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1.
The reaction scheme of methionyl-tRNA synthetase from Escherichia coli with the initiator tRNAsMet from E. coli and rabbit liver, respectively, has been resolved. The statistical rate constants for the formation, kR, and for the dissociation, kD, of the 1:1 complex of these tRNAs with the dimeric enzyme have been calculated. Identical kR values of 250 μm?1 s?1 reflect similar behaviour for antico-operative binding of both tRNAsMet to native methionyl-tRNA synthetase. Advantage was taken of the difference in extent of tryptophan fluorescence-quenching induced by the bacterial and mammalian initiator tRNAsMet to measure the mode of exchange of these tRNAs antico-operatively bound to the enzyme. Analysis of the results reveals that antico-operativity does not arise from structural asymmetric assembly of the enzyme subunits. Indeed, both subunits can potentially bind a tRNA molecule. Exchange between tRNA molecules can occur via a transient complex in which both sites are occupied. Either strong and weak sites reciprocate between subunits on the transient complex or occupation of the weak site induces symmetry of this complex. While in the present case, these two alternatives are kinetically indistinguishable, they do account for the observation that, upon increasing the concentration of the competing mammalian tRNA, the rate of exchange of the E. coli initiator tRNAMet is enhanced, due to its faster rate of dissociation from the transient complex. Finally, it has been verified that in the case of the trypsin-modified methionyl-tRNA synthetase which cannot provide more than one binding site for tRNA, exchange of enzymebound bacterial tRNA by mammalian tRNA does proceed to a limiting rate independent of the mammalian tRNA concentration present in the solution.  相似文献   

2.
Mitoxantrone (1,4-dihydroxy-5,8-bis[[2-[(2-hydroxyethyl)amino]ethyl]amino]-9,10-anthracenedione) is a synthetically designed antineoplastic agent and structurally similar to classical anthracyclines. It is widely used as a potent chemotherapeutic component against various kinds of cancer and possesses lesser cardio-toxic effects with respect to naturally occurring anthracyclines. In the present study, we have investigated the binding features of mitoxantrone–tRNA complexation at physiological pH using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, circular dichroism (CD) spectroscopy, isothermal titration calorimetry, and UV–visible absorption spectroscopic techniques. FTIR analysis reveals that mitoxantrone interacts mainly with heterocyclic base residues of tRNA along with slight external binding with phosphate–sugar backbone. In particular, mitoxantrone binds at uracil (C=O) and adenine (C=N) sites of biomolecule (tRNA). CD spectroscopic results suggest that there is no major conformational transition in native A-form of tRNA upon mitoxantrone–tRNA adductation except an intensification in the secondary structure of tRNA is evident. The association constant calculated for mitoxantrone–tRNA association is found to be 1.27?×?105 M?1 indicating moderate to strong binding affinity of drug with tRNA. Thermodynamically, mitoxantrone–tRNA interaction is an enthalpy-driven exothermic reaction. Investigation into drug–tRNA interaction can play an essential role in the rational development of RNA targeting chemotherapeutic agents, which also delineate the structural–functional relationship between drug and its target at molecular level.  相似文献   

3.
Number of tRNA binding sites on 80 S ribosomes and their subunits   总被引:1,自引:0,他引:1  
The ability of rabbit liver ribosomes and their subunits to form complexes with different forms of tRNAPhe (aminoacyl-, peptidyl- and deacylated) was studied using the nitrocellulose membrane filtration technique. The 80 S ribosomes were shown to have two binding sites for aminoacyl- or peptidyl-tRNA and three binding sites for deacylated tRNA. The number of tRNA binding sites on 80 S ribosomes or 40 S subunits is constant at different Mg2+ concentrations (5-20 mM). Double reciprocal or Scatchard plot analysis indicates that the binding of Ac-Phe-tRNAPhe to the ribosomal sites is a cooperative process. The third site on the 80 S ribosome is formed by its 60 S subunit, which was shown to have one codon-independent binding site specific for deacylated tRNA.  相似文献   

