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1.
J Chen  S Pongor    A Simoncsits 《Nucleic acids research》1997,25(11):2047-2054
Single-chain derivatives of the phage 434 repressor, termed single-chain repressors, contain covalently dimerized DNA-binding domains (DBD) which are connected with a peptide linker in a head-to-tail arrangement. The prototype RR69 contains two wild-type DBDs, while RR*69 contains a wild-type and an engineered DBD. In this latter domain, the DNA- contacting amino acids of thealpha3 helix of the 434 repressor are replaced by the corresponding residues of the related P22 repressor. We have used binding site selection, targeted mutagenesis and binding affinity studies to define the optimum DNA recognition sequence for these single-chain proteins. It is shown that RR69 recognizes DNA sequences containing the consensus boxes of the 434 operators in a palindromic arrangement, and that RR*69 optimally binds to non-palindromic sequences containing a 434 operator box and a TTAA box of which the latter is present in most P22 operators. The spacing of these boxes, as in the 434 operators, is 6 bp. The DNA-binding of both single-chain repressors, similar to that of the 434 repressor, is influenced indirectly by the sequence of the non-contacted, spacer region. Thus, high affinity binding is dependent on both direct and indirect recognition. Nonetheless, the single-chain framework can accommodate certain substitutions to obtain altered DNA-binding specificity and RR*69 represents an example for the combination of altered direct and unchanged indirect readout mechanisms.  相似文献   

2.
Single-chain repressor RRTRES is a derivative of bacteriophage 434 repressor, which contains covalently dimerized DNA-binding domains (amino acids 1-69) of the phage 434 repressor. In this single-chain molecule, the wild type domain R is connected to the mutant domain RTRES by a recombinant linker in a head-to-tail arrangement. The DNA-contacting amino acids of RTRES at the -1, 1, 2, and 5 positions of the a3 helix are T, R, E, S respectively. By using a randomized DNA pool containing the central sequence -CATACAAGAAAGNNNNNNTTT-, a cyclic, in vitro DNA-binding site selection was performed. The selected population was cloned and the individual members were characterized by determining their binding affinities to RRTRES. The results showed that the optimal operators contained the TTAC or TTCC sequences in the underlined positions as above, and that the Kd values were in the 1×10-12 mol/L-1×10-11mol/L concentration range. Since the affinity of the natural 434 repressor to its natural operator sites is in the 1×10-9 mol/L range, the observed binding affinity increase is remarkable. It was also found that binding affinity was strongly affected by the flanking bases of the optimal tetramer binding sites, especially by the base at the 5′ position. We constructed a new homodimeric single-chain repressor RTRESRTRES and its DNA-binding specificity was tested by using a series of new operators designed according to the recog-nition properties previously determined for the RTRES domain. These operators containing the con-sensus sequence GTAAGAAARNTTACN or GGAAGAAARNTTCCN (R is A or G) were recognized by RTRESRTRES specifically, and with high binding affinity. Thus, by using a combination of random selection and rational design principles, we have discovered novel, high affinity protein-DNA inter-actions with new specificity. This method can potentially be used to obtain new binding specificity for other DNA-binding proteins.  相似文献   

3.
Summary O c mutations in the operators of bacteriophage lambda have been used to analyze the functional organization of the operators. In each operator, repressor binding sites 1 and 2, as identified biochemically, were found to be primarily responsible for the repressor affinity of the operators in vitro and for the repression of lytic functions in vivo. In addition, both sites were shown to be involved in the action of cro product at the operators. The data obtained have been used to estimate the repressor affinities of the individual binding sites. These affinities suggest that repressor bound at O R1 and O R2 interacts cooperatively. The results obtained support a model for repression of the early lambda operons where repressor bound at binding sites 1 and 2 interferes with RNA polymerase binding to the promoter sites.  相似文献   

