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1.
Abstract

The binding of three analogues of the minor-groove binding antiviral antibiotic distamycin (Dst) with double-stranded (ds)-DNA were monitored using ds-DNA melting temperature (Tm) measurements, ethidium bromide (EtBr) displacement assay, footprinting analysis and induced circular dichroism (ICD). These compounds contained 3–5 N-methyl-pyrrole-car- boxamide units and lacked the N-terminal formamide unit present in Dst. These experiments suggested that the present analogues did not compromise their AT-specificity despite the deletion of the N-terminal formamide unit. The binding affinities, however, were significantly affected. Interestingly, the analogue with three N-methyl-pyrrole-carboxamide units exhibited an initial decrease in ICD at >40 mM salt concentrations. This was followed by a pronounced recovery of ICD at > 1.6 M salt concentrations, a phenomenon hitherto not observed with any other DNA binding molecules. The pentapyrrole analogue exhibited the highest binding affinity with CT-DNA under normal (40 mM) salt conditions. However, it suffered maximum relative dissociation under high salt conditions and did not exhibit any recovery in ICD at higher NaCl concentrations. The analogues possessing four and five pyrrole rings exhibited intense ICD signals with poly d(GC) in the ligand absorption region in the presence of 40 mM NaCl, unlike the one with three pyrrole rings. These ICD signals were however, highly susceptible to changes in ionic strength. Thus subtle modifications in the ligand molecular structure can have dramatic effect on their DNA binding properties.  相似文献   

2.
First examples of distamycin (Dst) analogs which lack hydrogen bond donor or acceptor groups at the N-terminus have been synthesized. The first molecule of this series, which is a bispyrrole peptide, did not exhibit any detectable binding with double-stranded (ds) DNA. However, all other analogs did bind strongly to AT-rich sequences of ds-DNA, with the binding affinities increasing as a function of the number of repeating pyrrole carboxamide units. These results imply that a hydrogen bond donor or acceptor atom per se at the N-terminus is not a prerequisite for DNA binding in the case of pyrrole carboxamide-based Dst analogs. However, in the absence of H-bond donor or acceptor at the N-terminus, a minimum of three pyrrole carboxamide units is necessary for the onset of DNA binding. Beyond this minimum number, the binding affinity increases as a function of the number of pyrrole units, as a result of the greater availability of hydrogen bonding and van der Waals surface. Experiments with poly[d(G-C)] have shown that the presence of the N-terminus formamide group is not inevitable for GC binding of this class of molecules. The observation that the N-terminus formamide unit can be dispensed with suggests that these molecules, which are much easier to synthesize and functionalize, can be used in place of the conventional analogs of distamycin for the development of novel minor groove binders with extended sequence recognition properties.  相似文献   

3.
Polyamides that are structural analogues of the naturally occurring DNA minor groove binding antibiotic distamycin (Dst) are promising candidates as gene modulators. Developing strategies for the large scale screening and monitoring of the cellular distribution of such ligands would aid the faster discovery of molecules, which would have eventual utility in molecular biology and medicine. Attachment of fluorescent tags would be a useful step towards this end. A fundamental question in this connection is whether the tag modifies the DNA binding affinity of the parent compounds. Towards answering this question, we have developed two oligopeptides that bear the dansyl (N, N-dimethylaminonaphthalene sulfonamido fluorophore) coupled directly to the N-terminus of the conjugated N-methylpyrrole carboxamide network, and possess three or four N-methyl pyrrole carboxamide units (abbreviated as Dn3 and Dn4 respectively). DNA binding abilities of these molecules were assessed from fluorescence titration experiments, duplex-DNA T(m) analysis (employing both UV and fluorescence spectroscopy), induced circular dichroism measurements (ICD), salt dependence of ICD and apparent binding constant measurements (K(app)) employing ethidium bromide (EtBr) displacement assay. Both these molecules reported DNA binding in the form of an enhanced fluorescence emission. As judged from the ICD measurements, salt dependence of ICD, T(m) analysis and K(app) measurements, the binding affinities of the molecules that possessed dansyl group at their N-termini were lower than the ones with equivalent number of amide units, but possessed N-methylpyrrole carboxamide unit at their N- termini. These results would have implications in the future design of fluorescent polyamides.  相似文献   

