 gene mutations [Arg-403 to Gln (R403Q) and Leu-908 to Val (L908V)] and found that the mutant message is present in skeletal muscle soleus) and that the mutant beta-myosin obtained from soleus muscle has abnormal in vitro motility activity. Having identified a second kindred with the R403Q mutation, and 3 other kindreds with two additional mutations (G741R and G256E), we performed histochemical analysis of soleus muscle biopsies from 25 HCM patients with one of these four mutations. Light microscopic examination of the NADH-stained biopsies revealed the presence of central core disease (CCD) of skeletal muscle, a rare autosomal dominant nonprogressive myopathy characterized by a predominance of type I "slow" fibers and an absence of mitochondria in the center of many type I fibers. CCD was present in 10 of 13 patients with the L908V mutation, 5 of 8 patients with the R403Q mutation, 1 of 3 patients with the G741R mutation, and 1 patient with the G256E mutation. Mild-to-moderate myopathic changes with muscle fiber hypertrophy were present in 16 patients. Notably, CCD was present in 2 adults and 3 children with the L908V mutation who did not have cardiac hypertrophy. In contrast, soleus muscle samples from 5 patients from 4 kindreds in which HCM was not linked to the MYH7 locus showed no myopathy or CCD. Soleus muscle biopsies from 5 control subjects also showed normal histology. This work demonstrates that (i) MYH7-associated HCM is often a disease of striated muscle but with predominant cardiac involvement and (ii) a subset of HCM patients with MYH7 gene missense mutations have CCD.
Controlled release of polypeptides from polyanhydrides.
Authors: Ron E , Turek T , Mathiowitz E , Chasin M , Hageman M , Langer R
Published: May 2006

The effects of both polymer hydrophobicity and addition of stabilizers on the release and integrity of polymer-encapsulated proteins were studied. By using very hydrophobic poly[1,3-bis(p-carboxyhydroxy)hexane anhydride] with sucrose as an excipient, both recombinant bovine somatotropin and zinc insulin were released intact over 3 weeks. The released proteins appeared to maintain their integrity as judged by acidic reverse-phase HPLC, size-exclusion HPLC, radioimmunoassay, and conformation-sensitive immunoassays. Our results also suggest how polymer hydrophobicity can be used to enhance protein stability.
The sizes of the CDR3 hypervariable regions of the murine T-cell receptor beta chains vary as a function of the recombined germ-line segments.
Authors: Pannetier C , Cochet M , Darche S , Casrouge A , Zöller M , Kourilsky P
Published: May 2006

A method using PCR amplification and primer extension with fluorescent oligonucleotides was developed to analyze T-cell repertoires. The sizes of the hypervariable CDR3-like regions of the murine T-cell antigen receptor beta chains were measured for all possible V beta-J beta combinations. This analysis shows that beta chains are distributed into at least 2000 groups, a value that provides a lower limit to their complexity. The CDR3 sizes appear to be dependent on the J beta and especially the V beta segment used and correlates with amino acid sequence motifs in the corresponding CDR1 region. This feature of T-cell receptors is discussed.
Interleukin 1 induces expression of the human immunodeficiency virus alone and in synergy with interleukin 6 in chronically infected U1 cells: inhibition of inductive effects by the interleukin 1 receptor antagonist.
Authors: Poli G , Kinter A L , Fauci A S
Published: May 2006