4.
Yeast arginyl-tRNA synthetase and aspartyl-tRNA synthetase like nucleotidyl transferases previously investigated interact with the Blue-Dextran-Sepharose affinity ligand through their tRNA binding domain: the enzymes are readily displaced from the affinity column by their cognate tRNAs but not by ATP or a mixture of ATP and the cognate amino acid in contrast to other aminoacyl-tRNA synthetases. In the absence of Mg++, the arginyl-tRNA synthetase can be dissociated from the column by tRNAAsp and tRNAPhe which have been shown to be able to form a complex with the synthetase, but in presence of Mg++ the elution is only obtained by the specific tRNA.The procedure described here can thus be used: (i) to detect polynucleotide binding sites in a protein; (ii) to estimate the relative affinities of different tRNAs for a purified synthetase; (iii) to purify an aminoacyl-tRNA synthetase by selective elution with the cognate tRNA.  相似文献   

5.
Measuring the binding affinities of 42 single-base-pair mutants in the acceptor and TΨC stems of Saccharomyces cerevisiae tRNAPhe to Thermus thermophilus elongation factor Tu (EF-Tu) revealed that much of the specificity for tRNA occurs at the 49-65, 50-64, and 51-63 base pairs. Introducing the same mutations at the three positions into Escherichia coli tRNACAGLeu resulted in similar changes in binding affinity. Swapping the three pairs from several E. coli tRNAs into yeast tRNAPhe resulted in chimeras with EF-Tu binding affinities similar to those for the donor tRNA. Finally, analysis of double- and triple-base-pair mutants of tRNAPhe showed that the thermodynamic contributions at the three sites are additive, permitting reasonably accurate prediction of the EF-Tu binding affinity for all E. coli tRNAs. Thus, it appears that the thermodynamic contributions of three base pairs in the TΨC stem primarily account for tRNA binding specificity to EF-Tu.  相似文献   

6.
Tetracycline blocks stable binding of aminoacyl-tRNA to the bacterial ribosomal A-site. Various tetracycline binding sites have been identified in crystals of the 30S ribosomal small subunit of Thermus thermophilus. Here we describe a direct photo- affinity modification of the ribosomal small subunits of Escherichia coli with 7-[3H]-tetracycline. To select for specific interactions, an excess of the 30S subunits over tetracycline has been used. Primer extension analysis of the 16S rRNA revealed two sites of the modifications: C936 and C948. Considering available data on tetracycline interactions with the prokaryotic 30S subunits, including the presented data (E.coli), X-ray data (T.thermophilus) and genetic data (Helicobacter pylori, E.coli), a second high affinity tetracycline binding site is proposed within the 3′-major domain of the 16S rRNA, in addition to the A-site related tetracycline binding site.  相似文献   

7.
It is generally believed that basic features of ribosomal functions are universally valid, but a systematic test still stands out for higher eukaryotic 80S ribosomes. Here we report: (i) differences in tRNA and mRNA binding capabilities of eukaryotic and bacterial ribosomes and their subunits. Eukaryotic 40S subunits bind mRNA exclusively in the presence of cognate tRNA, whereas bacterial 30S do bind mRNA already in the absence of tRNA. 80S ribosomes bind mRNA efficiently in the absence of tRNA. In contrast, bacterial 70S interact with mRNA more productively in the presence rather than in the absence of tRNA. (ii) States of initiation (Pi), pre-translocation (PRE) and post-translocation (POST) of the ribosome were checked and no significant functional differences to the prokaryotic counterpart were observed including the reciprocal linkage between A and E sites. (iii) Eukaryotic ribosomes bind tetracycline with an affinity 15 times lower than that of bacterial ribosomes (Kd 30 μM and 1–2 μM, respectively). The drug does not effect enzymatic A-site occupation of 80S ribosomes in contrast to non-enzymatic tRNA binding to the A-site. Both observations explain the relative resistance of eukaryotic ribosomes to this antibiotic.  相似文献   