4.
Two synthetic analogues of distamycin (Dst), PPA and PAP, containing a saturated beta-alanine moiety substituting for an N-methylpyrrole chromophore were studied for their interactions with the double-stranded alternating copolymer poly(dA-dT).poly(dA-dt) [abbreviated as poly(dA-dT)], with UV absorption and circular dichroism (CD) spectroscopy. The distinctive feature of these analogues is the difference in the extents of extended conjugation due to contiguous pyrrole rings: it decreases in the order Dst greater than PPA greater than PAP. Both these analogues bind to poly(dA-dT) in a way similar to Dst, as suggested from the observed red shift in the UV spectra of the ligands upon complexation and the appearance of induced Cotton effects (in the 290-350-nm region) in the CD spectra of the complexes. A comparative study of (i) the spectral features of the complexes between these ligands, Dst and netrospin (Nt) and poly(dA-dT), and (ii) the binding parameters for the association with the polynucleotide suggests that the number and relative positions of the pyrrole moieties influence the spectral features and thermodynamic stabilities of the complexes, and the latter show a progressive decrease in the order Dst greater than Nt greater than PPA greater than PAP. Implications of these results vis-à-vis the molecular basis of Dst-DNA interaction are discussed.  相似文献   

5.
In order to investigate ligand binding sites in alpha-thrombin that interact with nonpolymerized fibrin, fibrinogen was conjugated (with CNBr) to Sepharose 4B and converted to the nonpolymerized fibrin resin with alpha-thrombin. Human alpha-thrombin was bound to the resin at 22 degrees C and eluted with a linear NaCl gradient [50-300 mM in 50 mM tris(hydroxymethyl)aminomethane hydrochloride, pH 7.6] with midpeak elution occurring at an ionic strength that corresponds to 170 +/- 5 mM NaCl. Among various ligands examined, ATP and its analogues caused alpha-thrombin to elute with 125 mM or less salt. Apparent dissociation constants were estimated by the dependence of elution volume on ligand concentration. The most potent ligands for desorption from the column were anionic (e.g., adenine nucleotides), which also inhibit thrombin esterolytic/amidolytic and clotting activity [Conery, B. G., & Berliner, L. J. (1983) Biochemistry 22, 369-375]. The desorption series was at 10 mM concentrations: ATP = ADP greater than pyrophosphate greater than citrate greater than oxalate greater than PO4(3-). Contrastingly, serotonin and related apolar compounds did not cause dissociation of alpha-thrombin from the fibrin resin, even though several of these substances inhibit fibrinogen clotting and esterolytic/amidolytic activities of the enzyme. These data imply that independent sites for apolar and anionic binding in alpha-thrombin are required for converting fibrinogen into clottable fibrin and that alpha-thrombin-fibrin binding involves an anionic site.  相似文献   

6.
Abstract

Pulsed magnetic field (PMF) effects on soybean plant regeneration under salt stress conditions were investigated. Seedlings were raised from seeds pre-treated with 0.1, 1.0, 10.0 and 100.0 Hz PMF. Cotyledonary nodal (CN) explants from PMF exposed and unexposed seedlings were cultured in media containing different concentrations of NaCl (0, 10, 20, 30 and 40 mM). In CN explants from unexposed seedlings, increasing salt concentration progressively suppressed the regeneration and development of shoots and roots. Plantlets were regenerated only on medium containing 0, 10, 20 and 30 mM NaCl. The highest dose of NaCl (40 mM) failed to induce shoot formation and strongly reduced the number of roots which also exhibited reduced length. Cotyledonary nodal explants from PMF exposed seedlings, cultured at 10, 20 and 30 mM NaCl, exhibited a higher frequency of shoot and root regeneration, as well as a higher number and length of shoots and roots compared to unexposed ones, with 1.0 Hz frequency resulting the most efficient in promoting regeneration. At 40 mM NaCl, the promotive effect of different PMFs frequencies was related to the induction of a greater number of roots and the enhancement of root length. Our results suggest that PMF pre-treatment could help the regeneration of soybean under salt stressed condition.  相似文献   

