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1.
Summary Derivatives of gramicidin S (GS) and its mono- and di-d-cyclohexylalanined-Cha) analogs possessing various protecting groups on Orn side chains were prepared.1H NMR spectra of the unsymmetrically protected analogs [Orn(X)2, Orn(X)2′,d-Cha4]GS were similar to the composites of the spectra of the symmetrical derivatives [Orn(X)2,2′,d-Cha4,4′]GS and [Orn(X)2,2′]Gs, revealing the proximity of the protecting groups of NδH of Orn residues at the 2 and 2 positions to the side chains ofd-Phe (ord-Cha) residues at the 4 and 4 positions, respectively. The results indicated the presence of H-bonds between the N°H of Orn and the carbonyl ofd-Phe residues in the i→i+2 sense and not in i→i-3, which was also supported by the ROESY analysis. The substantially strong H-bonds can explain the observed resistance of the urethane NH of the Orn side chains in the GS derivatives to the N-methylation with CH3I−Ag2O in DMF.  相似文献   

2.
We report the first high-resolution structure for a protein containing a fluorinated side chain. Recently we carried out a systematic evaluation of phenylalanine to pentafluorophenylalanine (Phe --> F(5)-Phe) mutants for the 35-residue chicken villin headpiece subdomain (c-VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe --> F(5)-Phe mutations are interesting because aryl-perfluoroaryl interactions of optimal geometry are intrinsically more favorable than either aryl-aryl or perfluoroaryl-perfluoroaryl interactions, and because perfluoroaryl units are more hydrophobic than are analogous aryl units. Only one mutation, Phe10 --> F(5)-Phe, was found to provide enhanced tertiary structural stability relative to the native core (by approximately 1 kcal/mol, according to guanidinium chloride denaturation studies). The NMR structure of this mutant, described here, reveals very little variation in backbone conformation or side chain packing relative to the wild type. Thus, although Phe --> F(5)-Phe mutations offer the possibility of greater tertiary structural stability from side chain-side chain attraction and/or side chain desolvation, the constraints associated with the native c-VHP fold apparently prevent the modified polypeptide from taking advantage of this possibility. Our findings are important because they complement several studies that have shown that fluorination of saturated side chain carbon atoms can provide enhanced conformational stability.  相似文献   

3.
Summary A series of six tetrapeptides, analogues of AS-I phytotoxin, pathogenic to sunflower, have been synthesized either in solution and/or by solid phase methods and have been tested for phytotoxic activity in various plants and cytotoxic activity in three cancer cell lines. These peptides were identified as model compounds by fast atom bombardment (FAB), plasma desorption (PD), electrospray ionization (ESI) mass spectrometry and by1H,1H-1H,13C and1H-13C NMR. The data presented show that in protected tetrapeptides the molecular ion was easily identified whereas some difficulties appeared with the fully deprotected peptides. NMR spectra are given.  相似文献   

4.
The syntheses of new oxamide derivatives of methyl 2-amino-2-deoxy-alpha-D-glucopyranoside and amino acid or peptide esters are presented. The reaction of methyl 3,4,6-tri-O-acetyl-2-acetamido-2-deoxy-alpha-D-glucopyranoside and oxalyl chloride gave N-(methyl 3,4,6-tri-O-acetyl-2-deoxy-alpha-D-glucopyranosid-2-yl) oxamic acid chloride which on reaction with the ester of Gly, L-Ala, L-Phe, GlyGly, Gly-L-Phe and Gly-L-Ala afforded N-(methyl 3,4,6-tri-O-acetyl-2-deoxy-alpha-D-glucopyranosid-2-yl), N'-oxalyl-amino acid or dipeptide esters. The structure of the oxamides was studied using 1H, 13C NMR in solution and solid state.  相似文献   

5.
Artifacts associated with the measurement of methyl 1H single quantum CPMG-based relaxation dispersion profiles are described. These artifacts arise due to the combination of cross-correlated spin relaxation effects involving intra-methyl 1H–1H dipolar interactions and imperfections in 1H refocusing pulses that are applied during CPMG intervals that quantify the effects of chemical exchange on measured transverse relaxation rates. As a result substantial errors in extracted exchange parameters can be obtained. A simple work-around is presented where the 1H chemical shift difference between the exchanging states is extracted from a combination of 13C single quantum and 13C–1H multiple quantum dispersion profiles. The approach is demonstrated with an application to a folding/unfolding reaction involving a G48M mutant Fyn SH3 domain.  相似文献   

