Influence of magnesium and manganese on some biological and physical properties of tetracycline

Accumulation of (3)H-tetracycline in nonproliferating cells of susceptible and resistant strains of Escherichia coli and Staphylococcus aureus in tris(hydroxymethyl)aminomethane (Tris) buffer (10 mm, pH 7.5) was significantly decreased in the presence of 5 to 40 mm MgCl(2) and increased in the presence of 5 to 10 mm MnCl(2). When the bacteria first accumulated (3)H-tetracycline in plain Tris.HCl, and the metal salts were thereafter added, a prompt decrease or increase in radioactivity of the cells was observed after the addition of Mg(2+) or Mn(2+), respectively. In phosphate buffer (10 mm, pH 7.5), the effect of Mg(2+) was delayed. Three minutes after addition of (3)H-tetracycline, uptake was as in the control cell suspension, but thereafter it dropped rapidly. When (3)H-tetracycline was incubated with Mg(2+) before addition to the bacterial suspension, uptake was scarcely measurable. The addition of Mg(2+) to growing cultures of S. aureus and E. coli caused a marked decrease in susceptibility; in contrast, no increase in susceptibility could be demonstrated when Mn(2+) was added. It was also demonstrated that Mg(2+) and Mn(2+) had distinct influences on the absorption spectrum, the optical rotatory dispersion, the circular dichroism, and the lipid solubility of tetracycline.     

Isoionic titration and isopycnic density gradient centrifugation studies of magnesium activation and subunit dissociation in yeast enolase.

Isopycnic density gradient centrifugations were performed on yeast enolase A in cesium chloride and sulfate at the isoionic pH (6.0–6.5) and at pH 8.1. The dissociation of the enzyme appears to be greater at the more alkaline pH. No large effect of the cofactor magnesium or pH or dissociation on the isopycnic point was found. Isoionic titrations were carried out in the presence and absence of magnesium using both salts. The metal reduces net anion binding by isoionic enzyme and net cation binding by pH 8.1 enzyme by about 1.6 – 3.4 equivalents at 0.05 ionic strength and somewhat less at the isopycnic ionic strengths. It is concluded that the metal does not significantly affect net hydration of the enzyme and that subunit dissociation is not accompanied by large changes in hydration or salt binding.     

Molecular level probing of preferential hydration and its modulation by osmolytes through the use of pyranine complexed to hemoglobin

Two spectroscopic probes are used to expose molecular level changes in hydration shell water interactions that directly relate to such issues as preferential hydration and protein stability. The major focus of the present study is on the use of pyranine (HPT) fluorescence to probe as a function of added osmolytes (PEG, urea, trehalose, and magnesium), the extent to which glycerol is preferentially excluded from the hydration shell of free HPT and HPT localized in the diphosphoglycerate (DPG) binding site of hemoglobin in both solution and in Sol-Gel matrices. The pyranine study is complemented by the use of vibronic side band luminescence from the gadolinium cation that directly exposes the changes in hydrogen bonding between first and second shell waters as a function of added osmolytes. Together the results form the basis for a water partitioning model that can account for both preferential hydration and water/osmolyte-mediated conformational changes in protein structure.     

Crystallographic and energetic analysis of binding of selected anions to the yellow variants of green fluorescent protein

The fluorescence emission of yellow fluorescent proteins (YFPs) has been shown to respond rapidly and reversibly to changes in the concentration of some small anions such as halides; this allows for the use of YFPs as genetically encodable Cl(-) sensors that may be targeted to specific organelles in living cells. Fluorescence is suppressed due to protonation of the chromophore upon anion binding, with a stronger level of interaction at low pH values. At pH 6.0, the apparent dissociation constant (K(app)) for Cl(-) is 32 mM for YFP and 22 mM for YFP-H148Q, whereas at pH 7.5, K(app) is 777 mM and 154 mM, respectively. In the cytosol, YFP-H148Q appears most promising as a halide sensor due to its high degree of sensitivity towards I(-) (K(app)=23 mM at pH 7.5). To aid in the design of variants with improved levels of specificity and affinity for Cl(-), we solved apo and I(-)-bound crystal structures of YFP-H148Q to 2.1 A resolution. The halide-binding site is found near van der Waals contact with the chromophore imidazolinone oxygen atom, in a small buried cavity adjacent to Arg96, which provides electrostatic stabilization. The halide ion is hydrogen bonded to the phenol group of T203Y, consistent with a mutational analysis that indicates that T203Y is indispensible for tight binding. A series of conformational changes occurs in the amphiphilic site upon anion binding, which appear to be propagated to the beta-bulge region around residue 148 on the protein surface. Anion binding raises the chromophore pK(a) values, since delocalization of the phenolate negative charge over the chromophore skeleton is suppressed. Extraction of microscopic binding constants for the linked equilibrium between anion and proton binding indicates that anion selectivity by YFP is related to hydration forces. Specific suggestions to improve Cl(-) binding to YFP-H148Q based on size and hydration energy are proposed.     