4.
Streptomyces lividans 1326 carries inducible mercury resistance genes on the chromosome, which are arranged in two divergently transcribed operons. Expression of the genes is negatively regulated by the repressor MerR, which binds in the intercistronic region between the two operons. The merR gene was expressed in E. coli using a T7 RNA polymerase/promoter expression system, and MerR was purified to around 95% homogeneity by ammonium sulfate precipitation, gel filtration and affinity chromatography. Gel filtration showed that the native MerR is a dimer with a molecular mass of 31 kDa. Two DNA binding sites were identified in the intercistronic mer promoter region by footprinting experiments. No evidence for cooperativity in the binding of MerR to the adjacent operator sequences was observed in gel mobility shift assays. The dissociation constants (KD) for binding of MerR were: binding site I, 8.5 × 10−9 M; binding site II, 1.2 × 10−8 M; and for the complete promoter/operator region 1 × 10−8 M. The half-life of the MerR-DNA complex was 19.4 min and 18.8 min for binding site I and binding site II, respectively. The KD value for binding of mercury(II)chloride to MerR, again determined by mobility shift assay, was 1.1 × 10−7 M. Received: 18 August 1998 / Accepted: 5 May 1999  相似文献   

5.
Combinatorial mutant libraries of the single-chain 434 repressor were used to discover novel DNA-binding specificities. Members of the library contain one wild type domain and one mutant domain which are connected by a recombinant peptide linker. The mutant domain contains randomized amino acids in place of the DNA-contacting residues. The single-chain derivatives are expected to recognize artificial operators containing the DNA sequence of ACAA — 6 base-pairs — NNNN, where ACAA is bound by the wild-type and NNNN by the mutant domain. An invivo library screening method was used to isolate mutant DNA-binding domains which recognize the TTAA site of an asymmetric operator. Several mutants showed high affinity binding to the selection target and also strong (up to 80 fold) preference for TTAA over the wild type TTGT sequence. Some of the isolated mutants bound with very high affinities (10–50 pM) to operators containing the TTAC sequence, a close homologue of the TTAA selection target.This revised version was published online in October 2005 with corrections to the Cover Date.  相似文献   

6.
Abbreviations: 434(1–63) – N-terminal 63-residue DNA-binding domain of the phage 434 repressor; dh434(0–63) – variant 434 repressor DNA-binding domain devoid of hydroxyl groups; P22c2(1–76) – N-terminal 76-residue fragment of the phage P22 c2 repressor; SDS-PAGE – SDS polyacrylamide gel electrophoresis; COSY – correlation spectroscopy; TOCSY – total correlation spectroscopy; NOE – nuclear Overhauser effect; RMSD – root-mean-square deviation.  相似文献   

7.
The antibacterial effect of cationic surfactants against the pure culture of phosphate (P)-accumulating bacterium Acinetobacter junii was investigated. The estimated EC50 values of the N-dodecylpyridinium chloride (DPC) for growth inhibition was 1.4±0.5 × 10−6 mol L−1 and for the inhibition of the P-uptake rates 7.3±2.6 × 10−5 mol L−1. The estimated EC50 values of the N-cetylpyridinium chloride (CPC) for growth inhibition was 4.9±1.3 × 10−7 mol L−1 and for the inhibition of the P-uptake rates 7.7±2.9 × 10−6 mol L−1. This suggests the importance of controlling the amounts of cationic surfactants in influent of the wastewater treatment systems in order to avoid the possible failure of the biological P removal from wastewaters.  相似文献   

8.
Two approaches to determine the fraction (μ) of mitochondrial respiration sustained during illumination by measuring CO2 gas exchange are compared. In single leaves, the respiration rate in the light (`day respiration' rate Rd) is determined as the ordinate of the intersection point of A–ci curves at various photon flux densities and compared with the CO2 evolution rate in darkness (`night respiration' rate Rn). Alternatively, using leaves with varying values of CO2 compensation concentration (Γ), intracellular resistance (ri) and Rn, an average number for μ can be derived from the linear regression between Γ and the product riċRn. Both methods also result in a number c* for that intercellular CO2 concentration at which net CO2 uptake rate is equal to –Rd. c* is an approximate value of the photocompensation point Γ* (Γ in the absence of mitochondrial respiration), which is related to the CO2/O2 specificity factor of Rubisco Sc/o. The presuppositions and limitations for application of both approaches are discussed. In leaves of Nicotiana tabacum, at 22 °C, single leaf measurements resulted in mean values of μ = 0.71 and c* = 34 μmol mol−1. At the photosynthetically active photon flux density of 960 μmol quanta m−2 s−1, nearly the same numbers were derived from the linear relationship between Γ and riċRn. c* and Rd determined by single leaf measurements varied between 31 and 41 μmol mol−1 and between 0.37 and 1.22 μmol m−2 s−1, respectively. A highly significant negative correlation between c* and Rd was found. From the regression equation we obtained estimates for Γ* (39 μmol mol−1), Sc/o (96.5 mol mol−1) and the mesophyll CO2 transfer resistance (7.0 mol−1 m2 s). This revised version was published online in June 2006 with corrections to the Cover Date.  相似文献   

