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111.
6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter 总被引:8,自引:1,他引:7
6S RNA is an abundant noncoding RNA in Escherichia coli that binds to sigma70 RNA polymerase holoenzyme to globally regulate gene expression in response to the shift from exponential growth to stationary phase. We have computationally identified >100 new 6S RNA homologs in diverse eubacterial lineages. Two abundant Bacillus subtilis RNAs of unknown function (BsrA and BsrB) and cyanobacterial 6Sa RNAs are now recognized as 6S homologs. Structural probing of E. coli 6S RNA and a B. subtilis homolog supports a common secondary structure derived from comparative sequence analysis. The conserved features of 6S RNA suggest that it binds RNA polymerase by mimicking the structure of DNA template in an open promoter complex. Interestingly, the two B. subtilis 6S RNAs are discoordinately expressed during growth, and many proteobacterial 6S RNAs could be cotranscribed with downstream homologs of the E. coli ygfA gene encoding a putative methenyltetrahydrofolate synthetase. The prevalence and robust expression of 6S RNAs emphasize their critical role in bacterial adaptation. 相似文献
112.
Ankyrin repeat polypeptides contain repeated structural elements that pack to produce modular architectures lacking in close contacts between distant segments of the polypeptide chain. Despite this lack of sequence-distant contacts, ankyrin repeat polypeptides have been shown to fold in a cooperative manner. To determine the distance over which cooperative interactions can be propagated in a repeat protein, and to investigate the tolerance to internal duplication and deletion of modules, we have constructed a series of ankyrin repeat variants of the Notch ankyrin domain in which repeat number is varied by duplication and deletion of internal repeats. A construct with two copies of the fifth ankyrin repeat shows a modest increase in stability compared to the parent construct and retains apparent two-state unfolding behavior. Although constructs containing three and four copies of the fifth repeat retain this increased resistance to urea, they exhibit broad, multi-state unfolding transitions compared to the parent construct. For the Notch ankyrin domain, these larger constructs may represent a limit beyond which full cooperativity cannot be maintained. Deletions of internal repeats from the Notch ankyrin domain significantly destabilize the domain. This severe destabilization, which is larger than that resulting from end-repeat deletion, may arise from unfavorable interactions within the new non-native interfaces produced by internal repeat deletion. These results demonstrate both an asymmetry between the duplication and deletion of internal repeats, and a difference between deletion of internal and end-repeats, suggesting preferred mechanisms for evolution of repeat proteins. 相似文献
113.
(1) The mean delta18O(BP) ( per thousandSMOW) for any given bone sampled from captive alligators maintained at high constant temperature was lower (indicative of higher temperatures of bone deposition) than that of the same bone from wild alligators caught in Northern Florida, but these differences were only greater than two standard deviations from the mean for the thoracic vertebrae and metatarsal bones. (2) Inter-bone variability of delta18O(BP) ( per thousandSMOW) was similar for captive alligators maintained at constant temperatures and the wild alligators, but intra-bone variability was much greater in wild alligators. (3) The order of mean delta18O(BP) ( per thousandSMOW) of bones (from highest to lowest) differed between treatment groups. However, intra-bone variability obscured the significance of those differences. Nevertheless, the thoracic vertebra had the highest mean delta18O(BP) ( per thousandSMOW), indicative of lower temperatures, and the lowest variability of bones in both groups of alligators. Conversely, the tibia was one of the warmest and more variable bones in both groups of alligators. (4) The pattern of delta18O(BP) ( per thousandSMOW) values across sites within long bones were identical between alligator treatment groups for the femur and humerus but differed between groups for the tibia and metatarsus, and differed between different long bones. The predicted intra-bone pattern for long bones of increasing delta18O(BP) ( per thousandSMOW) indicative of lower temperatures in more distal sampling sites was only obtained from the femurs. (5) Paired cortical and cancellous bone samples from the same site from all individuals in both treatment groups were available for proximal humeri and distal femurs. delta18O(BP) ( per thousandSMOW) values from cortical bone were more variable than those from cancellous bone for both bones. (6) Cortical bone had lower delta18O(BP) ( per thousandSMOW) values indicative of warmer temperatures than cancellous bone at sites sampled on the proximal humeri and distal femurs of all three animals from both treatment groups. 相似文献
114.
Barrick D 《Proteins》2000,39(4):291-308
The trans-substituted histidine to glycine mutant of sperm whale myoglobin (H93G Mb) is used to study energetics of proximal hydrogen bonding, proximal ligand-heme interactions, and coupling to distal ligand binding. Comparison of mono- and dimethylimidazole structural isomers shows that the hydrogen bond between the proximal ligand and the neighboring Ser92 hydroxyl (position F7) is stabilizing. The range of hydrogen bond stabilities measured here for different distal ligand complexes ranges from -0.7 kcal/mol (monomethylimidazole isomers to MbCO) to -4.1 kcal/mol (dimethylimidazole isomers to MbCN). This range of hydrogen bond stabilities, which is similar to that seen in protein mutagenesis unfolding studies, demonstrates the high sensitivity of the hydrogen bond to modest structural perturbations. The degree to which the 2-methyl group destabilizes proximal ligand binding is found to depend inversely on the total electronic spin. For monomethylimidazole proximal ligands, distal ligand binding weakens the proximal hydrogen bond compared to deoxyMb. Surprisingly, this trend is largely reversed for the dimethylimidazole proximal ligands. These results demonstrate strong coupling between the proximal protein matrix and distal ligand binding. These results provide an explanation for the strong avoidance of hydrogen bonding residues at position F7 in hemoglobin sequences. 相似文献
115.
