The compact conformation of fibronectin is determined by intramolecular ionic interactions.
(9/1497)
Fibronectin exists in a compact or extended conformation, depending upon environmental pH and salt concentration. Using recombinant fragments expressed in bacteria and baculovirus, we determined the domains responsible for producing fibronectin's compact conformation. Our velocity and equilibrium sedimentation data show that FN2-14 (a protein containing FN-III domains 2 through 14) forms dimers in low salt. Experiments with smaller fragments indicates that the compact conformation is produced by binding of FN12-14 of one subunit to FN2-3 of the other subunit in the dimer. The binding is weakened at higher salt concentrations, implying an electrostatic interaction. Furthermore, segment FN7-14+A, which contains the alternatively spliced A domain between FN11 and 12, forms dimers, whereas FN7-14 without A does not. Segment FN12-14+A also forms dimers, but the isolated A domain does not. These data imply an association of domain A with FN12-14, and the presence of A may favor an open conformation by competing with FN2-3 for binding to FN12-14. (+info)
Fluorescence studies of the carboxyl-terminal domain of smooth muscle calponin effects of F-actin and salts.
(10/1497)
The fluorescence parameters of the environment-sensitive acrylodan, selectively attached to Cys273 in the C-terminal domain of smooth muscle calponin, were studied in the presence of F-actin and using varying salt concentrations. The formation of the F-actin acrylodan labeled calponin complex at 75 mm NaCl resulted in a 21-nm blue shift of the maximum emission wavelength from 496 nm to 474 nm and a twofold increase of the fluorescent quantum yield at 460 nm. These spectral changes were observed at the low ionic strengths (< 110 mm) where the calponin : F-actin stoichiometry is 1 : 1 as well as at the high ionic strengths (> 110 mm) where the binding stoichiometry is a 1 : 2 ratio of calponin : actin monomers. On the basis of previous three-dimensional reconstruction and chemical crosslinking of the F-actin-calponin complex, the actin effect is shown to derive from the low ionic strength interaction of calponin with the bottom of subdomain-1 of an upper actin monomer in F-actin and not from its further association with the subdomain-1 of the adjacent lower monomer which occurs at the high ionic strength. Remarkably, the F-actin-dependent fluorescence change of acrylodan is qualitatively but not quantitatively similar to that earlier reported for the complexes of calponin and Ca2+-calmodulin or Ca2+-caltropin. As the three calponin ligands bind to the same segment of the protein, encompassing residues 145-182, the acrylodan can be considered as a sensitive probe of the functioning of this critical region. A distance of 29 A was measured by fluorescence resonance energy transfer between Cys273 of calponin and Cys374 of actin in the 1 : 1 F-actin-calponin complex suggesting that the F-actin effect was allosteric reflecting a global conformational change in the C-terminal domain of calponin. (+info)
Ultraviolet Raman examination of the environmental dependence of bombolitin I and bombolitin III secondary structure.
(11/1497)
Bombolitin I and III (BI and BIII) are small amphiphilic peptides isolated from bumblebee venom. Although they exist in predominately nonhelical conformations in dilute aqueous solutions, we demonstrate, using UV Raman spectroscopy, that they become predominately alpha-helical in solution at pH > 10, in high ionic strength solutions, and in the presence of trifluoroethanol (TFE) and dodecylphosphocholine (DPC) micelles. In this paper, we examine the effects of electrostatic and hydrophobic interactions that control folding of BI and BIII by systematically monitoring their secondary structures as a function of solution conditions. We determine the BI and BIII secondary structure contents by using the quantitative UV Raman methodology of Chi et al. (1998. Biochemistry. 37:2854-2864). Our findings suggest that the alpha-helix turn in BIII at neutral pH is stabilized by a salt bridge between residues Asp2 and Lys5. This initial alpha-helical turn results in different BI and BIII alpha-helical folding mechanisms observed in high pH and high salt concentrations: BIII folds from its single alpha-helix turn close to its N-terminal, whereas the BI alpha-helix probably nucleates within the C-terminal half. We also used quasielastic light scattering to demonstrate that the BI and BIII alpha-helix formation in 0.2 M Ca(ClO4)2 is accompanied by formation of trimers and hexamers, respectively. (+info)
Partial purification of the yeast U2 snRNP reveals a novel yeast pre-mRNA splicing factor required for pre-spliceosome assembly.
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We have partially purified the U2 snRNP of Saccharomyces cerevisiae. Identification of some proteins consistently found in the purified fractions by nanoelectrospray mass spectrometry indicated the presence of a novel splicing factor named Rse1p. The RSE1 gene is essential and codes for a 148.2 kDa protein. We demonstrated that Rse1p associates specifically with U2 snRNA at low salt concentrations. In addition, we showed that Rse1p is a component of the pre-spliceosome. Depletion of Rse1p and analysis of a conditional mutant indicated that Rse1p was required for efficient splicing in vivo. In vitro Rse1p is required for the formation of pre-spliceosomes. Database searches revealed that Rse1p is conserved in humans and that it belongs to a large protein family that includes polyadenylation factors and DNA repair proteins. The characteristics of Rse1p suggest that its human homologue could be a subunit of the SF3 splicing factor. (+info)
Induction of gadd153 mRNA by nutrient deprivation is overcome by glutamine.