8.
Four subunits of the acetylcholine receptor molecule, obtained from the electric organ of Torpedo ocellata, have been isolated using polyacrylamide gel electrophoresis, and assayed by titration with a fluorescent lanthanide, terbium, and by affinity-labeling with p-(N-maleimido)benzyl [trimethyl-3H] ammonium iodide. The site with which the activator-analogue affinity label reacts, as well as the terbium-binding sites, are mainly associated with the smallest of the subunits of an apparent molecular weight of 40,000. Calcium competes with terbium for these binding sites. The affinity for terbium is the same in the intact molecule as in the subunit (KTb ? 19 ± 1 μM), but the affinity for calcium decreases by a factor of 4 (KCa ? 4 mM) in the subunit. Hydrolysis of the receptor, catalyzed by trypsin and chymotrypsin, to peptides with an apparent molecular weight of 8000 or less, does not affect the terbium-binding sites. These experiments indicate that the binding sites for neural activators and for calcium are associated with the same subunit, and that the terbium- and calcium-binding sites reflect structural properties of the polypeptide chain rather than the three-dimensional structure of the protein.  相似文献   

9.
In the presence of methanol 50S ribosomal subunits reveal two independents sites for binding of deacylated tRNA and/or AcPhe-tRNA. The site with lower affinity was identified with the donor (P') site as the dissociation constant (Ka) for AcPhe-tRNA was equal to the Michaelis constant for its reaction with puromycin both at 0 degrees C and 25 degrees C. Log Ka increases linearly with methanol concentration. This suggests that there are no conformational transitions of the interacting components, the affinity increases only quantatively due to lowering of the dielectric constant of water, and the site can exist even in the absence of methanol, but its Ka may be too low to be measured. It follows from these data that the higher-affinity site, which is observed both in the absence and presence of methanol, cannot be the P' site as it was generally believed. By all its properties it is more like the additional E site, which has been recently found on 70S ribosomes. Specifically, its affinity for deacylated tRNA is about 1000-fold higher than for AcPhe-tRNA (in the P'-site they are almost the same).  相似文献   

10.
The refined crystal structure of the ternary complex of yeast Phe-tRNAPhe, Thermus aquaticus elongation factor EF-Tu and the non-hydrolyzable GTP analog, GDPNP, revelas many details of the EF-Tu recognition of aminoacylated tRNA (aa-tRNA). EF-Tu-GTP recognizes the aminoacyl bond and one side of the backbone fold of the acceptor helix and has a high affinity for all ordinary elongator aa-tRNAs by binding to this aa-tRNA motif. Yet, the binding of deacylated tRNA, initiator tRNA, and selenocysteine-specific tRNA (tRNASec) is effectively discriminated against. Subtle rearrangements of the binding pocket may occur to optimize the fit to any side chain of the aminoacyl group and interactions with EF-Tu stabilize the 3′-aminoacyl isomer of aa-tRNA. A general complementarity is observed in the location of the binding sites in tRNA for synthetases and for EF-Tu. The complex formation is highly specific for the GTP-bound conformation of EF-Tu, which can explain the effects of various mutants.  相似文献   

11.
The effects of apomorphine on the binding properties of striatal muscarinic receptors were investigated using the specific muscarinic antagonist, [3H](?)3-quinuclidinyl benzilate ([3H](?)QNB). When binding measurements were made in 50 mM sodium/HEPES buffer, pH 7.4, containing Mg+2, the binding of [3H](?)QNB was consistent with the presence of two binding sites; 57% of the sites had a high affinity dissociation constant of 0.030 nM whereas the remaining sites had a low affinity dissociation constant of 0.64 nM. Apomorphine (1.0 μM) enhanced the binding of [3H](?)QNB by an apparent conversion of low to high affinity sites. A variety of other agents were screened for their ability to enhance [3H](?)QNB binding, and a pattern generally consistent with a dopaminergic effect was observed although some evidence for a β-adrenergic effect was demonstrable. The potent neuroleptics haloperidol, spiperone and sulpiride failed to antagonize the apomorphine enhancement of [3H](?)QNB binding as well as some adrenergic antagonists. However, the potent inhibitors of the dopamine-sensitive adenylate cyclase, α-flupenthixol and fluphenazine, specifically blocked the apomorphine enhancement of [3H](?)QNB binding with Ki values of approximately 0.1 μM.  相似文献   