9.
The harmful effects of surfactants to the environment are well known. We were interested in investigating their potential toxicity in a pure culture of Acinetobacter junii, a phosphate (P)-accumulating bacterium. Results showed a high acute toxicity of sodium dodecyl sulfate (SDS) and hexadecyltrimethylammonium bromide (HDTMA) against A. junii. The estimated EC50 values of the HDTMA for the inhibition of CFUs in the pure culture of A. junii was 3.27 ± 1.12 × 10−7 mol L−1 and for the inhibition of the P-uptake rates 2.47 ± 0.51 × 10−6 mol L−1. For SDS, estimated EC50 values for the inhibition of CFUs in the pure culture of A. junii was 5.00 ± 2.95 × 10−6 mol L−1 and for the inhibition of the P-uptake rates 3.33 ± 0.96 × 10−4 mol L−1. The obtained EC50 values in the standardised yeast toxicity test using Saccharomyces cerevisiae were 3.03 ± 0.38 × 10−4 and 4.33 ± 0.32 × 10−5 mol L−1 for SDS and HDTMA, respectively. These results emphasized the need to control concentrations of surfactants entering the activated sludge system. The negative effects of these toxicants could greatly decrease populations of P-accumulating bacteria, as well as eukaryotic organisms, inhabiting activated sludge systems, which in turn could result in the decrease of the system efficiency.  相似文献   

10.
Chlorogenic acid, 3’-O-caffeoyl D-quinic acid, is an inherent ligand present inHelianthus annuus L. The effect of pH on chlorogenic acid binding to helianthinin suggests that maximum binding occurs at pH 6.0. The protein-polyphenol complex precipitates as a function of time. The association constant of the binding of chlorogenic acid to helianthinin, determined by equilibrium dialysis, at 31°C has a value of 3.5 ± 0.1 × 104M−-1 resulting in a ΔG value of − 6.32 ± 0.12 kcal /mol. The association constantK ais 1.0 ± 0.1 × 104M−1 as determined by ultraviolet difference spectral titration at 25°C with ΔG° of -5.46 ± 0.06 kcal/mol. From fluorescence spectral titration at 28°C, theK avalue is 1.38 ± 0.1 × 1 0 4M−1 resulting in a ΔG of − 5.70 ± 0.05 kcal/mol. The total number of binding sites on the protein are 420 ± 50 as calculated from equilibrium dialysis. Microcalorimetric data of the ligand-protein interaction at 23°C suggests mainly two classes of binding. The thermal denaturation temperature,T mof the protein decreases from 76°C to 72°C at 1 × 10−3M chlorogenic acid concentration upon complexation. This suggests that the complexation destabilizes the protein. The effect of temperature onK aof chlorogenic acid shows a nonlinear increase from 10.2°C to 45°C. Chemical modification of both lysyl and tryptophanyl residues of the protein decreases the strength of binding of chlorogenic acid. Lysine, tryptophan and tyrosine of protein are shown to be present at the binding site. Based on the above data, it is suggested that charge-transfer complexation and entropically driven hydrophobic interaction are the predominant forces that are responsible for binding of chlorogenic acid to the multisubunit protein, helianthinin. Publication No. 324.  相似文献   