6.
Coxon B 《Carbohydrate research》2005,340(10):1714-1721
Complete 1H and 13C NMR chemical shift assignments have been generated from a series of acetamidodeoxy and aminodeoxy sugar derivatives. For free sugars, the enhanced sensitivity of an NMR cryoprobe allowed simple 1D and 2D NMR spectra to be obtained from essentially single anomers, before significant mutarotation had occurred. The NMR assignments have been used to characterize deuterium isotope effects on 13C chemical shifts measured under conditions of slow NH to ND exchange in single solutions. Within a range of 0 to −0.138 ppm, β, γ, δ, and ζ deuterium isotope effects have been observed, thus providing additional reference data for assignment of the 13C NMR spectra of nitrogenous saccharides.  相似文献   

7.
A series of 5-aryl-3-alkylidenedihydrofuran-2(3H)-ones 6ag″ and 11a,b as well as 5-aryl-3-methylidenepyrrolidin-2-ones 10ac and 12 were synthesized starting from 4-aryl-2-diethoxyphosphoryl-4-oxobutanoates 3ag. Reaction sequence includes reduction or reductive amination of the carbonyl group, lactonization or lactamization step and finally the Horner–Wadsworth–Emmons olefination of aldehydes using thus obtained 5-aryl-3-diethoxyphosphoryl-3,4-dihydrofuran-2(5H)-ones 5ag″ or 5-aryl-3-diethoxyphosphorylpyrrolidin-2-ones 9ac. Furanones 6 and 11, as well as pyrrolidinones 10 and 12, were evaluated in vitro against mouse leukemia cell line L-1210 and two human leukemia cell lines HL-60 and NALM-6. Several of the obtained furanones proved to be very potent against all three cell lines with IC50 values lower than 6 μM. Structure–activity relationships of these compounds, as well as 5-alkyl or 5-arylmethyl-3-methylidenedihydrofuran-2(3H)-ones 13ae, previously obtained in our laboratory, are discussed.  相似文献   

8.
The binding of trimethoprim and [1,3,2-amino-15N3]-trimethoprim to Lactobacillus casei dihydrofolate reductase has been studied by 15N and 1H NMR spectroscopy. 15N NMR spectra of the bound drug were obtained by using polarisation transfer pulse sequences. The 15N chemical shifts and 1H-15N spin-coupling constants show unambiguously that the drug is protonated on N1 when bound to the enzyme.The N1-proton resonance in the complex has been assigned using the 15N-enriched molecule. The temperature-dependence of the linewidth of this resonance has been used to estimate the rate of exchange of this proton with the solvent: 160±10s-1 at 313 K, with an activation energy of 75 (±9) kJ·mole-1. This is considerably faster than the dissociation rate of the drug from this complex, demonstrating that there are local fluctuations in the structure of the complex.  相似文献   

9.
An 1H NMR (nuclear magnetic resonance) spectroscopic structural analysis of Cd2+ complexes formed with the pentapeptide phytochelatin, (NH3)+−(ψ-Glu-Cys)2−Gly−COO−(PC2), at a pH of 7.5 showed that the two thiol groups of the Cys residues and either the carbonyl or amide group of the peptide bond between Glu1 and Cys1 act as possible donor groups in the complexes at Cd2+/PC2 ratios up to 0.4. As the ratio increases, the carboxylate group of Glu2 and either the carbonyl or amide group of the peptide bond between Cys1 and Glu2 comes to serve as a donor group. The manner in which Cd2+ forms complexes with PC2 is distinctly different from Zn2+ and might account for the role of phytochelatin in Cd2+ detoxification. Electron absorption spectrometry demonstrated that the Cd2+ complexes are coordinated in a tetrahedral fashion by four thiol groups and that several sulfur atoms might bridge Cd2+ ions, resulting in the formation of polynuclear complexes. This contrasts with Zn2+ complex formation, which consists exclusively of a 1:1 complex.  相似文献   

10.
A novel NMR spectroscopic approach to the direct biochemical characterization of bacterial culture broths is presented. A variety of one- and two-dimensional 1H NMR spectroscopic methods were used to characterize low-molecular-weight organic components of broth supernatants from cultures of Streptomyces citricolor. By applying 1H NMR spectroscopy to analyze whole, untreated culture supernatants, it was possible to identify and monitor simultaneously a range of media substrates and excreted metabolites. Identified metabolites include 2-phenylethylamine, trehalose, succinate, acetate, uridine, and aristeromycin, a secondary metabolite with antibiotic properties. Directly coupled HPLC-NMR spectroscopy was also applied to the analysis of broth supernatants for the first time, to aid spectral assignments, especially where signals were extensively overlapped in the 1H NMR spectra of the whole broth mixtures. Two-dimensional NMR methods such as 1H-1H correlation spectroscopy, 1H-13C heteronuclear single quantum correlation, and 1H-13C heteronuclear multiple bond correlation aided the structure elucidation and peak assignments of individual components in the mixtures by providing information on 1H-1H coupling networks and 13C chemical shifts. This work shows that high-resolution NMR spectroscopic methods provide a rapid and efficient means of investigating microbial metabolism directly without invasive or destructive sample pretreatment.  相似文献   