Relation between ovalbumin hydration and the nature of cations, their concentration and temperature

The influence of temperature, nature and concentration and alkali metal chlorides on the hydration degree of ovalbumin (W) was studied by the method of proton magnetic relaxation. It is shown that W of ovalbumin at low temperatures is conditioned by the sum of W by strong and weak water binding sites of the protein molecule. The standard binding enthalpy of water by weak sites is independent of the nature and concentration of the low-molecular weight salt and comprises about 40 KJ mol-1. The addition of such salts to the protein solution leads to changes of W conditioned by the changes of the strong site hydration. The liotropic effect of Li+ and Cs+ on the protein solution is complicated by their interactions with the peptide groups of protein.     

Problems of resistance of the causative agent of melioidosis to antibiotics]

It was shown that the pathogen causing melioidosis was highly resistant to antibiotics including beta-lactams. Antibiotic sensitive mutants of P. pseudomallei were isolated after mutagenesis induced by nitrosoguanidine. Permeability for 3H-tetracycline and tetracycline sensitivity of the mutant cells was respectively 3 and 20 times as high as those of the initial parent strain. Gas liquid chromatography revealed quantitative and qualitative changes in separate sugars of the lipopolysaccharide structure in antibiotic sensitive mutants as compared to the initial strain.     

Synthesis of homologous fluorescent carboxylates and their application to the study of bovine serum albumin

The synthesis of four fluorescent carboxylate probes with spacer groups comprising 1 to 12 atoms between the dansyl and carboxylate functions is described. These probes bind specifically to bovine serum albumin with changes in fluorescence properties. Dansyl glycine shows significantly different behavior in comparison with its longer homologs. Probe binding to protein is diminished in the presence of fatty acids. Evaluation of binding stoichiometries, dissociation constants, and limiting fluorescence values suggests that dansyl glycine binds at a site distinct from the binding site for the longer homologs.     

Regulation of formyl peptide receptor binding to rabbit neutrophil plasma membranes. Use of monovalent cations, guanine nucleotides, and bacterial toxins to discriminate among different states of the receptor

The regulation by monovalent cations, guanine nucleotides, and bacterial toxins of [3H]FMLP binding to rabbit neutrophil plasma membranes was studied by using dissociation techniques to identify regulatory effects on separate receptor states. Under conditions of low receptor occupancy (1 nM [3H]FMLP) and in both Na+ and K+ buffers, dissociation is heterogenous, displaying two distinct, statistically significant off rates. [3H]FMLP binding was enhanced by substituting other monovalent cations for Na+. In particular, enhanced binding in the presence of K+ relative to Na+ was caused by additional binding to both rapidly and slowly dissociating receptors. Three receptor dissociation rates, two of which appear to correspond to the two affinity states detected in equilibrium binding studies, were defined by specific GTP and pertussis toxin (PT) treatments. Neither GTP, nor PT or cholera toxins (CT) had an effect on the rate of dissociation of [3H]FMLP from the rapidly dissociating form of the receptor. Both 100 microM GTP and PT treatments increased the percentage of rapidly dissociating receptors, correspondingly decreasing the percentage of slowly dissociating receptors. The observed changes in the rapidly and slowly dissociating receptors after GTP, PT, and CT treatments were caused by an absolute decrease in the amount of binding to the slowly dissociating receptors. However, complete inhibition of slowly dissociating receptor binding by GTP, PT, or both was never observed. Both GTP and PT treatments, but not CT treatment, increased by two-fold the rate of dissociation of 1 nM [3H]FMLP from the slowly dissociating form of the receptor, resulting in a third dissociation rate. Thus, slowly dissociating receptors comprise two different receptor states, a G protein-associated guanine nucleotide and PT-sensitive state and a guanine nucleotide-insensitive state.     