12.
J L Leroy  M Guéron 《Biopolymers》1977,16(11):2429-2446
The binding of Mn2+ to yeast tRNAPhe at 25°C is measured by esr, and found to depend strongly on the concentration of monovalent cations, showing the importance of electrostatic effects. In low sodium (<15mM/l.), the affinity is high and the Scatchard plots are distinctly curved. In high sodium (>50mM/l.), the affinity and the curvature are reduced. In a limited range of sodium concentrations (15–30mM/l.), the folding of tRNA which is induced by the divalent ions results in cooperative binding, leading to upwards convexity of the Scatchard plot. An electrostatic model is developed, based on a single type of binding site which we take to be the phosphates, with a binding constant for Mn2+ in the range of that found for ApA, 10 l./M. We compute the change in the binding constant due to the electrostatic potential of the distant charges (other phosphates and counterions), using a single set of parameters for all sodium concentrations. The model predicts that the plots in low sodium are curved, and a good fit to the experimental results is obtained: it is therefore not legitimate or necessary to interpret these results in terms of two types of binding sites. In high salt, the model gives plots that are only slightly curved, corresponding to weaker electrostatic effects. This shows that a search for sites with a special binding mode should be done in high salt. The computed plots are in good agreement with the data, except for slight differences concerning the first bound ions, which give a possible indication in favor of special binding. Given the observation of one special site for Mg2+ at 4°C in high sodium [Stein, A. & Crothers, D. M. (1976) Biochemistry 15 , 157–160] in E. coli tRNAfMet, we have measured the binding of Mn2+ at lower temperature. At 12°C, in both yeast tRNAPhe and E. coli tRNAfMet, the plots clearly indicate special binding. A site found in high sodium is on a very different footing from the four to six so-called strong sites unduly derived from low-salt binding plots.  相似文献   

13.
Studies of the localization of the Na+-dependent sugar transport in monolayers of LLC PK1 cells show that the uptake of a methyl α-d-glucoside, a nonmetabolizable sugar which shares the glucose-galactose transport system, occurs mainly from the apical side of the monolayer. Kinetics of [3H]phlorizin binding to monolayers of LLC PK1 cells were also measured. These studies demonstrate the presence of two distinct classes of receptor sites. The class comprising high affinity binding sites had a dissociation constant (Kd) of 1.2 μM and a concentration of high affinity receptors of 0.30 μmol binding sites per g DNA. The other class involving low affinity sites had a Kd of 240 μM with the number of binding sites equal to 12 μmol/g DNA. Phlorizin binding at high affinity binding sites is a Na+-dependent process. Binding at the low affinity sites on the contrary is Na+-independent. The mode of action of Na+ on the high affinity binding sites was to increase the dissociation constant without modifying the number of binding sites. The Na+ dependence and the matching of Kd for high affinity binding sites with the Ki of phlorizin for the inhibition of methyl α-d-glucoside strongly suggest that the high affinity phlorizin binding site is, or is part of the methyl α-d-glucoside transport system. Binding studies from either side of the monolayer also show that the binding of phlorizin at the Na+ dependent high affinity binding sites occurs mainly from the apical rather than the basolateral side. The specific location of the Na+-dependent sugar transport system in the apical membrane of LLC PK1 cells is, therefore, another expression of the functional polarization of epithelial cells that is retained under tissue culture condition. In addition, since this sugar transport almost disappears after the cells are brought into suspension, it can be used as a marker to study the development of the apical membrane in this cell line.  相似文献   