11.
 Short oligopeptides (14 residues) derived from the DNA recognition helix of the phage 434 repressor (434R) have been tethered onto the metallointercalating [Rh(phi)2(phen′)]3+, and the DNA recognition characteristics of the resultant metal-peptide complexes have been examined. DNA sequence selectivities for the family of metal-peptide complexes, determined in photoactivated DNA cleavage experiments, reproduce features of operator recognition by the native 434R. Binding to the DNA duplex depends both on the appended peptide and upon the metallointercalating unit, as determined through variations in the peptide sequence and in the diastereomeric configuration of the metal-peptide. The complexes preferentially target 5′-ACAA-3′ operator sites and single-base variants, bind at 50 nM concentrations, and, as determined by chemical footprinting, protect 7–10 bp of DNA around the target sites. Comparative cleavage studies on synthetic oligonucleotides containing variations in operator sequence, furthermore, reveal a hierarchy in sequence preference which resembles the native protein, but highest affinity for the metal-peptides, unlike 434R, is found for 5′-ACGA-3′. These studies illustrate a new route to the rational design of small, artificial repressors through the construction of metal-peptide complexes. Received: 18 June 1997 / Accepted: 11 September 1997  相似文献   

12.
We report for the first time the presence of a sex steroid-binding protein in the plasma of green sea turtles Chelonia mydas, which provides an insight into reproductive status. A high affinity, low capacity sex hormone steroid-binding protein was identified in nesting C. mydas and its thermal profile was established. In nesting C. mydas testosterone and oestradiol bind at 4°C with high affinity (K a = 1.49 ± 0.09 × 109 M−1; 0.17 ± 0.02 × 107 M−1) and low binding capacity (B max = 3.24 ± 0.84 × 10−5 M; 0.33 ± 0.06 × 10−4 M). The binding affinity and capacity of testosterone at 23 and 36°C, respectively were similar to those determined at 4°C. However, oestradiol showed no binding activity at 36°C. With competition studies we showed that oestradiol and oestrone do not compete for binding sites. Furthermore, in nesting C. mydas plasma no high-affinity binding was observed for adrenocortical steroids (cortisol and corticosterone) and progesterone. Our results indicate that in nesting C. mydas plasma temperature has a minimal effect on the high-affinity binding of testosterone to sex steroid-binding protein, however, the high affinity binding of oestradiol to sex steroid-binding protein is abolished at a hypothetically high (36°C) sea/ambient/body temperature. This suggests that at high core body temperatures most of the oestradiol becomes biologically available to the tissues rather than remaining bound to a high-affinity carrier.  相似文献   

13.
A novel metalloproteinase, recombinant fibrinogenase IV (rFIVa), was expressed and purified from Agkistrodon acutus venom. It is a single-chain protein with an apparent molecular weight of 27 kDa. Western blot showed that it had a good immunological reaction against anti-FIVa rabbit serum. The kinetic parameters Km and Kcat of rFIVa on the substrate T6140 were 7.471×10−4 mol/l and 5.103×10−5 s−1. RFIVa cleaved preferentially the α-chain, and the β- and γ-chains of fibrinogen were also cleaved when the incubation time was prolonged. The administration of rFIVa (1.8 and 5.4 mg/kg) to animals with acute blood-stasis model produced a decrease in fibrinogen to control values. To our knowledge, this is the first report of the expression, purification, and evaluation of recombinant fibrinogenase IV, which belongs to class P-I metalloproteinase from A. acutus venom.  相似文献   

14.
To gain insight into the metabolic design of the amino acid carrier systems in fish, we injected a bolus of 15N amino acids into the dorsal aorta in mature rainbow trout (Oncorhynchus mykiss). The plasma kinetic parameters including concentration, pool size, rate of disappearance (R d), half-life and turnover rate were determined for 15 amino acids. When corrected for metabolic rate, the R d values obtained for trout for most amino acids were largely comparable to human values, with the exception of glutamine (which was lower) and threonine (which was higher). R d values ranged from 0.9 μmol 100 g−1 h−1 (lysine) to 22.1 μmol 100 g−1 h−1 (threonine) with most values falling between 2 and 6 μmol 100 g−1 h−1. There was a significant correlation between R d and the molar proportion of amino acids in rainbow trout whole body protein hydrolysate. Other kinetic parameters did not correlate significantly with whole body amino acid composition. This indicates that an important design feature of the plasma-free amino acids system involves proportional delivery of amino acids to tissues for protein synthesis.  相似文献   

