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1.
Quantitative φ-dihedral angle determinations of non-glycine and non-proline residues in Desulfovibrio vulgaris flavodoxin are carried out on the exclusive basis of 3 J coupling constants. In total 124 3 JHNH α , 123 3 JHNC ′i , 118 3 JHNC β , 117 3 JC′ i–1Hα , 109 3 JC′ i–1C′i , and 103 3 JC′ i–1Hβ values form the experimental basis for translating J coupling data into geometry information using various combinations of Karplus parameters given in the literature. In addition, each backbone torsional angle φ is adjusted assuming different models of local geometry, either a rigid torsion, a Gaussian distribution centered at a distinct angle, or a two-site jump model. Numerical optimization is followed by a statistical significance evaluation to assess the results. It is found that experimental coupling constants of most of the residues involved in secondary structure elements agree best with those predicted from rigid local conformations. For dihedral angles in loop regions, mobility effects are not negligible, and a single torsion (Glu 42) is likely to adopt two distinct adjustments. However, α-helix conformations with –60° < φ < –45° give rise to an alternate solution with φ≈+170° with similar statistical significance when using the four traditionally determined proton-involved 3 J couplings. This ambiguity is efficiently avoided only when taking advantage of the complete data set comprising six available experimental 3 J coupling constants and of the degeneracy intrinsic to the Karplus relation. The optimized φ conformations are compared with reference values from the crystal structure of flavodoxin.  相似文献   

2.
Measurement of isotope ratios in 1α,2α,3β-trihydroxy-p-menthane, which has been biosynthesized in Fusicoccum amygdali from 3H- and 14C-labelled mevalonate and in its degradation product diosphenol indicates that: (a) four tritium atoms arising from [5-3H2, 2-14C]MVA are retained, one more than suggested from the hydroxylation pattern, (b) menth-2-ene-1-ol is generated from an α-terpinyl cation through a 1,3-hydride shift and (c) trans-cleavage of an α-epoxide by hydrolysis gives 1α,2α,3β-trihydroxy-p-menthane.  相似文献   

3.
4.
IS2-IS2 and IS3-IS3 relative recombination frequencies in F integration   总被引:5,自引:0,他引:5  
The relative integrative recombination frequencies of the F plasmid IS2 and IS3 elements were determined at two Escherichia coli K-12 chromosomal sites by hybridization analysis of Hfr DNA. The sequence organizations of the independent Hfr strains formed by F integration atα3β3 indicate that the relative recombinational frequencies at the two F plasmid IS3 elementsα1β1 and α2β2 are not significantly different. A comparison of the relative recombinational frequencies of the IS2 and IS3 elements of F was provided by analysis of DNA from Hfr strains having F integrated betweenlacandproC (i.e., at the IS2 or at the IS3 element (α5β5) located in this region). No instances of F integration atα5β5 were detected, indicating that integrative recombination at IS2 is significantly more frequent than at IS3 in this chromosomal region.  相似文献   

5.
Recent publications defined requirements for inter-subunit contacts in a benzodiazepine-sensitive GABAA receptor (GABAARα1β3γ2). There is strong evidence that the heteropentameric receptor contains two α1, two β3, and one γ2 subunit. However, the available data do not distinguish two possibilities: When viewed clockwise from an extracellular viewpoint the subunits could be arranged in either γ2β3α1β3α1 or γ2α1β3α1β3 configurations. Here we use molecular modeling to thread the relevant GABAAR subunit sequences onto a template of homopentameric subunits in the crystal structure of the acetylcholine binding protein (AChBP). The GABAA sequences are known to have 15-18% identity with the acetylcholine binding protein and nearly all residues that are conserved within the nAChR family are present in AChBP. The correctly aligned GABAA sequences were threaded onto the AChBP template in the γ2β3α1β3α1 or γ2α1β3α1β3  arrangements. Only the γ2α1β3α1β3 arrangement satisfied three known criteria: (1) α1 His102 binds at the γ2 subunit interface in proximity to γ2 residues Thr142, Phe77, and Met130; (2) α1 residues 80-100 bind near γ2 residues 91-104; and (3) α1 residues 58-67 bind near the β3 subunit interface. In addition to predicting the most likely inter-subunit arrangement, the model predicts which residues form the GABA and benzodiazepine binding sites.  相似文献   