7.
Fless GM  Halfman CJ  Kirk EW 《Biochemistry》2000,39(10):2740-2747
Lipoprotein(a) [Lp(a)] exhibits many of the same properties as plasminogen, owing to a similar structural makeup from a composite of multiple kringle domains. Shared behavior includes induction of an expanded conformation by lysine analogues, inhibition of this effect, and creation of a compact conformation by NaCl. Here, we examine in detail the independent and mutual effects of NaCl and 6-aminohexanoic acid (6-AHA) on the structure of Lp(a) and the relationship between the binding of the two ligands. We find that NaCl promotes the compact conformation while binding to Lp(a) homogeneously. In the absence of salt, 6-AHA leads to the complete unfolding of Lp(a), a process that is accompanied by cooperative binding. Reversal of conformation and weakening of binding occurred when one ligand was added to Lp(a) in the presence of the other, suggesting competitive binding. High concentrations of NaCl completely reversed the expansion of Lp(a) in 100 mM 6-AHA, and high concentrations of 6-AHA unfolded Lp(a) in the presence of 100 mM NaCl, but only by 30% in the case of the 15 kringle IV Lp(a) studied. Induction of the compact form of Lp(a) appears to be an effect in common with all salts examined and cannot be attributed solely to the anion, as in the case of plasminogen. The results were summarized in terms of a model of Lp(a) depicting the conformational alterations of apo(a) caused by the binding of the two ligands. In the compact conformation in NaCl, apo(a) is apposed to the particle surface. The fully expanded form in 6-AHA results from release of both the variable and constant kringle domains. In the intermediate form in water and in a solution containing both NaCl and 6-AHA, only the variable domain is released from the particle surface.  相似文献   

8.
The kinetic properties of cruciform extrusion in supercoiled DNA molecules fall into two main classes. C-type cruciforms extrude in the absence of added salt, at relatively low temperatures, with large activation energies, while S-type cruciforms exhibit no extrusion in the absence of salt, and maximal rates at 50 mM NaCl, with activation energies about one quarter those of the C-type. These diverse properties are believed to reflect two distinct pathways for the extrusion process, and are determined by the nature of the sequences which form the context of the inverted repeat. C-type kinetics are conferred by A + T rich sequences, implying a role of helix stability in the selection. In this study we have shown that: 1. Helix-destabilising solvents (dimethyl formamide and formamide) facilitate extrusion by normally S-type molecules at low temperatures in the absence of salt. 2. C-type extrusion is strongly suppressed by low concentrations (2-4 microM) distamycin, at which concentrations S-type extrusion is enhanced. 3. Some extrusion occurs in a C-type construct in the presence of 50 mM NaCl. This is increased by addition of 3 microM distamycin, under which conditions extrusion becomes effectively S-type. Thus S-type constructs can behave in a quasi-C-type manner in the presence of helix-destabilising solvents, and C-type extrusion is suppressed by binding a compound which stabilises A + T rich regions of DNA. Helix destabilisation leads to C-type behaviour, while helix stabilisation results in S-type properties. These studies demonstrate the influence of contextual helix stability on the selection of kinetic mechanism of cruciform extrusion.  相似文献   

9.
Abstract

Salt stress is one of the major environmental factors limiting crop growth and yield. To understand the effect of salt stress on plant growth, we investigated the response of three perilla varieties (Suyin 1, Ziye 7, and Ziye 10) to NaC1 exposure at concentrations of 0, 50, 100, 150, 200, and 250 mM in terms of seed germination, seedling growth, root activity, contents of soluble sugar, proline, and malondialdehyde (MDA), and peroxidase (POD) enzyme activity. Germination characteristics, such as the percentage of seed germination, tended to decrease with increasing NaC1 concentrations. After three weeks of salt stress, the three varieties exhibited different salt tolerance in terms of seed germination, seedling growth, and physiological changes: seedling growth was inhibited to various degrees, seedling vigor and root activities decreased, and MDA, proline, and soluble sugar contents increased with increasing NaCl concentrations. POD enzyme activity, a protective mechanism against salt stress, increased at low NaC1 concentrations in Suyin1 (0–150 mM) and Ziye 7 (0–100 mM), and then decreased at higher NaCl concentrations. In Ziye 10, on the other hand, POD activity dropped significantly with increasing NaCl concentrations. These results suggest that among the three varieties Suyin 1 is more salt tolerant than Ziye 7 and Ziye 10, and that Ziye 10 is the most sensitive to salt stress.  相似文献   