15.
Mg2+ in various concentrations was added to purified Rubisco in vitro to gain insight into the mechanism of molecular interactions between Mg2+ and Rubisco. The enzyme activity assays showed that the reaction between Rubisco and Mg2+ was two order, which means that the enhancement of Rubisco activity was accelerated by low concentration of Mg2+ and slowed by high concentration of Mg2+. The kinetics constant (K m) and V max was 1.91 μM and 1.13 μmol CO2 mg−1 protein∙min−1, respectively, at a low concentration of Mg2+, and 3.45 μM and 0.32 μmol CO2∙mg−1 protein∙min−1, respectively, at a high concentration of Mg2+. By UV absorption and fluorescence spectroscopy assays, the Mg2+ was determined to be directly bound to Rubisco; the binding site of Mg2+ to Rubisco was 0.275, the binding constants (K A) of the binding site were 6.33 × 104 and 5.5 × 104 l·mol−1. Based on the analysis of the circular dichroism (CD) spectra, it was concluded that the binding of Mg2+ did not alter the secondary structure of Rubisco, suggesting that the observed enhancement of Rubisco carboxylase activity was caused by a subtle structural change in the active site through the formation of the complex with Mg2+.  相似文献   

16.
Single-chain derivatives of the 434 repressor containing one wild-type and one mutant DNA-binding domain recognize the general operator ACAA-6 base pairs-NNNN, where the ACAA operator subsite is contacted by the wild-type and the NNNN tetramer by the mutant domain. The DNA-binding specificities of several single-chain mutants were studied in detail and the optimal subsites of the mutant domains were determined. The characterized mutant domains were used as building units to obtain homo- and heterodimeric single-chain derivatives. The DNA-binding properties of these domain-shuffled derivatives were tested with a series of designed operators of NNNN-6 base pairs-NNNN type. It was found that the binding specificities of the mutant domains were generally maintained in the new environments and the binding affinities for the optimal DNA ligands were high (with K(d) values in the range of 10(-11)-10(-10) M). Considering that only certain sequence motifs in place of the six base pair spacer can support optimal contacts between the mutant domains and their subsites, the single-chain 434 repressor mutants are highly specific for a limited subset of 14 base pair long DNA targets.  相似文献   

17.
Human serum heme–albumin (HSA-heme) displays globin-like properties. Here, the allosteric inhibition of ferric heme [heme-Fe(III)] binding to human serum albumin (HSA) and of ferric HSA–heme [HSA-heme-Fe(III)]-mediated peroxynitrite isomerization by isoniazid and rifampicin is reported. Moreover, the allosteric inhibition of isoniazid and rifampicin binding to HSA by heme-Fe(III) has been investigated. Data were obtained at pH 7.2 and 20.0 °C. The affinity of isoniazid and rifampicin for HSA [K 0 = (3.9 ± 0.4) × 10−4 and (1.3 ± 0.1) × 10−5 M, respectively] decreases by about 1 order of magnitude upon heme-Fe(III) binding to HSA [K h = (4.3 ± 0.4) × 10−3 and (1.2 ± 0.1) × 10−4 M, respectively]. As expected, the heme-Fe(III) affinity for HSA [H 0 = (1.9 ± 0.2) × 10−8 M] decreases by about 1 order of magnitude in the presence of saturating amounts of isoniazid and rifampicin [H d = (2.1 ± 0.2) × 10−7 M]. In the absence and presence of CO2, the values of the second-order rate constant (l on) for peroxynitrite isomerization by HSA-heme-Fe(III) are 4.1 × 105 and 4.3 × 105 M−1 s−1, respectively. Moreover, isoniazid and rifampicin inhibit dose-dependently peroxynitrite isomerization by HSA-heme-Fe(III) in the absence and presence of CO2. Accordingly, isoniazid and rifampicin impair in a dose-dependent fashion the HSA-heme-Fe(III)-based protection of free l-tyrosine against peroxynitrite-mediated nitration. This behavior has been ascribed to the pivotal role of Tyr150, a residue that either provides a polar environment in Sudlow’s site I (i.e., the binding pocket of isoniazid and rifampicin) or protrudes into the heme-Fe(III) cleft, depending on ligand binding to Sudlow’s site I or to the FA1 pocket, respectively. These results highlight the role of drugs in modulating heme-Fe(III) binding to HSA and HSA-heme-Fe(III) reactivity.  相似文献   