6.
7.
Four flavonol glycosides isolated from non-flowering leafy shoots of Iberis saxatilis (Brassicaceae) were characterised by spectroscopic and chemical methods as saxatilisins A–D, the 3-O-β-d-glucopyranosyl-(1  3)-α-l-rhamnopyranosyl-(1  2)[β-d-glucopyranosyl-(1  2)-α-l-rhamnopyranosyl-(1  6)]-β-d-glucopyranoside, 3-O-β-d-glucopyranosyl-(1  3)-α-l-rhamnopyranosyl-(1  2)[α-l-rhamnopyranosyl-(1  6)]-β-d-glucopyranoside, 3-O-(6-O-E-sinapoyl)-β-d-glucopyranosyl-(1  3)-α-l-rhamnopyranosyl-(1  2)[β-d-glucopyranosyl-(1  2)-α-l-rhamnopyranosyl-(1  6)]-β-d-glucopyranoside, and 3-O-(6-O-E-feruloyl)-β-d-glucopyranosyl-(1  3)-α-l-rhamnopyranosyl-(1  2)[β-d-glucopyranosyl-(1  2)-α-l-rhamnopyranosyl-(1  6)]-β-d-glucopyranoside of isorhamnetin (3,5,7,4′-tetrahydroxy-3′-methoxyflavone), respectively. Analysis of 2JHC correlations detected with the H2BC (heteronuclear two-bond correlation) pulse sequence aided the unambiguous assignment of glycosidic resonances in the 1H and 13C NMR spectra of these compounds. Saxatilisins A, C, and D, are the first flavonol glycosides to be described with a pentasaccharide chain at a single glycosylation site. Several pentaglycosides of kaempferol and quercetin, tentatively assigned as saxatilisin analogues from LC–MS/MS analyses, were present as minor constituents of the extracts.  相似文献   

8.
In this study thirty-three novel indole derivatives were designed and synthesized based on the structure of deformylflustrabromine B (1), a metabolite isolated from the marine bryozoan Flustra foliacea L. The syntheses were carried out using standard methodologies and in good yields. The molecules were tested for their affinities for the α4β21, α3β41, α71 and (α1)2β1γδ nicotinic acetylcholine receptor (nAChR) subtypes. Binding assays showed that, among these ligands, compound 7c exhibited the highest affinity with Ki = 136.1, 93.9 and 862.4 nM for the α4β21, α3β41, and α71 nAChRs subtypes, respectively. These results indicated that the indole core might be a useful scaffold for the development of new potent and selective nAChR ligands.  相似文献   

9.
A novel polyhydroxylated C29-sterol, 25ξ-methyl-22-homo-5α-cholest-7,22-diene-3β,6β,9α-triol, designated globosterol (1), together with one known tetrahydroxylated ergosterol (22E, 24R)-ergosta-7,22-diene-3β,5α,6β,9α-tetraol (2) has been isolated from the cultures of an endophytic fungus, Chaetomium globosum ZY-22 originated from the plant Ginkgo biloba. The structures and relative configurations of 1 and 2 were established on the basis of extensive spectroscopic analyses including 1D and 2D NMR (1H-1H COSY, HSQC, HMBC, and NOESY) experiments and comparison with the literature. Globosterol (1) possesses an unprecedented 25-methyl Δ22-C10-side chain and Δ7-3β,6β,9α-hydroxy-steroid nucleus, which represents the first example for C29-steroids of the group.  相似文献   