116.
117.
Single-copy nuclear DNAs (scnDNAs) of eight species of arvicoline and six
species of murine rodents were compared using DNA-DNA hybridization. The
branching pattern derived from the DNA comparisons is congruent with the
fossil evidence and supported by comparative biochemical, chromosomal, and
morphological studies. The recently improved fossil record for these
lineages provides seven approximate divergence dates, which were used to
calibrate the DNA-hybridization data. The average rate of scnDNA divergence
was estimated as 2.5%/Myr. This is approximately 10 times the rate in the
hominoid primates. These results agree with previous reports of accelerated
DNA evolution in muroid rodents and extend the DNA-DNA hybridization data
set of Brownell.
相似文献
118.
Carbohydrates have been suggested to account for some IgE cross- reactions
between various plant, insect, and mollusk extracts, while some IgG
antibodies have been successfully raised against plant glycoproteins. A rat
monoclonal antibody raised against elderberry abscission tissue (YZ1/2.23)
and rabbit polyclonal antiserum against horseradish peroxidase were
screened for reactivity in enzyme-linked immunosorbent assay against a
range of plant glycoproteins and extracts as well as neoglycoproteins, bee
venom phospholipase, and several animal glycoproteins. Of the
oligosaccharides tested, Man3XylFucGlcNAc2(MMXF3) derived from horseradish
peroxidase was the most potent inhibitor of the reactivity of both YZ1/2.23
and anti- horseradish peroxidase to native horseradish peroxidase
glycoprotein. The reactivity of YZ1/2. 23 and anti-horseradish peroxidase
against Sophora japonica lectin was most inhibited by a neoglycoconjugate
of bromelain glycopeptide cross-linked to bovine serum albumin, while the
defucosylated form of this conjugate was inactive as an inhibitor. A wide
range of plant extracts was found to react against YZ1/2.23 and
anti-horseradish peroxidase, with particularly high reactivities recorded
for grass pollen and nut extracts. All these reactivities were inhibitable
with the bromelain glycopeptide/bovine serum albumin conjugate. Bee venom
phospholipase and whole bee venom reacted weakly with YZ1/2.23 but more
strongly with anti-horseradish peroxidase in a manner inhibitable with the
bromelain glycopeptide/bovine serum albumin conjugate, while hemocyanin
from Helix pomatia reacted poorly with YZ1/2.23 but did react with
anti-horseradish peroxidase. It is concluded that the alpha1, 3-fucose
residue linked to the chitobiose core of plant glycoproteins is the most
important residue in the epitope recognized by the two antibodies studied,
but that the polyclonal anti-horseradish peroxidase antiserum also contains
antibody populations that recognize the xylose linked to the core mannose
of many plant and gastropod N-linked oligosaccharides.
相似文献
119.
Structural comparison of fibroblast growth factor-specific heparan sulfates derived from a growing or differentiating neuroepithelial cell line 总被引:3,自引:1,他引:2
Brickman YG; Nurcombe V; Ford MD; Gallagher JT; Bartlett PF; Turnbull JE 《Glycobiology》1998,8(5):463-471
Heparan sulfate (HS) glycosaminoglycans are essential modulators of
fibroblast growth factor (FGF) activity both in vivo and in vitro, and
appear to act by cross-linking particular forms of FGF to appropriate FGF
receptors. We have recently isolated and characterized two separate HS
pools derived from immortalized embryonic day 10 mouse neuroepithelial 2.3D
cells: one from cells in log growth phase, which greatly potentiates the
activity of FGF-2, and the other from cells undergoing contact-inhibition
and differentiation, which preferentially activates FGF-1. These two pools
of HS have very similar functional activities to those species isolated
from primary neuroepithelial cells at corresponding stages of active
proliferation or differentiation. We present here a structural comparison
between these cell line HS species to establish the nature of the changes
that occur in the biosynthesis of HS. A combination of chemical and
enzymatic cleavage, low pressure chromatography and strong anion-exchange
HPLC were used to generate full chain models of each species. Overall, the
HS pools synthesized in the dividing cell line pools possessed less complex
sulfation than those derived from more differentiated, growth arrested
cells.
相似文献
120.
MOTIVATION: Recently, we described a Maximum Weighted Matching (MWM) method
for RNA structure prediction. The MWM method is capable of detecting
pseudoknots and other tertiary base-pairing interactions in a
computationally efficient manner (Cary and Stormo, Proceedings of the Third
International Conference on Intelligent Systems for Molecular Biology, pp.
75-80, 1995). Here we report on the results of our efforts to improve the
MWM method's predictive accuracy, and show how the method can be extended
to detect base interactions formerly inaccessible to automated RNA modeling
techniques. RESULTS: Improved performance in MWM structure prediction was
achieved in two ways. First, new ways of calculating base pair likelihoods
have been developed. These allow experimental data and combined statistical
and thermodynamic information to be used by the program. Second, accuracy
was improved by developing techniques for filtering out spurious base pairs
predicted by the MWM program. We also demonstrate here a means by which the
MWM folding method may be used to detect the presence of base triples in
RNAs. AVAILABILITY: http://www.cshl.org/mzhanglab/tabaska/j axpage. html
CONTACT: tabaska@cshl.org
相似文献