18.
In this research, the enhancement of electron-transfer activity of hemoglobin (Hb) in lauric acid film was investigated for the first time. This type of composite film was made on a glassy carbon electrode by a casting method. Cyclic voltammetric result of the modified electrode displays a well-defined redox peak, which was attributed to the direct electrochemical response of Hb. Our results illustrate that Hb exchange electrons directly with electrode and exhibits the characteristics of peroxidase. When we use this modified electrode as a biosensor, it gives excellent performance in the electrocatalytic reduction of hydrogen peroxide (H2O2). The parameters such as pH and applied potential of the biosensor influencing in H2O2 detection were optimized carefully. Through the optimal conditions, the proposed biosensor shows the linear range for H2O2 determination was from 1×10−5 to 1.25×10−4 mol L−1 with a detection limit of 1×10−7 mol L−1. The biosensor retained more than 90% of the initial response after 14 d.  相似文献   

19.
Noncovalent DIDS binding to Band 3 (AE1) protein in human erythrocyte membranes, modified by non-penetrating, water soluble 1-ethyl-3-(4-azonia-4,4-dimethylpentyl)-carbodiimide iodide (EAC), was studied at 0°C in the presence of 165 mM KCl. Under experimental conditions applied up to (48 ± 5) % of irreversible chloride self-exchange inhibition was observed. The apparent dissociation constant, KD, for “DIDS-Band 3” complex, determined from the chloride transport experiments, was (34 ± 3) nM and (80 ± 12) nM for control and EAC-treated resealed ghosts, respectively. The inhibition constant, Ki, for DIDS was (35 ± 6) nM and (60 ± 8) nM in control and EAC-treated ghosts, respectively. The reduced affinity for DIDS reversible binding was not a result of negative cooperativity of DIDS binding sites of Band 3 oligomer since Hill’s coefficients were indistinguishable from 1 (within the limit error) both for control and EAC-treated ghosts. By using tritium-labeled DIDS, 4,4’-diisothiocyanato-2,2’-stilbenedisulfonate ([3H]DIDS), the association rate constant, k+1 (M−1s−1), was measured. The mean values of (4.3 ± 0.7) × 105 M−1s−1 for control and (2.7 ± 0.7) × 105 M−1s−1 for EAC-treated ghosts were obtained. The mean values for KD, evaluated from [3H]DIDS binding measurements, were (37 ± 9) nM and (90 ± 21) nM for control and EAC-modified ghosts, respectively. The results demonstrate that EAC modification of AE1 reduces about 2-fold the affinity of AE1 for DIDS. It is suggested that half of the subunits are modified near the transport site by EAC.  相似文献   

20.
This study investigated vasodilator mechanisms in the dorsal aorta of the elephant fish, Callorhinchus milii, using anatomical and physiological approaches. Nitric oxide synthase could only be located in the perivascular nerve fibres and not the endothelium of the dorsal aorta, using NADPH histochemistry and immunohistochemistry. In vitro organ bath experiments demonstrated that a NO/soluble guanylyl cyclase (GC) system appeared to be absent in the vascular smooth muscle, since the NO donors SNP (10−4 mol l−1) and SIN-1 (10−5 mol l−1) were without effect. Nicotine (3 × 10−4 mol l−1) mediated a vasodilation that was not affected by ODQ (10−5 mol l−1), l-NNA (10−4 mol l−1), indomethacin (10−5 mol l−1), or removal of the endothelium. In contrast, the voltage-gated sodium channel inhibitor, tetrodotoxin (10−5 mol l−1), significantly decreased the dilation induced by nicotine, suggesting that it contained a neural component. Pre-incubation of the dorsal aorta with the calcitonin gene-related peptide (CGRP) receptor antagonist, CGRP8–37 (10−6 mol l−1) also caused a significant decrease in the nicotine-induced dilation. We propose that nicotine is mediating a neurally-derived vasodilation in the dorsal aorta that is independent of NO, prostaglandins and the endothelium, and partly mediated by CGRP.  相似文献   

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