14.
The RNA subunit of the ribonucleoprotein enzyme ribonuclease P (RNase P (P RNA) contains the active site, but binding of Escherichia coli RNase P protein (C5) to P RNA increases the rate constant for catalysis for certain pre-tRNA substrates up to 1000-fold. Structure-swapping experiments between a substrate that is cleaved slowly by P RNA alone (pre-tRNAf-met605) and one that is cleaved quickly (pre-tRNAmet608) pinpoint the characteristic C(+ 1)/A(+ 72) base pair of initiator tRNAf-met as the sole determinant of slow RNA-alone catalysis. Unlike other substrate modifications that slow RNA-alone catalysis, the presence of a C(+ 1)/A(+ 72) base pair reduces the rate constant for processing at both correct and miscleavage sites, indicating an indirect but nonetheless important role in catalysis. Analysis of the Mg2+ dependence of apparent catalytic rate constants for pre-tRNAmet608 and a pre-tRNAmet608 (+ 1)C/(+ 72)A mutant provides evidence that C5 promotes rate enhancement primarily by compensating for the decrease in the affinity of metal ions important for catalysis engendered by the presence of the CA pair. Together, these results support and extend current models for RNase P substrate recognition in which contacts involving the conserved (+ 1)G/C(+ 72) pair of tRNA stabilize functional metal ion binding. Additionally, these observations suggest that C5 protein has evolved to compensate for tRNA variation at positions important for binding to P RNA, allowing for tRNA specialization.  相似文献   

15.
The iron requirement of a cell line of Chinese hamster fibroblasts is met more efficiently by human transferrin than by bovine transferrin or conalbumin. One possible explanation is that the binding of these transferrins to the Chinese hamster V79 cells may differ. Binding studies now show that the affinity of V79 cells for human transferrin is about 40 times greater than for bovine transferrin. Conalbumin has no detectable affinity for the human transferrin binding sites. Human apotransferrin has approximately one-sixth the affinity for the transferrin binding sites. The binding constant for the relation of human transferrin with the V79 cell is about 2.3·1061· mole−1, and the approximate number of binding sites per cell is 9 · 105.  相似文献   

16.
Letters to the editor: Accessibility of 5 S RNA in 50 S ribosomal subunits   总被引:5,自引:0,他引:5  
Only two sites in 5 S RNA react with Kethoxal in 50 S ribosomal subunits. These two sites, G13 and G41, have previously been found to be accessible in free 5 S RNA. Nucleotide sequences which have been suggested as possible binding sites for the T-ψ-C-G loop of tRNA are not accessible.  相似文献   

17.
Biogenic polyamines are found to modulate protein synthesis at different levels. This effect may be explained by the ability of polyamines to bind and influence the secondary structure of tRNA, mRNA, and rRNA. We report the interaction between tRNA and the three biogenic polyamines putrescine, spermidine, spermine, and cobalt(III)hexamine at physiological conditions, using FTIR spectroscopy, capillary electrophoresis, and molecular modeling. The results indicated that tRNA was stabilized at low biogenic polyamine concentration, as a consequence of polyamine interaction with the backbone phosphate group. The main tRNA reactive sites for biogenic polyamine at low concentration were guanine-N7/O6, uracil-O2/O4, adenine-N3, and 2′OH of the ribose. At high polyamine concentration, the interaction involves guanine-N7/O6, adenine-N7, uracil-O2 reactive sites, and the backbone phosphate group. The participation of the polycation primary amino group, in the interaction and the presence of the hydrophobic contact, are also shown. The binding affinity of biogenic polyamine to tRNA molecule was in the order of spermine > spermidine > putrescine with KSpm = 8.7 × 105 M−1, KSpd = 6.1 × 105 M−1, and KPut = 1.0 × 105 M−1, which correlates with their positively charged amino group content. Hill analysis showed positive cooperativity for the biogenic polyamines and negative cooperativity for cobalt-hexamine. Cobalt(III)hexamine contains high- and low-affinity sites in tRNA with K1 = 3.2 × 105 M−1 and K2 = 1.7 × 105 M−1, that have been attributed to the interactions with guanine-N7 sites and the backbone PO2 group, respectively. This mechanism of tRNA binding could explain the condensation phenomenon observed at high Co(III) content, as previously shown in the Co(III)–DNA complexes.  相似文献   