In the present study we have observed that interleukin (IL) 1 alpha or IL-1 beta directly induced expression of human immunodeficiency virus (HIV) in the latently infected human promonocytic cell line U1. In addition, IL-1 synergized with IL-6, but not with tumor necrosis factor, in the upregulation of virus expression in U1 cells as measured by accumulation of steady-state mRNAs and production of reverse transcriptase activity. The HIV inductive effect of IL-1 was blocked by transforming growth factor beta, anti-IL-1 antibodies, or monoclonal antibodies directed to the type 1, but not to the type 2, cell surface receptor for IL-1; the latter actually caused enhancement of the IL-1-mediated effect. Unlike tumor necrosis factor alpha, IL-1 either alone or in combination with IL-6 did not induce activation of the transcription activating factor NF-kappa B above the constitutive levels of unstimulated U1 cells. Finally, the IL-1 receptor antagonist effectively blocked IL-1-mediated direct and synergistic inductive effects on virus production. Thus, IL-1 may be an important mediator of HIV expression, and blocking of IL-1 expression and/or its effects may have a potential therapeutic role in the inhibition of HIV expression in infected individuals.
Strain-specific and tissue-specific expression of mouse mast cell secretory granule proteases.
Authors: Stevens R L , Friend D S , McNeil H P , Schiller V , Ghildyal N , Austen K F
Published: May 2006

As assessed by RNA blot analyses with gene-specific probes, we report that the perivascular connective tissue mast cells (CTMCs) in the ear and skin of BALB/cJ mice contain abundant levels of the mouse mast cell protease (mMCP) 7 transcript, in addition to those protease transcripts present in their serosal mast cells (SMCs). High levels of the mMCP-7 transcript also were detected in the ears of WBB6F1/J(-)+/+, WCB6F1/J(-)+/+, WB/ReJ(-)+/+, and WC/ReJ(-)+/+ mice. However, the ears of these four strains and the SMCs from the WCB6F1/J(-)+/+ strain but not the BALB/cJ strain also contained high steady-state levels of the mMCP-2 transcript. The mMCP-2, mMCP-4, mMCP-5, mMCP-6, and mMCP-7 transcripts were not detected in the ears of mast-cell-deficient WBB6F1/J-W/Wv and WCB6F1/J-Sl/Sld mice, indicating that mast cells were the source of these protease transcripts in the +/+ animals. When immunohistochemical analyses of serial sections of ear and skin from WBB6F1/J(-)+/+ mice were performed with anti-mMCP-2 IgG and anti-mMCP-5 IgG, the perivascular CTMCs in these tissues were found to express both mMCP-2 and mMCP-5 in their granules. The prominent expression of mMCP-7 in constitutive perivascular CTMCs indicates that this mast cell has an extended protease phenotype relative to the SMCs of the same strains. Further, the perivascular CTMCs and SMCs of the +/+ strains differ from those in BALB/cJ mice in their prominent expression of mMCP-2.
Epidermal growth factor-receptor mutant lacking the autophosphorylation sites induces phosphorylation of Shc protein and Shc-Grb2/ASH association and retains mitogenic activity.
Authors: Gotoh N , Tojo A , Muroya K , Hashimoto Y , Hattori S , Nakamura S , Takenawa T , Yazaki Y , Shibuya M
Published: May 2006

Epidermal growth factor (EGF) receptor (EGFR) can induce cell growth and transformation in a ligand-dependent manner. To examine whether the autophosphorylation of EGFR correlates with the capacity of the activated EGFR to induce cell growth and transformation, we truncated the human EGFR just after residue 1011, removing all three major autophosphorylation sites (DEL1011). Further, a point mutation was introduced at another autophosphorylation site, Tyr-992-->Phe (DEL1011+F992). The wild-type and mutant receptors were stably expressed in a NIH 3T3 variant cell line that expresses an extremely low level of endogenous EGFR and does not grow with EGF. As expected, DEL1011 and DEL1011+F992 were found to be severely impaired in EGF-induced autophosphorylation, due to the deletion of the appropriate target tyrosines. However, mutant receptors still could induce EGF-dependent DNA synthesis, morphological transformation, and anchorage-independent growth, although the extent of these was significantly reduced when compared with wild-type EGFR. EGF-induced tyrosine phosphorylation of Ras-GTPase activating protein-associated protein p62 and phospholipase C gamma 1 was dramatically reduced in the cells expressing DEL1011 and DEL1011+F992. On the other hand, tyrosine phosphorylation of Shc, complex formation of Shc-Grb2/Ash, and activation of microtubule-associated protein kinase were still fully induced upon EGF stimulation without binding of Shc or Grb2/Ash to the mutant receptor. Thus, tyrosine phosphorylation of Shc may play a crucial role for activating Ras and generating mitotic signals by the activated EGFR mutant.
A glutamine-rich hydrophobic patch in transcription factor Sp1 contacts the dTAFII110 component of the Drosophila TFIID complex and mediates transcriptional activation.
Authors: Gill G , Pascal E , Tseng Z H , Tjian R
Published: May 2006