10.
Channel functions of the neuronal α4β2 nicotinic acetylcholine receptor (nAChR), one of the most widely expressed subtypes in the brain, can be inhibited by volatile anesthetics. Our Na+ flux experiments confirmed that the second transmembrane domains (TM2) of α4 and β2 in 2:3 stoichiometry, (α4)2(β2)3, could form pentameric channels, whereas the α4 TM2 alone could not. The structure, topology, and dynamics of the α4 TM2 and (α4)2(β2)3 TM2 in magnetically aligned phospholipid bicelles were investigated using solid-state NMR spectroscopy in the absence and presence of halothane and isoflurane, two clinically used volatile anesthetics. 2H NMR demonstrated that anesthetics increased lipid conformational heterogeneity. Such anesthetic effects on lipids became more profound in the presence of transmembrane proteins. PISEMA experiments on the selectively 15N-labeled α4 TM2 showed that the TM2 formed transmembrane helices with tilt angles of 12° ± 1° and 16° ± 1° relative to the bicelle normal for the α4 and (α4)2(β2)3 samples, respectively. Anesthetics changed the tilt angle of the α4 TM2 from 12° ± 1° to 14° ± 1°, but had only a subtle effect on the tilt angle of the (α4)2(β2)3 TM2. A small degree of wobbling motion of the helix axis occurred in the (α4)2(β2)3 TM2. In addition, a subset of the (α4)2(β2)3 TM2 exhibited counterclockwise rotational motion around the helix axis on a time scale slower than 10- 4 s in the presence of anesthetics. Both helical tilting and rotational motions have been identified computationally as critical elements for ion channel functions. This study suggested that anesthetics could alter these motions to modulate channel functions.  相似文献   

11.
An extension to HN(CO-α/β-N,Cα-J)-TROSY (Permi and Annila in J Biomol NMR 16:221–227, 2000) is proposed that permits the simultaneous determination of the four coupling constants 1 J N′(i)Cα(i), 2 J HN(i)Cα(i), 2 J Cα(i−1)N′(i), and 3 J Cα(i−1)HN(i) in 15N,13C-labeled proteins. Contrasting the original scheme, in which two separate subspectra exhibit the 2 J CαN′ coupling as inphase and antiphase splitting (IPAP), we here record four subspectra that exhibit all combinations of inphase and antiphase splittings possible with respect to both 2 J CαN′ and 1 J N′Cα (DIPAP). Complementary sign patterns in the different spectrum constituents overdetermine the coupling constants which can thus be extracted at higher accuracy than is possible with the original experiment. Fully exploiting data redundance, simultaneous 2D lineshape fitting of the E.COSY multiplet tilts in all four subspectra provides all coupling constants at ultimate precision. Cross-correlation and differential-relaxation effects were taken into account in the evaluation procedure. By applying a four-point Fourier transform, the set of spectra is reversibly interconverted between DIPAP and spin-state representations. Methods are exemplified using proteins of various size.  相似文献   

12.
M. T. Cung  M. Marraud 《Biopolymers》1982,21(5):953-967
We use the nmr data concerning the CαH? CβH fragment in eight peptides with rigid side chains to parametrize a Karplus correlation between the vicinal proton Jαβ coupling constant and the dihedral angle θ. When considering molecules containing the fragment CαHα? CβHβHβ′, the three-dimensional structure of the model peptides does not need to be known with accurate precision, since each set of Jαβ and Jαβ′ coupling constants is then related to the coefficients of the Karplus equation. A good correlation is observed with the Karplus equation, which is in substantial agreement with the Jαβ coupling constants reported for rigid as well as rotating Cα? Cβ bonds in peptides.  相似文献   