10.
11.
The interaction of tubulin with simple analogues of colchicine that contain both its tropolone and trimethoxyphenyl rings has been characterized, and the results were analyzed in terms of the simple bifunctional ligand model developed for the binding of colchicine [ Andreu , J. M., & Timasheff , S. N. (1982) Biochemistry 21, 534-543] on the basis of interactions of tubulin with single-ring analogues. The compound 2-methoxy-5-(2,3,4-trimethoxyphenyl)-2,4,6- cycloheptatrien -1-one has been found to bind reversibly to 0.86 +/- 0.06 site of purified calf brain tubulin with an equilibrium constant of (4.9 +/- 0.3) X 10(5) M-1 (25 degrees C), delta H degrees app = -1.6 +/- 0.7 kcal mol-1, and delta S degrees app = 20.5 +/- 2.5 eu. The binding appears specific for the colchicine site. The closely related compound 2-methoxy-5-[[3-(3,4,5-trimethoxyphenyl)-propionyl]amino] -2,4,6- cycloheptatrien -1-one interacts weakly with tubulin. Binding of the first analogue is accompanied by ligand fluorescence appearance, quenching of protein fluorescence, perturbation of the far-ultraviolet circular dichroism of tubulin, and induction of the tubulin GTPase activity, similarly to colchicine binding. Substoichiometric concentrations of the analogue inhibit microtubule assembly in vitro. Excess analogue concentration under microtubule-promoting conditions induces an abnormal cooperative polymerization of tubulin, similar to that of the tubulin-colchicine complex.  相似文献   

12.
HU is one of the most abundant proteins in bacterial chromosomes and participates in nucleoid compaction and gene regulation. We report experiments using DNA stretching that study the dependence of DNA condensation by HU on force, salt and HU concentration. Previous experiments at sub-physiological salt levels revealed that low concentrations of HU could compact DNA, whereas larger HU concentrations formed a DNA-stiffening complex. Here we report that this bimodal binding behavior depends sensitively on salt concentration. Only the compaction mode was observed for 150 mM and higher NaCl levels, i.e. for physiological salt concentrations. Similar results were obtained for the more physiological salt K-glutamate. Real-time studies of dissociation kinetics revealed that HU unbound slowly (minutes to hours under the conditions studied) but completely for salt concentrations at or above 100 mM NaCl; the lifetime of HU complexes was observed to increase with the HU concentration at which the complexes were formed, and to decrease with salt concentration. Higher salt levels of 300 mM NaCl completely eliminated observable HU binding to DNA. Finally, we observed that the dissociation kinetics depend on force applied to the DNA: increased applied force in the sub-piconewton range accelerates dissociation, suggesting a mechanism for DNA tension to regulate chromosome structure and gene expression.  相似文献   

13.
The in vitro response of kiwifruit (Actinidia deliciosa) to increasing concentrations of boron (B) and NaCl in the culture medium was studied. Kiwifruit shoot cultures were grown in vitro for 12 weeks on an MS medium containing two B concentrations (0.1 and 2 mM) combined with five NaCl concentrations (0, 10, 20, 40 and 80 mM). Kiwifruit produced the longest shoots with 2 mM B when NaCl concentration was 0--20 mM. More shoots were produced with 2 mM B for all NaCl treatments. More shoots were produced with 2 mM B and 10 and 20 mM NaCl. High B concentrations in the culture medium significantly increased shoot proliferation. Explants exhibited a moderate chlorotic appearance with 40 mM NaCl and shoots died with 80 mM NaCl. With 2 mM B, the B concentration of explants was 5--9X greater for the various NaCl treatments compared to the control. Increasing the NaCl concentration from 10 to 80 mM, resulted in higher Na and Cl concentrations in explants for all B treatments, while K and Ca concentrations decreased. Phosphorus concentration in the explants was significantly increased by increasing the NaCl concentration reaching a maximum value at 80 mM NaCl for the two B concentrations.  相似文献   

