Accessibility to bacterial nucleic acids of the intercalating drug aliphatic amino acid ellipticinium derivatives in Escherichia coli and Salmonella typhimurium

The fluorescence of the aliphatic (amino acido)-N2-methyl-9-hydroxyellipticinium (AA-NMHE) derivatives [Auclair, C., Voisin, E., Banoun, H., Bernardou, J., Meunier, B., & Paoletti, C. (1984) J. Med. Chem. 27, 1161-1166], namely, dehydroglycino-NMHE, dehydroalanino-NMHE, dehydrovalino-NMHE, and dehydroleucino-NMHE, has been characterized. The changes in the fluorescence properties of the drugs, including increase in quantum yields, increase in fluorescence lifetimes, and occurrence of energy transfer upon binding to DNA in vitro, have been further investigated. The measurement of the fluorescence increment of AA-NMHE when bound to fluorescent sites inside intact bacteria has been found to be suitable for the determination of the accessibility of the drugs to bacterial nucleic acids according to the method of Lambert and Le Pecq [Lambert, B., & Le Pecq, J.B. (1984) Biochemistry 23, 166-176]. With this methodology, the kinetics of drug uptake, the ability of the drug to reach the bacterial nucleic acids at equilibrium, and the nature of the ligand binding model have been determined in two AA-NMHE-sensitive strains, Escherichia coli BL 101 (Lambert & Le Pecq, 1984) and Salmonella typhimurium TA 98 [Ames, B.N., Lee, F.D., & Durston, W.E. (1973) Proc. Natl. Acad. Sci. U.S.A. 70, 782-786]. The main results obtained are the following: At nonsaturating concentrations, each AA-NMHE exhibits a marked difference in its ability to reach the bacterial nucleic acids. This parameter seems to be correlated with the antibacterial efficiency of the drugs.(ABSTRACT TRUNCATED AT 250 WORDS)     

Peroxidase-catalyzed covalent binding of the antitumor drug N2-methyl-9-hydroxyellipticinium to DNA in vitro

In the presence of DNA, the antitumor drug N2-methyl-9-hydroxyellipticinium (elliptinium; NMHE) [Le Pecq, J. B., Gosse, C., Dat-Xuong, N., & Paoletti, C. (1975) C. R. Seances Acad. Sci., Ser. D 281, 1365-1367] is oxidized by the horseradish peroxidase-hydrogen peroxide (HRP-H2O2) system to the quinone imine derivative N2-methyl-9-oxoellipticinium (NMOE) [Auclair, C., & Paoletti, C. (1981) J. Med. Chem. 24, 289-295], which interacts with DNA according to the intercalation mode. When excess H2O2 was used, the major part of the quinone imine was further oxidized to the o-quinone N2-methyl-9,10-dioxoellipticinium [Bernadou, J., Meunier, G., Paoletti, C., & Meunier, B. (1983) J. Med. Chem. 26, 574-579]. In the presence of stoichiometric amounts of H2O2 (H2O2/NMHE = 1), NMOE reacts with DNA, yielding a fluorescent compound irreversibly linked to the nucleic acid, which is related to the covalent binding of the ellipticinium chromophore. Under optimal reaction conditions, NMHE binding occurs according to a first-order process (k = 4.3 X 10(-3) min-1) with a linear increase with respect to drug to nucleotide ratio up to a maximum binding of 1 NMHE per 20 base pairs (r = 0.05). The fluorescence spectra (ex, 330 nm; em, 548 nm) of NMHE bound to DNA, the occurrence of energy transfer from the DNA to the drug, and the DNA length increase of the DNA-NMHE adduct suggest that the binding occurs at the intercalating site with limited denaturation of the DNA helix.(ABSTRACT TRUNCATED AT 250 WORDS)     

A reexamination of the problem of resonance energy transfer between DNA intercalated chromophores using bisintercalating compounds.

The rate of energy transfer between DNA intercalated ethidium cations calculated by Paoletti and Le Pecq1 using the Forster theory differs from the measured one by a factor of twenty two, if the proper geometrical factors are taken into account. By changing some of the parameters used in the calculation, the discrepancy can be reduced but not eliminated. This led us to the study of other systems where experimental and calculated results can be more directly compared. The apparent rate of energy transfer between ethidium and one of its non fluorescent analogues and between various pairs of intercalated chromophores has been studied. The fluorescence anisotropy decay of acridine dimers in glycerol or bisintercalated in DNA has been measured. These studies show that the Forster theory of energy transfer does not apply to the case of identical chromophores when they are relatively close to each other.     