Incorporation and stabilization of 3H-tetracycline in embryonic chick bone: an autoradiographic study

Tibiae from 11-day-old chick embryos, injected with 3H-tetracycline, were autoradiographically analyzed at different stages to localize and study the dynamics of the initial phases of bone mineralization. 3H-tetracycline was localized within newly formed trabeculae, but only at the surfaces of older trabeculae, indicating that the incorporation of tetracycline into bone occurs at active sites of calcification. It takes between 24 and 36 h for injected tetracycline to become stabilized and incorporated into the mineralized matrix. Absence of 3H-tetracycline grains over the osteoblasts suggests a paracellular pathway for incorporation of tetracycline into the mineralizing bone matrix.     

Hydration changes accompanying the binding of minor groove ligands with DNA

4',6-diamidino-2-phenylindole (DAPI), netropsin, and pentamidine are minor groove binders that have terminal -C(NH2)2+ groups. The hydration changes that accompany their binding to the minor groove of the (AATT)2 sequence have been studied using the osmotic stress technique with fluorescence spectroscopy. The affinity of DAPI for the binding site decreases with the increasing osmolality of the solution, resulting in acquisition of 35+/-1 waters upon binding. A competition fluorescence assay was utilized to measure the binding constants and hydration changes of the other two ligands, using the DNA-DAPI complex as the fluorescence reporter. Upon their association to the (AATT)2 binding site, netropsin and pentamidine acquire 26+/-3 and 34+/-2 additional waters of hydration, respectively. The hydration changes are discussed in the context of the terminal functional groups of the ligands and conformational changes in the DNA.     

Circular dichroism and fluorescence studies on the binding of ligands to the alpha subunit of tryptophan synthase.

Binding to the alpha subunit of tryptophan synthase induces extrinsic Cotton effects in the substrates indole (IND), indoleglycerol phosphate (IGP), and D-glyceraldehyde-3-P (D-GAP) and in the inhibitor indolepropanol phosphate (IPP). These effects disappear when the enzyme is denatured in guanidinium chloride. The induced circular dichroism (CD) was used to determine the dissociation constant and the number of binding sites for IPP. The dissociation constant so determined is equal to 48 muM and is in good agreement with the value of 48 muM obtained by equilibrium dialysis. From the temperature dependence of the dissociation constant, a value of -2.8 kcal/mol for the binding enthalpy was obtained. The determination of dissociation constants by means of extrinsic Cotton effects is shown to be quite feasible. CD competition experiments with glycerol phosphate (GP) suggest that IPP binds bifunctionally to the enzyme: via its indole part and its phosphate group. Indolepropanol, which lacks the phosphate group, does not show an extrinsic Cotton effect. Since the induced CD is strongly dependent on the binding geometry, the close similarity between the induced spectra in IPP and IGP is additional evidence that IPP is a good substrate analog. Binding to the enzyme results in a blue shift of the IPP fluorescence emission maximum. The dissociation constant determined by fluorescence titration equals 46 muM and agrees well with the values determined by the other two methods. Previous biochemical and fast kinetic studies suggested the existence of multiple conformational states for the enzyme and of ligand-induced conformational changes. No evidence was found in the far-uv CD spectra for conformational changes upon binding of IND and D-GAP. For IPP a very small effect was observed.     

The osmotic sensitivity of netropsin analogue binding to DNA

The binding of a netropsin analogue to random sequence DNA, monitored by CD, is seen dependent on the concentration of neutral solutes. The binding free energy decreases linearly with solute osmolal concentration and the magnitude of the effect is insensitive to the chemical identity of the solute fur betaine, sorbitol, and triethylene glycol. These solutes appear to modulate binding through their effect on water activity and changes in the hydration of the drug and DNA in the complex reaction, not through a direct interaction with the reactants or the product. The dependence of binding constant on solute concentration can be interpreted as an additional binding of some 50–60 extra solute excluding water molecules by the complex. A water sensitivity of drug binding is further seen from the dependence of binding constants on the type of anion in solution. Anions in the Hofmeister series strongly affect bulk water free energies and entropies. The differences in netropsin analogue binding to DNA with Cl⁻, F⁻, and CIO are consistent with the effect observed with neutral solutes. The ability to measure changes in water binding associated with a specific DNA interaction is a first step toward correlating changes in hydration with the strength and specificity of binding. © 1995 John Wiley & Sons, Inc.     