13.
Oversaturated deoxy-α2β2T4V aggregated instantly without a delay time, which is in contrast to the delay time before the generation of fibers of deoxy-HbS and deoxy-α2β2E6V,D73H. Solubility of deoxy-α2β2T4V was ∼10-fold lower than that of deoxy-HbS and was similar to oxy- and deoxy-α2β2E6V,T4V. These results indicate that β4Val in HbA in the oxy and deoxy forms with or without β6Val facilitates hydrophobic interaction of the A-helix with the EF helix of adjacent molecules without forming a β4/β73 hydrogen bond. Deoxy-HbA generated crystals following aggregation as does HbC-Harlem(α2β2E6V,D73N), while α2β2T4V and α2β2D73H as well as HbS, α2β2E6V,D73H and α2β2E6V,T4V in the oxy and deoxy forms did not form crystals, indicating in addition to the strength of β6 amino acid hydrophobicity that the synergism between the β4Thr hydrogen bond and β6 hydrophobic interaction free energies on the A-helix play a critical role in formation of fibers versus crystalline nuclei during phase transition.  相似文献   

14.
The specificity of the sialidase activity present in rat kidney cortex (12 000 × g pellet) was studied with various tritiated oligosaccharidic substrates: (i) αNeuAc2 → 3βGall → 4Glc-itol[3H], αNeuAc2 → 6βGall → 4Glc-itol[3H] and αNeuAc2 → 8αNeuAc2 → 3βGall → 4Glc-itol[3H] from bovine colostrum; (ii) α-NeuAc2 → 6βGall → 4βGlcNAc-itol[3H], αNeuAc2 → 3βGal1 → 4βGlcNAcl → 2αManl → 3βMan1 → 4GlcNAc-itol[3H]. αNeuAc2 → 6βGall → 4βGlcNAcl → 2αManl α 3(βGall → 4GlcNAcl → 2αManl → 6)βManl → 4GlcNAc-itol [3H]et αNeuAc2 → 6βGall → 4βGlcNAcl → 2αManl-3(αNeuAc2 → 6βGall → 4βGlcNAcl → 2αManl → 6)βManl 4GlNAc-itol[3H] isolated from the urine of a patient with mucolipidosis I. The enzyme cleaves α2 → 3 and α2 → 8 linkages at a greater rate than the α2 → 6 bonds. Its activity decreases with the length of the oligosaccharidic chain. Substitution of a glucose moiety by Nacetylglucosamine results in diminished activity. The specificity of rat kidney sialidase differs from that reported for other mammalian of viral sialidases.  相似文献   

15.
Dβ (or D-iso)- and Lβ- (or iso)- aspartyl (Asp) residues are accumulated in aged lens crystallins and amyloid beta (Aβ) proteins, respectively, as a result of spontaneous, nonenzymatic isomerization of normal Lα-Asp. To explore why such uncommon Asp isomers are accumulated, the stability of Lα-, Lβ-, and Dβ-Asp was compared in view of the staggered side-chain conformers. By using cylindrin (KVKVLGD7VIEV) from αB-crystallin and Aβ17-25 (L17VFF20AED23)VG25) containing Asp isomers, the vicinal spin-spin coupling constants of Asp Hα-Hβ1 and Hα-Hβ2 were quantified by high-resolution solution 1H NMR. It was found that the trans conformer was extremely preferred in Dβ-Asp7 side-chain of cylindrin. In Aβ17–25, the side chain of Lβ-Asp23 was likely to adopt trans conformer, while gauche conformers were rather rich in Lα-Asp23. In gauche conformers, the close distance between Asp carboxylate carbon (CCOO-) and backbone nitrogen (N) next to Asp is advantageous to the intramolecular cyclization to form succinimide intermediate, followed by the conversion from α- to β-Asp. The cyclization is limited in the trans conformer because of the long distance between CCOO- and N, to keep Dβ- or Lβ-Asp stable. This would be the reason for the site specificity of Asp isomerization in proteins. The higher population of trans conformer in Asp side chain, the less isomerization of Asp as shown as Asp76 in αA-crystallin. The stability and less reactivity of normal Asp and its isomers are the potential factors to determine whether or not the abnormal accumulation is permitted in aged crystallins and Aβ.  相似文献   