11.
Summary A technique is described for measuring the approximate exchange rates of the more labile amide protons in a protein. The technique relies on a comparison of the intensities in1H–15N correlation spectra recorded with and without presaturation of the water resonance. To distinguish resonance attenuation caused by hydrogen exchange from attenuation caused by cross relation, the experiment is repeated at several different pH values and the difference in attenuation of any particular amide resonance upon presaturation is used for calculating its exchange rate. The technique is demonstrated for calmodulin and for calmodulin complexed with its binding domain of skeletal muscle myosin light chain kinase. Upon complexation, increased amide exchange rates are observed for residues Lys75 through Thr79 located in the central helix of calmodulin, and for the C-terminal residues Ser147 and Lys148. In contrast, a decrease in amide exchange rate is observed at the C-terminal end of the F helix, from residues Thr110 through Glu114.Istituto Guido Donegani, Novara, Italy  相似文献   

12.
O,O′-Dipropyldithiophosphate and O,O′-dibutyldithiophosphate (Dtph) cadmium(II) complexes were prepared and studied by means of heteronuclear 31P, 113Cd, 31C CP/MAS NMR spectroscopy and single-crystal X-ray diffraction. Linear-chain polynuclear structures have been established for both cadmium(II) complexes, in which each pair of equivalent dithiophosphate groups, playing the same bridging structural function, asymmetrically links the neighbouring cadmium atoms. One remarkable structural feature of the synthesised cadmium(II) compounds is defined by the alternation of two types of conformationally different (‘chair’-‘saddle’) eight-membered rings [Cd2S4P2] in the polymeric chains. Therefore, in both 31P NMR and XRD data, the bridging dithiophosphate ligands exhibit structural inequivalence in pairs. The structural states of both Dtph ligands and cadmium atoms have been characterised by the 31P and 113Cd chemical shift tensors, which display a profound axially symmetric and mainly rhombic characters, respectively. All experimental 31P resonances were assigned to the phosphorus structural sites in both resolved structures.  相似文献   

13.
Water-soluble N-(4-carboxybutyroyl) chitosan derivatives with different degrees of substitution (DS) were synthesized to enhance the antimicrobial activity of chitosan molecule against plant pathogens. Chitosan in a solution of 2% aqueous acetic acid-methanol (1:1, v/v) was reacted with 0.1, 0.3, 0.6 and 1 mol of glutaric anhydride to give N-(4-carboxybutyroyl) chitosans at DS of 0.10, 0.25, 0.48 and 0.53, respectively. The chemical structures and DS were characterized by 1H and 13C NMR spectroscopy, which showed that the acylate reaction took place at the N-position of chitosan. The synthesized derivatives were more soluble than the native chitosan in water and in dilute aqueous acetic acid and sodium hydroxide solutions. The antimicrobial activity was in vitro investigated against the most economic plant pathogenic bacteria of Agrobacterium tumefaciens and Erwinia carotovora and fungi of Botrytis cinerea, Pythium debaryanum and Rhizoctonia solani. The antimicrobial activity of N-(4-carboxybutyroyl) chitosans was strengthened than the un-modified chitosan with the increase of the DS. A compound of DS 0.53 was the most active one with minimum inhibitory concentration (MIC) of 725 and 800 mg/L against E. carotovora and A. tumefaciens, respectively and also in mycelial growth inhibiation against B. cinerea (EC50 = 899 mg/L), P. debaryanum (EC50 = 467 mg/L) and R. solani (EC50 = 1413 mg/L).  相似文献   