Investigations of alkaline phosphatase Ca+2-ATPase and Na+, K+-ATPase during beta-APN-induced initial bone mineralization inhibition

Tibias of 6-day-old white Leghorn chick embryos treated with beta-aminopropionitrile (beta-APN; 0.1 mg/egg/day) for 4 days and injected with 3H-proline or 3H-tetracycline on the 11th day were analyzed for incorporation of 3H-proline and 3H-tetracycline. The incorporation of 3H-proline was comparable in the controls and beta-APN-treated embryos. However, the incorporation of 3H-tetracycline was significantly lower in beta-APN-treated embryos. The bone ash contents were also lower in the latter group. Alkaline phosphatase and Ca+2-ATPase were found to be significantly lower in beta-APN-treated embryonic bones. There was, however, no difference in the activity of Na+, K+-ATPase. The histochemical examination showed the alkaline phosphatase to be present on osteoblasts and matrix vesicle plasma membranes at the periosteal surface. The chick embryonic liver tissue showed no significant differences in the activities of any of the above enzymes. The results suggest that beta-APN-induced inhibition of the bone mineralization may be due to the bone-specific inhibition of alkaline phosphatase and Ca+2-ATPase.     

An NMR study elucidating the binding of Mg(II) and Mn(II) to spinach plastocyanin. Regulation of the binding of plastocyanin to subunit PsaF of photosystem I

In this work we address the question whether light-induced changes in the Mg(II) content in the chloroplast lumen can modulate the electron donation to photosystem I, in particular the electrostatic interaction between plastocyanin (Pc) and the photosystem 1 subunit PsaF. For this, we have used 2D NMR spectroscopy to study the binding of Mg(II) ions and the isolated luminal domain of PsaF to (15)N-labelled Pc. From the chemical-shift perturbations in the (1)H-(15)N HSQC spectra, dissociation constants of (4.9 ± 1.7) mM and (1.4 ± 0.2) mM were determined for the Pc-Mg(II) and Pc-PsaF complexes, respectively. In both cases, significant chemical-shift changes were observed for Pc backbone amide groups belonging to the two acidic patches, residues 42-45 and 59-61. In addition, competitive effects were observed upon the addition of Mg(II) ions to the Pc-PsaF complex, further strengthening that Mg(II) and PsaF bind to the same region on Pc. To structurally elucidate the Mg(II) binding site we have utilized Mn(II) as a paramagnetic analogue of Mg(II). The paramagnetic relaxation enhancement induced by Mn(II) results in line broadening in the Pc HSQC spectra which can be used to estimate distances between the bound ion and the affected nuclear spins. The calculations suggest a location of the bound Mn(II) ion close to Glu43 in the lower acidic patch, and most likely in the form of a hexaquo complex embedded within the hydration shell of Pc. The results presented here suggest a specific binding site for Mg(II) that may regulate the binding of Pc to photosystem 1 in vivo.     

Analysis of peptide affinity to major histocompatibility complex proteins for the two-step binding mechanism

A novel approach to the analysis of an equilibrium two-step peptide-protein binding is developed and applied to the experimental data. The first step of the process is the release of an endogenous peptide from a binding groove and the second is the binding of an added peptide. The method developed enables us to determine consequently the maximum protein occupancy level (protein-binding capacity), the dissociation constant of an endogenous peptide, and the dissociation constant of a binding (antigenic) peptide. It is shown and confirmed by experimental data that the value of an equilibrium dissociation constant of a binding peptide could be much less than the experimental value of ED(50) (concentration of added peptide required to bind half of the protein), but not equal to that commonly assumed for major histocompatibility complex (MHC)-peptide binding. The model considered gives a clear understanding of why some peptides may be good binders to MHC protein in vitro, but do not exhibit anticipated activity on the cellular level and vice versa.     