Activation of transcription by the promoter-specific factor Sp1 requires coactivators that are tightly associated with the TATA-box-binding protein (TBP) in the TFIID complex. Recent work has shown that the two glutamine-rich activation domains of Sp1, A and B, can interact with at least one component of this complex, the TBP-associated factor dTAFII110. Here we report the mapping of a region of Sp1 with alternating glutamine and hydrophobic residues which is required for the interaction with dTAFII110 and is important for mediating transcriptional activation. Substitution of bulky hydrophobic residues within this region decreased both interaction with dTAFII110 and transcriptional activation in Drosophila cells. In contrast, mutation of glutamine residues in this region had no effect. Thus, the strength of the Sp1-TAF interaction correlates with the potency of Sp1 as a transcriptional activator, indicating that this activator-TAF interaction is an important part of the mechanism of transcriptional activation. Sequence comparison of three activation domains shown to bind dTAFII110 suggests that different activators that utilize dTAFII110 as a coactivator may share common sequence features that we have determined to be important for the Sp1-dTAFII110 interaction.
Crystal structure of peanut lectin, a protein with an unusual quaternary structure.
Authors: Banerjee R , Mande S C , Ganesh V , Das K , Dhanaraj V , Mahanta S K , Suguna K , Surolia A , Vijayan M
Published: May 2006

The x-ray crystal structure of the tetrameric T-antigen-binding lectin from peanut, M(r) 110,000, has been determined by using the multiple isomorphous replacement method and refined to an R value of 0.218 for 22,155 reflections within the 10- to 2.95-A resolution range. Each subunit has essentially the same characteristic tertiary fold that is found in other legume lectins. The structure, however, exhibits an unusual quaternary arrangement of subunits. Unlike other well-characterized tetrameric proteins with identical subunits, peanut lectin has neither 222 (D2) nor fourfold (C4) symmetry. A noncrystallographic twofold axis relates two halves of the molecule. The two monomers in each half are related by a local twofold axis. The mutual disposition of the axes is such that they do not lead to a closed point group. Furthermore, the structure of peanut lectin demonstrates that differences in subunit arrangement in legume lectins could be due to factors intrinsic to the protein molecule and, contrary to earlier suggestions, are not necessarily caused by interactions involving covalently linked sugar. The structure provides a useful framework for exploring the structural basis and the functional implications of the variability in the subunit arrangement in legume lectins despite all of them having nearly the same subunit structure, and also for investigating the general problem of "open" quaternary assembly in oligomeric proteins.
The lung amiloride-sensitive Na+ channel: biophysical properties, pharmacology, ontogenesis, and molecular cloning.
Authors: Voilley N , Lingueglia E , Champigny G , Mattéi M G , Waldmann R , Lazdunski M , Barbry P
Published: May 2006

Water balance in the lung is controlled via active Na+ and Cl- transport. Electrophysiological measurements on lung epithelial cells demonstrated the presence of a Na+ channel that is inhibited by amiloride (K0.5 = 90 nM) and some of its derivatives such as phenamil (K0.5 = 19 nM) and benzamil (K0.5 = 14 nM) but not by ethylisopropylamiloride. An amiloride-sensitive Na+ channel of 4 pS was recorded from outside-out patches excised from the apical membrane. This channel is highly selective for Na+ (PNa+/PK+ > or = to 10). Isolation of a human lung cDNA led to the primary structure of the lung Na+ channel. The corresponding protein is 669 residues long and has two large hydrophobic domains. An amiloride-sensitive Na(+)-selective current apparently identical to the one observed in lung epithelial cells was recorded after expression of the cloned channel in oocytes. The level of the mRNA for the Na+ channel was highly increased from fetal to newborn and adult stages. This observation indicates that the increased Na+ reabsorption that occurs at birth as a necessary event to pass to an air-breathing environment is probably associated with control of transcription of this Na+ channel. The human gene for the lung Na+ channel was mapped on chromosome 12p13.
A granulocyte inhibitory protein overexpressed in chronic renal disease regulates expression of interleukin 6 and interleukin 8.
Authors: Ziesche R , Roth M , Papakonstantinou E , Nauck M , Hörl W H , Kashgarian M , Block L H
Published: May 2006