14.
Interaction of two synthetic analogs of distamycin (Dst), PPA and PAP, containing a saturated beta-alanine moiety replacing one N-methylpyrrole ring, with different polynucleotides and natural DNAs were studied using UV and CD spectroscopy. The results indicate that, similar to Dst, these analogs bind to DNA via the minor groove with a specificity towards AT-base pairs. It may be proposed that pyrrole chromophores in Dst probably do not play a role in the AT-base selectivity exhibited by Dst.  相似文献   

15.
Lai JR  Huck BR  Weisblum B  Gellman SH 《Biochemistry》2002,41(42):12835-12842
Protegrins are short, cationic peptides that display potent, broad-spectrum antimicrobial activity. PG-1, the first of the five natural analogues discovered, forms a rigid antiparallel two-stranded beta-sheet that is stabilized by two disulfide bonds. The two strands of the sheet are linked by a short two-residue loop segment. Removal of the disulfide bridges (e.g., in Cys --> Ala analogues) is known to cause marked loss of antimicrobial activity. We have used basic principles of beta-hairpin design to develop linear analogues of PG-1 that lack cysteine but nevertheless display PG-1-like activity. Our most potent reengineered molecules contain three essential design features: (i) the four cysteine residues of PG-1 are replaced by residues that have high propensity for beta-strand conformation, (ii) D-proline is placed at the i + 1 position of the reverse turn to promote a type II' beta-turn, and (iii) amino functionality is incorporated at the gamma-carbon of the D-proline residue to mimic the charge distribution of the natural beta-hairpin. Structural studies revealed that the antimicrobial potency of the non-disulfide-bonded peptides can be correlated to the stability of the beta-hairpin conformations they adopt in aqueous solution. The presence of 150 mM NaCl was found to have little effect on the antimicrobial activity of PG-1, but one of our linear analogues loses some potency under these high salt conditions. Despite this discrepancy in salt sensitivity, NMR and CD data indicate that neither PG-1 nor our linear analogue experiences a significant decrease in beta-hairpin conformational stability in the presence of 150 mM NaCl. Thus, salt inactivation is not due to destabilization of the beta-hairpin conformation. Furthermore, our results show that beta-sheet design principles can be used to replace conformation-stabilizing disulfide bridges with noncovalent conformation-stabilizing features.  相似文献   

16.
The in vitro response of kiwifruit (Actinidia deliciosa) to increasing concentrations of boron (B) and NaCl in the culture medium was studied. Kiwifruit shoot cultures were grown in vitro for 12 weeks on an MS medium containing two B concentrations (0.1 and 2 mM) combined with five NaCl concentrations (0, 10, 20, 40 and 80 mM). Kiwifruit produced the longest shoots with 2 mM B when NaCl concentration was 0--20 mM. More shoots were produced with 2 mM B for all NaCl treatments. More shoots were produced with 2 mM B and 10 and 20 mM NaCl. High B concentrations in the culture medium significantly increased shoot proliferation. Explants exhibited a moderate chlorotic appearance with 40 mM NaCl and shoots died with 80 mM NaCl. With 2 mM B, the B concentration of explants was 5--9X greater for the various NaCl treatments compared to the control. Increasing the NaCl concentration from 10 to 80 mM, resulted in higher Na and Cl concentrations in explants for all B treatments, while K and Ca concentrations decreased. Phosphorus concentration in the explants was significantly increased by increasing the NaCl concentration reaching a maximum value at 80 mM NaCl for the two B concentrations.  相似文献   