14.
The effect of fosmidomycin and mevinoline, inhibitors of the nonmevalonate and the mevalonate pathways of isoprenoid biosynthesis, respectively, on the growth of 34 anaerobic and 10 aerobic prokaryotic strains was studied. Fosmidomycin at the concentrations used was shown to inhibit the growth of 9 (of 10) representatives of the family Microbacteriaceae, 4 (of 5) strains of Thermoanaerobacter, and 11 (of 12) strains of Clostridium, whereas mevinoline inhibited the growth of lactobacilli (Carnobacterium), methanogenic and sulfate-reducing bacteria insensitive to fosmidomycin. During the late growth phase, four strains of actinobacteria (of nine) accumulated the compound, which, upon oxidation, generates a long-lived free radical; three strains synthesized 2-C-methyl-D-erythritol-2,4-cyclopyrophosphate (MEC). It was concluded that the difference in the sensitivity of the organisms to fosmidomycin and mevinoline might serve as a test to differentiate several representatives of the family Microbacteriaceae. The use of mevinoline for inhibiting methanogens in ecological investigations seems to be promising.__________Translated from Mikrobiologiya, Vol. 74, No. 2, 2005, pp. 185–190.Original Russian Text Copyright © 2005 by Trutko, Dorofeeva, Shcherbakova, Chuvilskaya, Laurinavichus, Binyukov, Ostrovskii, Hintz, Wiesner, Jomaa, Akimenko.  相似文献   

15.
Shabalina  S. A. 《Molecular Biology》2002,36(3):359-364
The results of computer analysis of complementarity regions in the sequences of E. coli 16S rRNA, mRNAs and tRNAs are reported in this article. The potential regions of intermolecular RNA–RNA hybridization, or clinger fragments, in 16S rRNA, which are complementary to the sites frequently occurring in mRNAs and tRNAs, were found. Major clinger fragments on 16S rRNA are universal for genes that belong to different functional groups. Our results show there are adaptations of the structural organization of the 16S rRNA molecule to messenger and transport RNA sequences. RNA interaction with clinger fragments may contribute to upregulation of the translation process through increasing the local concentration of mRNAs and tRNAs in the vicinity of the ribosome and their proper positioning, as well as decrease the efficiency of translation through nonspecific mRNA–16SrRNA interactions.  相似文献   

16.
Summary A method is proposed to generate initial structures in cases where the distance geometry method may fail, such as when the set of1H NMR NOE-based distance constraints is small in relation to the size of the protein. The method introduces an initial correlation between the and backbone angles (based on empirical observations) which is relaxed in later stages of the calculation. The obtained initial structures are refined by well-established methods of energy minimization and restrained molecular dynamics. The method is applied to determine the solution structure of Ribonuclease A (124 residues) from a NOE basis consisting of 467 NOE cross-correlations (97 intra-residue, 206 sequential, 23 medium-range and 141 long-range) obtained at 360 MHz. The global shape and backbone overall fold of the eight final refined structures are close to those shown by the crystal structure. A meaningful difference in the positioning of the catalytically important His119 side chain in the solution and crystal structures has been detected.  相似文献   

17.
The cationic β-sheet cyclic tetradecapeptide cyclo[VKLdKVdYPLKVKLdYP] (GS14dK4) is a diastereomeric lysine ring-size analog of the potent naturally occurring antimicrobial peptide gramicidin S (GS) which exhibits enhanced antimicrobial but markedly reduced hemolytic activity compared to GS itself. We have previously studied the binding of GS14dK4 to various phospholipid bilayer model membranes using isothermal titration calorimetry [Abraham, T. et al. (2005) Biochemistry 44, 2103-2112]. In the present study, we compare the ability of GS14dK4 to bind to and disrupt these same phospholipid model membranes by employing a fluorescent dye leakage assay to determine the ability of this peptide to permeabilize large unilamellar vesicles. We find that in general, the ability of GS14dK4 to bind to and to permeabilize phospholipid bilayers of different compositions are not well correlated. In particular, the binding affinity of GS14dK4 varies markedly with the charge and to some extent with the polar headgroup structure of the phospholipid and with the cholesterol content of the model membrane. Specifically, this peptide binds much more tightly to anionic than to zwitterionic phospholipids and much less tightly to cholesterol-containing than to cholesterol-free model membranes. In addition, the maximum extent of binding of GS14dK4 can also vary considerably with phospholipid composition in a parallel fashion. In contrast, the ability of this peptide to permeabilize phospholipid vesicles is only weakly dependent on phospholipid charge, polar headgroup structure or cholesterol content. We provide tentative explanations for the observed lack of a correlation between the affinity and extent of GS14dK4 binding to, and degree of disruption of the structure and integrity of, phospholipid bilayers membranes. We also present evidence that the lack of correlation between these two parameters may be a general phenomenon among antimicrobial peptides. Finally, we demonstrate that the affinity of binding of GS14dK4 to various phospholipid bilayer membranes is much more strongly correlated with the antimicrobial and hemolytic activities of this peptide than with its effect on the rate and extent of dye leakage in these model membrane systems.  相似文献   