Growing evidence suggests that cytokine expression is influenced by locally produced mediators, thus modifying the pluripotential effects of cytokines toward a tissue-specific inflammatory reaction. The granulocyte inhibitory protein (GIP), a 23-kDa protein found to be significantly overexpressed in patients with chronic renal failure, increases autocrine transcription and expression of interleukin (IL) 6 and IL-8 in human mesangial cells. Moreover, GIP alone induced the transcription of c-jun mRNA; however, in combination with IL-6, it stimulated de novo synthesis of DNA and the transcription of both c-jun and c-fos genes. The data suggest that the overall effect of GIP results in the modulation of the glomerular response to injury and contributes to the progression of glomerulosclerosis.
Direct observation of better hydration at the N terminus of an alpha-helix with glycine rather than alanine as the N-cap residue.
Authors: Harpaz Y , Elmasry N , Fersht A R , Henrick K
Published: May 2006

The structural basis for the stability of N termini of helices has been analyzed by thermodynamic and crystallographic studies of three suitably engineered mutants of the barley chymotrypsin inhibitor 2 with Ser, Gly, or Ala at the N-cap position (residue 31). Each mutant has a well-organized shell of hydration of the terminal NH groups of the helix. The three structures are virtually superimposable (rms separations for all atoms, including the common water molecules, are 0.15-0.17 A) and show neither changes in conformation at the site of substitution nor changes in the crystal packing. The only changes on going from Ser-31 to Ala-31 to Gly-31 are in the position of a water molecule (Wat-116). This is bound to the Ser-O gamma atom in the Ser-31 structure but is in a weak hydrogen bonding position with the NH of residue 34 (O ... N = 3.28 A) in the Ala-31 mutant, partly replacing the strong Ser-31-O gamma ... N34 hydrogen bond (O ... N = 2.65 A). The corresponding water molecule completely replaces the Ser hydroxyl hydrogen bond to N34 on mutation to Gly (2.74 A). The only other change between the three structures is an additional water molecule in the Ala-31 structure (Wat-150) that partly compensates for the weak Wat-116 ... N34 hydrogen bond. Perturbation of solvation by the side chain of Ala is consistent with earlier hypotheses on the importance of exposure of the termini of helices to the aqueous solvent.
Role of septal vasopressin innervation in paternal behavior in prairie voles (Microtus ochrogaster).
Authors: Wang Z , Ferris C F , De Vries G J
Published: May 2006

After being paired with females, male prairie voles show major changes in their social behaviors among which is an increase in paternal responsiveness. These changes are accompanied by fluctuations in the density of the [Arg8]vasopressin-immunoreactive (AVP-ir) fibers in the lateral septum, suggesting that septal AVP might be involved in these changes. To explore a possible involvement of septal AVP in paternal responsiveness, we tested whether injections of saline, AVP, or the V1a receptor antagonist [1-(beta-mercapto-beta, beta-cyclopentamethylenepropionic acid),2-(O-methyltyrosine]AVP [d(CH2)5Tyr(Me)AVP] into the lateral septum influenced the four most prominent paternal activities displayed by male prairie voles; grooming, crouching over, contacting, and retrieving pups. In a first experiment, sexually inexperienced males received a single injection of AVP, saline, or d(CH2)5Tyr(Me)AVP in the lateral septum, after which their paternal responsiveness was recorded during a 10-min period. AVP-injected animals spent more time contacting and crouching over pups, while d(CH2)5Tyr(Me)AVP-injected animals spent less time grooming pups than saline-injected animals. In a follow-up study, one group of animals received an injection of AVP preceded by an injection of saline or d(CH2)5Tyr(Me)-AVP into the lateral septum. A second group of animals received an injection of saline preceded by an injection of saline or d(CH2)5Tyr(Me)AVP into the lateral septum. In both groups, animals spent less time grooming, crouching over, and contacting pups if they had first been injected with d(CH2)5Tyr(Me)AVP. Control experiments suggested that the effects of AVP on paternal responsiveness were dose- and site-specific. These data suggest that septal AVP enhances paternal responsiveness by a V1a receptor-mediated mechanism.
Cloning of the cellular receptor for amphotropic murine retroviruses reveals homology to that for gibbon ape leukemia virus.
Authors: Miller D G , Edwards R H , Miller A D
Published: May 2006