16.
Brine shrimp are primitive crustacean arthropodal model organisms, second to daphnia, which can survive in high-salinity environments. Their oviposited cysts, cuticle-covered diapausing eggs, are highly resistant to dryness. To elucidate specialties of brine shrimp, this study characterized glycosphingolipids, which are signal transduction-associated material. A group of novel and complex fucosyl glycosphingolipids were separated and identified from cysts of the brine shrimp Artemia franciscana by repeated lipid extraction, alkaline methanolysis, acid treatment, successive column chromatography, and post-source decay measurements by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Structures of the glycosphingolipids were elucidated by conventional structural characterization and mass spectrometry, and the compounds were identified as GlcNAcβ1-3GalNAcβ1-4(GlcNAcα1-2Fucα1-3)GlcNAcβ1-3Manβ1-4Glcβ1-Cer, GalNAcβ1-4(Fucα1-3)GlcNAcβ1-3GalNAcβ1-4(GlcNAcα1-2Fucα1-3)GlcNAcβ1-3Manβ1-4Glcβ1-Cer, and GalNAcβ1-4(GlcNAcα1-2Fucα1-3)GlcNAcβ1-3GalNAcβ1-4(GlcNAcα1-2Fucα1-3)GlcNAcβ1-3Manβ1-4Glcβ1-Cer. These compounds also contained a branching, non-arthro-series disaccharide with an α-GlcNAc terminus, similar to that found in a previously reported ceramide hexasaccharide (III3(GlcNAcα2Fucα)-At4Cer). The glycans within these complex GSLs are longer than reported glycans of the animal kingdom containing α-GlcNAc terminus. These complex GSLs as well as the longest GSL with ten sugar residues, ceramide decasaccharide (CDeS), contain the fucosylated LacdiNAc sequence reported to associate with parasitism/immunosuppression and the α-GlcNAc terminus reported to show a certain antibacterial effect in other reports. CDeS, the longest GSL of this species, was found in the highest amount, which indicates that CDeS may be functionally important.  相似文献   

17.
Nucleic acid duplexes featuring a single alpha-anomeric thymidine inserted into each DNA strand via 3′-3′ and 5′-5′ phosphodiester linkages exhibit local conformational dynamics that are not adequately depicted by conventional restrained molecular dynamics (rMD) methods. We have used molecular dynamics with time-averaged NMR restraints (MDtar) to explore its applicability to describing the conformational dynamics of two α-containing duplexes – d(GCGAAT-3′-3′-αT-5′-5′-CGC)2 and d(ATGG-3′-3′-αT-5′-5′-GCTC)?r(gagcaccau). In contrast to rMD, enforcing NOE-based distance restraints over a period of time in MDtar rather than instantaneously results in better agreement with the experimental NOE and J-data. This conclusion is based on the dramatic decreases in average distance and coupling constant violations (Δd av, J rms, and ΔJ av) and improvements in sixth-root R-factors (R x). In both duplexes, the deoxyribose ring puckering behavior predicted independently by pseudorotation analysis is portrayed remarkably well using this approach compared to rMD. This indicates that the local dynamic behavior is encoded within the NOE data, although this is not obvious from the local R x values. In both systems, the backbone torsion angles comprising the 3′-3′ linkage as well as the (high S-) sugars of the α-nucleotide and preceding residue (α?1) are relatively static, while the conformations of the 5′-5′ linkage and the sugar in the neighboring β-nucleotide (α+1) show enhanced flexibility. To reduce the large ensembles generated by MDtar to more manageable clusters we utilized the PDQPRO program. The resulting PDQPRO clusters (in both cases, 13 structures and associated probabilities extracted from a pool of 300 structures) adequately represent the structural and dynamic characteristics predicted by the experimental data.  相似文献   