18.
The structural and electronic properties of 4′-epiadriamycin, adriamycin, and daunomycin have been studied using density functional theory (DFT) employing B3LYP exchange correlation. The chemical shifts of 1H and 13C resonances in nuclear magnetic resonance spectra have been calculated using Gauge-Invariant Atomic Orbital (GIAO) method as implemented in Gaussian 98 and compared with experimental spectra recorded at 500 MHz. 13C resonances of drugs have been assigned for the first time. A restrained molecular dynamics approach was used to get the optimized solution structure of drugs using inter-proton distance constraints obtained from 2D NOESY spectra. The glycosidic angle C7-O7-C1′-C2′ is found to show considerable flexibility by adopting 156°-161° (I), 142°-143° (II), and 38°-78° (III) conformations, of which the biological relevant structure appears to be the conformer II. The observed different conformations of the three drugs are correlated to the differential anticancer activity and the available biochemical evidence exhibited by these drugs.  相似文献   

19.
We and others have recently demonstrated that the pharmacological tolerance observed after prolonged exposure to plant and synthetic cannabinoids in adult individuals seems to have a pharmacodynamic basis, based on the observed down-regulation of cannabinoid receptors in the brain of cannabinoid-tolerant rats. However, we were unable to elicit a similar receptor down-regulation after a chronic exposure to anandamide, the first discovered endogenous cannabinoid, possibly because of its rapid metabolic breakdown in arachidonic acid and ethanolamine. The present study was designed to progress in these previous studies, by using R-methanandamide, a more stable analog, instead anandamide. In addition, we examined not only cannabinoid receptor binding, but also WIN-55,212-2-stimulated [35S]-GTPγS binding, by autoradiography, and cannabinoid receptor mRNA levels, by in situ hybridization. Results were as follows. The daily administration of R-methanandamide for a period of five days produced decreases in cannabinoid receptor binding in the lateral caudate-putamen, cerebellum, entopeduncular nucleus and substantia nigra. The remaining areas, the medial caudate-putamen, globus pallidus, cerebral cortex (layers I and VI), hippocampus (dentate gyrus and Ammon’s horn) and several limbic structures (nucleus accumbens, septum nuclei and basolateral amygdaloid nucleus), exhibited no changes in cannabinoid receptor binding. Similarly, the levels of cannabinoid receptor mRNA expression decreased in the lateral and medial caudate-putamen and in the CA1 and CA2 subfields of the Ammon’s horn in the hippocampus after the chronic exposure to R-methanandamide, whereas the remaining areas showed no changes. WIN-55,212-2-stimulated [35S]-GTPγS binding did not change in the lateral caudate-putamen, cerebral cortex (layer I), septum nuclei and hippocampal structures (dentate gyrus and Ammon’s horn) of animals chronically exposed to R-methanandamide, whereas a certain trend to decrease could be observed in the substantia nigra and deep layer (VI) of the cerebral cortex in these animals. In summary, as reported for other cannabinoid receptor agonists, the prolonged exposure of rats to R-methanandamide, a more stable analog of anandamide, was able to produce cannabinoid receptor-related changes in contrast with the absence of changes observed early with the metabolically labile anandamide. The observed changes exhibited an evident regional pattern with areas, such as basal ganglia, cerebellum and hippocampus, responding to chronic R-methanandamide treatment while regions, such as the cerebral cortex and limbic nuclei, not responding.  相似文献   

20.
A new synthesizing statistical methodology is proposed to resolve issues of signal-heterogeneity in data sets collected through high-resolution 1H nuclear magnetic resonance (NMR) spectroscopy. This signal-heterogeneity is typically caused by subjective operations for processing spectral profiles and measuring peak areas, non-homogeneous biological phases of experimental subjects, and variations of systems in multi-center. All these causes are likely to simultaneously impact signals of metabolic changes and their precision in a nonlinear fashion. As a combined effect, signal-heterogeneity chiefly manifests through non-homomorphic patterns of standardized treatment mean deviations spanning all experiments, and makes most remedial statistical models with linearity structure invalid. By avoiding a huge and very complex model, we develop a simple meta-ANOVA approach to synthesize many one-way-layout ANOVA analyses from individual experiments. A scale-invariant F-ratio statistic is taken as the summarizing sufficient statistic of a non-centrality parameter that supposedly captures the information about metabolic change from each experiment. Then a joint-likelihood function of a common non-centrality is constructed as the basis for maximum likelihood estimation and Chi-square likelihood ratio testing for statistical inference. We apply the meta-ANOVA to detect metabolic changes of three metabolites identified through pattern recognition on NMR spectral profiles obtained from muscle and liver tissues. We also detect effect differences among different treatments via meta-ANOVA multiple comparison.  相似文献   

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