The host and tissue specificity of retrovirus infection is largely determined by specific cellular receptors that mediate virus entry. Genes encoding these receptors are widely distributed in the genome, and the receptors identified to date show no sequence similarity. We have identified the cellular receptor for amphotropic murine retroviruses, Ram-1, by screening a rat cDNA expression library introduced into amphotropic virus-resistant hamster cells. The 656-amino acid receptor is homologous to the gibbon ape leukemia virus receptor at both hydrophobic termini but is highly divergent in the central hydrophilic region. Both receptors appear to be integral membrane proteins having multiple membrane-spanning regions. Identification of this family of receptors will help define the evolutionary relationship between retroviruses and their cellular receptors.
How frequent are correlated changes in families of protein sequences?
Authors: Neher E
Published: May 2006

A loss-of-function point mutation in a protein is often rescued by an additional mutation that compensates for the original physical change. According to one hypothesis, such compensation would be most effective in maintaining a structural motif if the two mutated residues were spatial neighbors. If this hypothesis were correct, one would expect that many such compensatory mutations have occurred during evolution and that present-day protein families show some degree of correlation in the occurrence of amino acid residues at positions whose side chains are in contact. Here, a statistical theory is presented which allows evaluation of correlations in a family of aligned protein sequences by assigning a scalar metric (such as charge or side-chain volume) to each type of amino acid and calculating correlation coefficients of these quantities at different positions. For the family of myoglobins it is found that there is a high correlation between fluctuations in neighboring charges. The correlation is close to what would be expected for total conservation of local charge. For the metric side-chain volume, on the other hand, no correlation could be found.
Reversal of resistance to Bacillus thuringiensis in Plutella xylostella.
Authors: Tabashnik B E , Finson N , Groeters F R , Moar W J , Johnson M W , Luo K , Adang M J
Published: May 2006

Continued success of the most widely used biopesticide, Bacillus thuringiensis, is threatened by development of resistance in pests. Experiments with Plutella xylostella (diamondback moth), the first insect with field populations resistant to B. thuringiensis, revealed factors that promote reversal of resistance. In strains of P. xylostella with 25- to 2800-fold resistance to B. thuringiensis compared with unselected strains, reversal of resistance occurred when exposure to B. thuringiensis was stopped for many generations. Reversal of resistance was associated with restoration of binding of B. thuringiensis toxin CryIA(c) to brush-border membrane vesicles and with increased biotic fitness. Compared with susceptible colonies, revertant colonies had a higher proportion of extremely resistant individuals. Revertant colonies responded rapidly to reselection for resistance. Understanding reversal of resistance will help to design strategies for extending the usefulness of this environmentally benign insecticide.
Hepatocyte growth factor prevents acute renal failure and accelerates renal regeneration in mice.
Authors: Kawaida K , Matsumoto K , Shimazu H , Nakamura T
Published: May 2006