(13/1497)
The growth arrest and DNA damage-inducible (gadd) genes are co-ordinately activated by a variety of genotoxic agents and/or growth-cessation signals. The regulation of gadd153 mRNA was investigated in renal proximal tubular epithelial cells (LLC-PK1) cultured in a nutrient- and serum-deprived medium. The addition of glutamine alone to LLC-PK1 cells cultured in Earl's balanced salt solution (EBSS) is sufficient to suppress gadd153 mRNA expression, and the removal of only glutamine from Dulbecco's modified Eagle's medium (DMEM) is also sufficient to induce gadd153 mRNA expression. Consistent with these findings, the inhibition of glutamine utilization with acivicin and 6-diazo-5-oxo-l-norleucine (DON) in cells grown in a glutamine-containing medium effectively induces gadd153 expression. Glutamine can be used as an energy source in cultured mammalian cells. However, it is unlikely that deficits in cellular energy stores (ATP) are coupled to gadd153 mRNA expression, because concentrations of ATP, UTP and GTP are all elevated in EBSS-exposed cells, and the addition of alpha-oxoglutarate to cells grown in EBSS has no effect on gadd153 mRNA expression. In contrast, concentrations of CTP decline substantially in EBSS and glutamine-deprived DMEM-cultured cells. Glutamine also serves as a precursor for the synthesis of protein and DNA. The addition of glutamine to cells grown in EBSS partly restores CTP concentrations. The addition of pyrimidine ribonucleosides (cytidine and uridine) to LLC-PK1 cells also restores CTP concentrations, in a manner commensurate with their relative abilities to overcome gadd153 expression. Finally, glutamine does not completely suppress DNA damage-induced gadd153 expression, suggesting that multiple signalling pathways lead to the expression of gadd153 mRNA under conditions of nutrient deprivation and DNA damage. (+info)
Purification and catalytic properties of human caspase family members.
(14/1497)
Members of the caspase family of cysteine proteases are known to be key mediators of mammalian inflammation and apoptosis. To better understand the catalytic properties of these enzymes, and to facilitate the identification of selective inhibitors, we have systematically purified and biochemically characterized ten homologues of human origin (caspases 1 - 10). The method used for production of most of these enzymes involves folding of active enzymes from their constituent subunits which are expressed separately in E. coli, followed by ion exchange chromatography. In cases where it was not possible to use this method (caspase-6 and -10), the enzymes were instead expressed as soluble proteins in E. coli, and partially purified by ion exchange chromatography. Based on the optimal tetrapeptide recognition motif for each enzyme, substrates with the general structure Ac-XEXD-AMC were used to develop continuous fluorometric assays. In some cases, enzymes with virtually identical tetrapeptide specificities have kcat/Km values for fluorogenic substrates that differ by more than 1000-fold. Using these assays, we have investigated the effects of a variety of environmental factors (e.g. pH, NaCl, Ca2+) on the activities of these enzymes. Some of these variables have a profound effect on the rate of catalysis, a finding that may have important biological implications. (+info)
Effects of salt concentration on analyte response using electrospray ionization mass spectrometry.
(15/1497)
The effect of salt concentration on analyte response using electrospray ionization mass spectrometry (ESI-MS) was measured and compared to that predicted by Enke's equilibrium partitioning model. The model predicts that analyte response will be proportional to concentration and that the response factor will decrease with increasing electrolyte concentration. The measured analyte response is proportional to concentration over four orders of magnitude when the electrolyte concentration is below 10(-3) M, as the model predicts. The concentration of excess charge ([Q]) generated by the ESI process increases significantly at 10(-3) M ionic concentration, but the response factor decreases at this concentration. Changes in shape of the spray that cause a loss of ion transmission efficiency may be the basis for the decrease in response. An increase in the analyte response factor with increasing electrolyte concentration is observed for electrolyte concentrations below 10(-3) M. An explanation for this based on the electrical double layer is proposed. (+info)
Evidence for involvement of gut-associated denitrifying bacteria in emission of nitrous oxide (N(2)O) by earthworms obtained from garden and forest soils.
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Earthworms (Aporrectodea caliginosa, Lumbricus rubellus, and Octolasion lacteum) obtained from nitrous oxide (N(2)O)-emitting garden soils emitted 0.14 to 0.87 nmol of N(2)O h(-1) g (fresh weight)(-1) under in vivo conditions. L. rubellus obtained from N(2)O-emitting forest soil also emitted N(2)O, which confirmed previous observations (G. R. Karsten and H. L. Drake, Appl. Environ. Microbiol. 63:1878-1882, 1997). In contrast, commercially obtained Lumbricus terrestris did not emit N(2)O; however, such worms emitted N(2)O when they were fed (i.e., preincubated in) garden soils. A. caliginosa, L. rubellus, and O. lacteum substantially increased the rates of N(2)O emission of garden soil columns and microcosms. Extrapolation of the data to in situ conditions indicated that N(2)O emission by earthworms accounted for approximately 33% of the N(2)O emitted by garden soils. In vivo emission of N(2)O by earthworms obtained from both garden and forest soils was greatly stimulated when worms were moistened with sterile solutions of nitrate or nitrite; in contrast, ammonium did not stimulate in vivo emission of N(2)O. In the presence of nitrate, acetylene increased the N(2)O emission rates of earthworms; in contrast, in the presence of nitrite, acetylene had little or no effect on emission of N(2)O. In vivo emission of N(2)O decreased by 80% when earthworms were preincubated in soil supplemented with streptomycin and tetracycline. On a fresh weight basis, the rates of N(2)O emission of dissected earthworm gut sections were substantially higher than the rates of N(2)O emission of dissected worms lacking gut sections, indicating that N(2)O production occurred in the gut rather than on the worm surface. In contrast to living earthworms and gut sections that produced N(2)O under oxic conditions (i.e., in the presence of air), fresh casts (feces) from N(2)O-emitting earthworms produced N(2)O only under anoxic conditions. Collectively, these results indicate that gut-associated denitrifying bacteria are responsible for the in vivo emission of N(2)O by earthworms and contribute to the N(2)O that is emitted from certain terrestrial ecosystems. (+info)