Hydrodynamic changes accompanying the loss of metal ions from concanavalin A.

The hydrodynamic changes which accompany the dissociation of metal ions, from concanavalin A at acid pH are a result of charge effects rather than of dissociation of metal ions as such. Measurements of the rotational relaxation time are discussed in terms of the hydration of the protein and its polymeric heterogeneity.     

Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: comparing the wild type to the R248Q mutant

Background

The protein p53 plays an active role in the regulation of cell cycle. In about half of human cancers, the protein is inactivated by mutations located primarily in its DNA-binding domain. Interestingly, a number of these mutations possess temperature-induced DNA-binding characteristics. A striking example is the mutation of Arg248 into glutamine or tryptophan. These mutants are defective for binding to DNA at 310 K although they have been shown to bind specifically to several p53 response elements at sub-physiological temperatures (298–306 K).

Methodology/Principal Findings

This important experimental finding motivated us to examine the effects of temperature on the structure and configuration of R248Q mutant and compare it to the wild type protein. Our aim is to determine how and where structural changes of mutant variants take place due to temperature changes. To answer these questions, we compared the mutant to the wild-type proteins from two different aspects. First, we investigated the systems at the atomistic level through their DNA-binding affinity, hydrogen bond networks and spatial distribution of water molecules. Next, we assessed changes in their long-lived conformational motions at the coarse-grained level through the collective dynamics of their side-chain and backbone atoms separately.

Conclusions

The experimentally observed effect of temperature on the DNA-binding properties of p53 is reproduced. Analysis of atomistic and coarse-grained data reveal that changes in binding are determined by a few key residues and provide a rationale for the mutant-loss of binding at physiological temperatures. The findings can potentially enable a rescue strategy for the mutant structure.     

Binding of ethidium to the nucleosome core particle. 1. Binding and dissociation reactions

We have examined binding properties of and dissociation induced by the intercalating dye ethidium bromide when it interacts with the nucleosome core particle under low ionic strength conditions. Ethidium binding to the core particle results in a reversible dissociation which requires the critical binding of 14 ethidium molecules. Under low ionic strength conditions, dissociation is about 90% completed in 5 h. The observed ethidium binding isotherm was corrected for the presence of free DNA due to particle dissociation. The corrected curve reveals that the binding of ethidium to the core particle itself is a highly cooperative process characterized by a low intrinsic binding constant of KA = 2.4 X 10(4) M-1 and a cooperativity parameter of omega = approximately 140. The number of base pairs excluded to another dye molecule by each bound dye molecule (n) is 4.5. Through the use of a chemical probe, methidiumpropyl-EDTA (MPE), we have localized the initial binding sites of ethidium in the core particle to consist of an average of 27 +/- 4 bp of DNA that are distributed near both ends of the DNA termini. MPE footprint analysis has also revealed that, prior to dissociation, the fractional population of core particles which bind the dye (f) may be as low as 50%. Comparison of the binding and dissociation data showed that the cooperative maximum of the binding curve occurred at or near the critical value, i.e., at the point where dissociation began. The data were used to generate a detailed model for the association of ethidium with chromatin at the level of the nucleosome.     

Despite similar binding to the Hfq protein regulatory RNAs widely differ in their competition performance

The binding of nine noncoding regulatory RNAs (sRNAs) to the E. coli Hfq protein was compared using a high-throughput double filter retention assay. Despite the fact that these sRNAs have different lengths, sequences and secondary structures their Hfq binding affinities were surprisingly uniform. The analysis of sRNAs binding to Hfq mutants showed that the proximal face of Hfq, known as the binding site for DsrA RNA, is a universal sRNA binding site. Moreover, all sRNAs bound Hfq with similar association rates limited only by the rate of diffusion, while the rates of dissociation, measured in the dilution experiments, were uniformly slow. Despite that, the data showed that there was a hierarchy of sRNAs in regard to their performance in competition for access to Hfq and in their ability to facilitate the dissociation of other sRNAs from Hfq. The sRNAs also differed in their salt dependence of binding to this protein. Overall, the results suggest that despite the uniform binding of different sRNAs to the same site on Hfq their exchange on this protein is dependent on the identities of the competing sRNAs.