18.
The photoinduced reaction of phenylalanyl-tRNA synthetase (E.C. 6.1.1.20) from E.coli MRE-600 with tRNAphe containing photoreative p-N3-C6H4-NHCOCH2-group attached to 4-thiouridine sU8 (azido-tRNAphe) was investigated. The attachment of this group does not influence the dissociation constant of the complex of Phe-tRNAphe with the enzyme,however it results in sevenfold increase of Km in the enzymatic aminoacylation of tRNAphe. Under irradiation at 300 nm at pH 5.8 the covalent binding of [14C]-Phe-azido-tRNAphe to the enzyme takes place 0.3 moles of the reagent being attached per mole of the enzyme. tRNA prevents the reaction. Phenylalanine, ATP,ADP,AMP, adenosine and pyrophosphate (2.5 × x 10−3 M) don't affect neither the stability of the tRNA-enzyme complex nor the rate of the affinity labelling. The presence of the mixture of either phenylalanine or phenylalaninol with ATP as well as phenylalaninol adenylate exibits 50% inhibition of the photoinduced reaction. Therefore, the reaction of [14C]-Phe-azido-tRNA with the enzyme is significantly less sensitive to the presence of the ligands than the reaction of chlorambucilyl-tRNA with the reactive group attached to the acceptor end of the tRNA studied in 1. It has been concluded that the kinetics of the affinity labelling does permit to discriminate the influence of the low molecular weight ligands of the enzyme on the different sites of the tRNA - enzyme interaction.  相似文献   

19.
Hocking  T. J.  Clapham  Jennifer  Cattell  K. J. 《Planta》1978,138(3):303-304
A centrifugation binding assay has been used to demonstrate the binding of [3H] (±) abscisic acid to membrane-rich fractions prepared from leaves of Vicia faba L. Kinetic analysis of this binding shows evidence of saturation of binding sites with increasing concentration of ligand. Scatchard analysis of these data yields a biphasic plot possibly indicating the presence of two types of binding sites. The dissocation constant for the high affinity site has been calculated to be 3.5×10-8 mol 1-1.  相似文献   

20.
《BBA》1986,849(1):121-130
The binding of 3′-O-(1-naphthoyl)adenosinetriphosphate (1-naphthoyl-ATP), ATP and ADP to TF1 and to the isolated α and β subunits was investigated by measuring changes of intrinsic protein fluorescence and of fluorescence anisotropy of 1-naphthoyl-ATP upon binding. The following results were obtained. (1) The isolated α and β subunits bind 1 mol 1-naphthoyl-ATP with a dissociation constant (KD(1-naphthoyl-ATP)) of 4.6 μM and 1.9 μM, respectively. (2) The KD(ATP) for α and β subunits is 8 μM and 11 μM, respectively. (3) The KD(ADP) for α and β subunits is 38 μM μM and 7 μM, respectively. (4) TF1 binds 2 mol 1-naphthoyl-ATP per mol enzyme with KD = 170 nM. (5) The rate constant for 1-naphthoyl-ATP binding to α and β subunit is more than 5 · 104 M−1s−1. (6) The rate constant for 1-naphthoyl-ATP binding to TF1 is 6.6 · 103 M−1 · s−1 (monophasic reaction); the rate constant for its dissociation in the presence of ATP is biphasic with a fast first phase (kA−1 = 3 · 10−3s−1) and a slower second phase (kA−2 < 0.2 · 10−3s−1). From the appearance of a second peak in the fluorescence emission spectrum of 1-naphthoyl-ATP upon binding it is concluded that the binding sites in TF1 are located in an environment more hydrophobic than the binding sites on isolated α and β subunits. The differences in kinetic and thermodynamic parameters for ligand binding to isolated versus integrated α and β subunits, respectively, are explained by interactions between these subunits in the enzyme complex.  相似文献   

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