17.
Dynamic light scattering (DLS) measurements were performed to study the binding of anionic surfactant alpha olefin sulfonate (AOS) to gelatin chains at various NaCl concentrations at 30 degrees C in aqueous sodium phosphate buffer (pH = 6.8) solutions. The surfactant concentration was varied from 0 to 80 mM and the NaCl concentrations chosen were 0.025, 0.05, and 0.1 M. AOS exhibited electrostatic binding to the positively charged sites of the polypeptide chain resulting in considerable reduction in its hydrodynamic radius up to critical micellar concentration (cmc = 8 mM for no salt, 0.01 and 0.025 M, and 5 mM for 0.05 M and 2 mM for 0.1 M solutions). The correlation function revealed the presence of two types of structures above cmc; namely the micelles of AOS and gelatin-AOS micelle complexes. The micellar radii (Rm), the effective gelatin-surfactant complex radii (Rc), have been determined as a function of salt concentration. No critical aggregation concentration (cac) was observed. The inter-gelatin-surfactant complex (kD1) and inter-micellar interactions (kD2), were determined by fitting the concentration dependence of Rm and Rc to a virial expansion in reduced concentration (c - cmc), which are compared. While kD1 showed strong ionic strength dependence, kD2 remained invariant of the same. The protein to surfactant binding ratio was found to be smaller than normal. Results have been discussed within the framework of the necklace-bead model of polymer-surfactant interactions.  相似文献   

18.
The ionic species of cytosol estrogen receptors from mature rat uteri have been compared by HPIEC on a SynChrom AX-1000 column when complexed with either [125I]iodoestradiol, [3H]estradiol or [3H]4-hydroxy tamoxifen. Three species of receptors (isoforms) each suppressible by excess competitor were fractionated at identical salt concentrations regardless of ligand employed. One species eluted in the column void volume (10 mM) and the others at congruent to 90 mM and congruent to 155 mM phosphate. Activation of receptor complexes by increasing time of incubation with ligand from 1 to 24 h at 4 degrees C or addition of 10 mM GTP increased the proportion of the congruent to 90 mM species for all 3 ligands. The addition of 10 mM molybdate to homogenization and HPIEC buffers resulted in only two species being resolved at 10 and 110 mM phosphate. These species were again identical regardless of ligand employed. Increasing concentrations of estradiol (1-40 nM) tamoxifen (20 nM-4 microM) and 4-hydroxy tamoxifen (2-400 nM) were able to compete for binding of [125I]iodoestradiol to each of the three ionic species. Binding to each species was inhibited equally by each concentration of competitor. There was no preferential or unique association of estrogen or antiestrogen with any of the ionic species and all ligands gave identical ionic species of non-activated and activated receptor complexes.  相似文献   

19.
Protection from salt stress was observed in the terms of yield (fresh and dry weight, chlorophyll and protein) and nitrogenase activity. Azollapinnata appeared highly sensitive to 40 mM external NaCl stress. Fronds of Azolla unable to grow beyond a concentration of 30 mM NaCl and accordingly death was recorded at 40 mM NaCl on the 6th day of incubation. Yield was inhibited by various levels of NaCl (0, 10, 20 and 30 mM). Addition of combined-N to the growth medium protected the association partially from salt toxicity. Among the N-sources (NO3-, NH4+ and urea) tried, urea mitigated the salt-induced toxicity most efficiently. Reduction in nitrogenase activity was observed when intact Azolla was grown in nutrient medium either supplemented with different levels of NaCl or combined nitrogen. Only NO3- (5 mM) protected the enzymatic activity from salt toxicity while other concentrations of ammonium, nitrate and urea slowed down the salt-induced inhibition of enzyme activity in Azolla-Anabaena association. These results suggested that an optimum protection from salt stress could be obtained by using a combination of combined nitrogen sources. The reason for this protection might be due to the availability of combined nitrogen to the association, nitrogen is only available through the biological nitrogen fixation which is the most sensitive to salt stress.  相似文献   

20.
High affinity binding for mu and kappa opioid receptors has been observed in analogues of cyclazocine, ethylketocyclazocine and naltrexone where the prototypic (of opiates) phenolic OH group was replaced with a formamide (-NHCHO) group. For the 8-formamide analogue of cyclazocine, binding is highly enantiospecific (eudismic ratios approximately 2000 for mu and kappa) with K(i) values 相似文献   

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