Although acute renal failure is encountered with administration of nephrotoxic drugs, ischemia, or unilateral nephrectomy, there has been no effective drug which can be used in case of acute renal failure. Hepatocyte growth factor (HGF) is a potent hepatotropic factor for liver regeneration and is known to have mitogenic, motogenic, and morphogenic activities for various epithelial cells, including renal tubular cells. Intravenous injection of recombinant human HGF into mice remarkably suppressed increases in blood urea nitrogen and serum creatinine caused by administration of cisplatin, a widely used antitumor drug, or HgCl2, thereby indicating that HGF strongly prevented the onset of acute renal dysfunction. Moreover, exogenous HGF stimulated DNA synthesis of renal tubular cells after renal injuries caused by HgCl2 administration and unilateral nephrectomy and induced reconstruction of the normal renal tissue structure in vivo. Taken together with our previous finding that expression of HGF was rapidly induced after renal injuries, these results allow us to conclude that HGF may be the long-sought renotropic factor for renal regeneration and may prove to be effective treatment for patients with renal dysfunction, especially that caused by cisplatin.
The sporulation-specific enzymes encoded by the DIT1 and DIT2 genes catalyze a two-step reaction leading to a soluble LL-dityrosine-containing precursor of the yeast spore wall.
Authors: Briza P , Eckerstorfer M , Breitenbach M
Published: May 2006

Dityrosine is a sporulation-specific component of the yeast ascospore wall that is essential for the resistance of the spores to adverse environmental conditions. Dityrosine in vivo exists in both the LL and DL configurations and is part of an insoluble macromolecule of unknown structure. Here we present data indicating that dityrosine of the yeast spore wall is biosynthesized by a different mechanism than dityrosine in other biological systems--e.g., the hard fertilization membrane of the sea urchin egg. We identified two soluble, low molecular weight LL-dityrosine-containing spore wall precursors in extracts of sporulating cells and one precursor containing L-tyrosine. By expression of the previously described sporulation-specific genes DIT1 and DIT2 in vegetative cells, it was shown that DIT1 catalyzes the reaction leading from L-tyrosine to the tyrosine-containing precursor. DIT2, which is a member of the cytochrome P450 superfamily, is responsible for the dimerization reaction leading to the dityrosine-containing precursors. Epimerization of LL- to DL-dityrosine is one of the latest steps in spore wall formation and takes place after the dityrosine-containing precursors are incorporated into the spore wall. On the basis of these findings we suggest a biosynthetic pathway for the top layer of the yeast spore wall.
Spontaneous generation of a biradical species of neocarzinostatin chromophore: role in DNA bulge-specific cleavage.
Authors: Hensens O D , Chin D H , Stassinopoulos A , Zink D L , Kappen L S , Goldberg I H
Published: May 2006

Detailed structure determination of the major and minor base-catalyzed degradation products of the chromophore of the enediyne anticancer antibiotic neocarzinostatin in the absence of DNA demonstrates that the enolate Michael addition reaction leading to a spirolactone cumulene intermediate is a spontaneous, stereoselective process. The implications of these findings for the mechanism of the thiol-independent, site-specific cleavage by the so-generated radical species of the drug at a DNA bulge are described.
Identification of Drosophila cytoskeletal proteins by induction of abnormal cell shape in fission yeast.
Authors: Edwards K A , Montague R A , Shepard S , Edgar B A , Erikson R L , Kiehart D P
Published: May 2006

To clone metazoan genes encoding regulators of cell shape, we have developed a functional assay for proteins that affect the morphology of a simple organism, the fission yeast Schizosaccharomyces pombe. A Drosophila melanogaster cDNA library was constructed in an inducible expression vector and transformed into S. pombe. When expression of the Drosophila sequences was induced, aberrant cell shapes were found in 0.2% of the transformed colonies. Four severe phenotypes representing defects in cytokinesis and/or cell shape maintenance were examined further. Each displayed drastic and specific reorganizations of the actin cytoskeleton. Three of the cDNAs responsible for these defects appear to encode cytoskeletal components: the actin binding proteins profilin and cofilin/actin depolymerizing factor and a membrane-cytoskeleton linker of the ezrin/merlin family. These results demonstrate that a yeast phenotypic screen efficiently identifies conserved genes from more complex organisms and sheds light on their potential in vivo functions.