18.
High subtype selectivity (α4β2 over α2β3) of neuronal nicotinic acetylcholine receptor (nAChR) agonists is critical for the rational design of less toxic drugs used for the treatment of neurodegenerative and psychiatric diseases. Here, three CoMFA models of pEC50(α4β2), pEC50(α2β3) and p[EC50(α4β2)/EC50(α2β3)] (pEC50(α4β2)pEC50(α2β3)) were developed to study the quantitative structure–activity relationship (QSAR) and quantitative structure–selectivity relationship (QSSR) of the 3,8-diazabicyclo[4.2.0]octane derivatives as nAChRs agonists. The parameters of the three models were 0.584, 0.792, and 0.599 for cross-validated r2 (r2CV), 0.924, 0.935 and 0.875 for conventional r2. Analyses indicated that both the steric and electrostatic factors should be considered in the rational design of more active and selective nAChR agonists.  相似文献   

19.

Background

Foot-and-mouth disease virus (FMDV) initiates infection via recognition of one of at least four cell-surface integrin molecules αvβ1, αvβ3, αvβ6, or αvβ8 by a highly conserved Arg-Gly-Asp (RGD) amino acid sequence motif located in the G-H loop of VP1. Within the animal host, the αvβ6 interaction is believed to be the most relevant. Sub-neutralizing levels of soluble secreted αvβ6 (ssαvβ6) was used as a selective pressure during passages in vitro to explore the plasticity of that interaction.

Results

Genetically stable soluble integrin resistant (SIR) FMDV mutants derived from A24 Cruzeiro were selected after just 3 passages in cell culture in the presence of sub-neutralizing levels of ssαvβ6. SIR mutants were characterized by: replication on selective cell lines, plaque morphology, relative sensitivity to ssαvβ6 neutralization, relative ability to utilize αvβ6 for infection, as well as sequence and structural changes. All SIR mutants maintained an affinity for αvβ6. Some developed the ability to attach to cells expressing heparan sulfate (HS) proteoglycan, while others appear to have developed affinity for a still unknown third receptor. Two classes of SIR mutants were selected that were highly or moderately resistant to neutralization by ssαvβ6. Highly resistant mutants displayed a G145D substitution (RGD to RDD), while moderately resistant viruses exhibited a L150P/R substitution at the conserved RGD + 4 position. VP1 G-H loop homology models for the A-type SIR mutants illustrated potential structural changes within the integrin-binding motif by these 2 groups of mutations. Treatment of O1 Campos with ssαvβ6 resulted in 3 SIR mutants with a positively charged VP3 mutation allowing for HS binding.

Conclusions

These findings illustrate how FMDV particles rapidly gain resistance to soluble receptor prophylactic measures in vitro. Two different serotypes developed distinct capsid mutations to circumvent the presence of sub-neutralizing levels of the soluble cognate receptor, all of which resulted in a modified receptor tropism that expanded the cell types susceptible to FMDV. The identification of some of these adaptive mutations in known FMDV isolates suggests these findings have implications beyond the cell culture system explored in these studies.  相似文献   

20.
Large-conductance Ca2+-activated K+ channel is formed by a tetramer of the pore-forming α-subunit and distinct accessory β-subunits (β1–β4) which contribute to BKCa channel molecular diversity. Accumulative evidences indicate that not only α-subunit alone but also the α + β subunit complex and/or β-subunit might play an important role in modulating various physiological functions in most mammalian cells. To evaluate the detailed pharmacological and biophysical properties of α + β1 subunit complex or β1-subunit in BKCa channel, we established an expression system that reliably coexpress hSloα + β1 subunit complex in HEK293 cells. The coexpression of hSloα + β1 subunit complex was evaluated by western blotting and immunolocalization, and then the single-channel kinetics and pharmacological properties of expressed hSloα + β1 subunit complex were investigated by cell-attached and outside-out patches, respectively. The results in this study showed that the expressed hSloα + β1 subunit complex demonstrated to be fully functional for its typical single-channel traces, Ca2+-sensitivity, voltage-dependency, high conductance (151 ± 7 pS), and its pharmacological activation and inhibition.  相似文献   

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