Nuclear magnetic resonance evidence for a structural intermediate at an early stage in the refolding of ribonuclease A

The kinetics of refolding of heat-unfolded ribonuclease A have been studied by Fourier transform proton nuclear magnetic resonance at 10 °C, pH 2. A single refolding reaction is observed: it corresponds to the slow-refolding reaction seen in stopped-flow studies of refolding at higher temperatures. There are two results of interest for the mechanism of protein folding. (1) A new resonance (X) is observed that shows the presence of a structural intermediate in refolding. (2) The α-helix close to the N-terminal end of ribonuclease A apparently forms rapidly when the unfolded protein is brought to refolding conditions.The folding intermediate has been studied by monitoring the C-2 protons of the four histidine residues. The intermediate contains one residue (X) in a partly folded environment and the other three residues in unfolded environments. The composite resonance (U) of these three protons at 10 °C agrees with the average chemical shift of the histidine residues in heat-unfolded ribonuclease A at high temperatures. During refolding at 10 °C, the resonance intensities of U and X disappear at the same rate that the spectrum of native ribonuclease A is regained.Partial deuteration experiments show that X is either histidine 12 or 119. Comparative studies of the amino-terminal fragment 1–20 of ribonuclease A indicate that X is histidine 12. The appearance of structure in this peptide can be followed by temperature-dependent changes in the chemical shift of histidine 12. At 10 °C the chemical shifts of histidine 12 and X agree closely. These results are consistent with the circular dichroism study of peptide 1–13 by Brown &; Klec (1971), who concluded that helix formation occurs at low temperatures.     

Helix-coil equilibria of poly (rA) · poly (rU)

Absorbance melting curves of the double-stranded (rA) · (rU) helix, made with fractionated homopolynucleotides of matched length, have been obtained over a 15-fold range of [Na⁺] and 30° range of temperature. An excellent fit of the observed profiles was obtained with theoretical curves calculated on the basis of the simplest interpretation for the occurrence of particular equilibria [1–3]; the complete molecular partition function being evaluated by the power series method developed by Applequist [4–6]. The stability constant was evaluated from literature values for the calorimetric enthalpy. The loop closure exponent was best represented by 2.22 ± 0.04 for the mismatching loop mode of melting and 1.22 for the matching mode and was independent of [Na⁺] and temperature. Assuming the applicability of the nonintersecting random walk value of 1.9 ± 0.1, these results would suggest a slight bias toward matched loop formation during melting of homopolynucleotides that might be expected to form only mismatched loops. The value of the stacking parameter at 60°C was only ~6% higher than that at 30°C, 0.0221 (0.0184 for the matching case). Calculated melting curves indicate the occurrence of a fifth-order phase transition when the mean helix length is only ~13 base-pairs, or about one full turn of the helix.     

Chain conformation in the collagen molecule.

Quantitative X-ray diffraction data have been collected from stretched kangaroo tail tendon and used to test models for the conformation of the polypeptide chains in the collagen molecule. The magnitude of the unit twist of the molecular helix was estimated to be 107.1 ° ± 0.6 °, which is close to the value expected for a helix with ten units in three turns. The intensity data were used to carry out a linked-atom least-squares refinement of models based on two possible interchain hydrogen bonding schemes suggested by Rich &; Crick (1955, 1961). No stereochemically acceptable solution could be found for the hydrogen bonding scheme of model I, but a stereochemically satisfactory solution was found for the scheme of model II which gave a crystallographic R factor of 0.272.     

Transition of bacterial flagella from helical to straight forms with different subunit arrangements.

We have found that several kinds of helical flagella from Salmonella and Escherichia become straight in the presence of 0·5 m-citric acid at pH values below 4·0, while the straight flagella from a mutant Salmonella (SJ814) are transformed into a helical shape under the same conditions. These transformations are reversible and transitional.Current models of bacterial flagella (Calladine, 1976,1978; Kamiya, 1976) predict that the family of distinct wave-forms should include two types of straight flagella, which have either an extreme right-handed twist (about 7 ° at the surface of the flagellum) or an extreme left-handed twist (2 ° to 3 °). As the inclination of the near-longitudinal rows of subunits in the Salmonella SJ814 flagellum (O'Brien &; Bennett, 1972) agrees closely with the degree of twisting predicted for the right-handed type, this flagellum has been considered to be the right-handed type. We have determined that the basic (1-start) helix in flagella is right-handed, using the method of Finch (1972). This fact, together with the selection rule (O'Brien &; Bennett, 1972), strongly suggests that the near-longitudinal rows in an SJ814 flagellum are right-handed, in agreement with the prediction. However, our optical diffraction and X-ray diffraction studies have revealed that the near-longitudinal rows of subunits in the citric acid-induced straight flagella and in the straight flagella from a mutant E. coli (Kondoh &; Yanagida, 1975) tilt at an angle of 2 ° to 3 ° with respect to the flagellar axis. This inclination is probably left-handed. Thus the predicted presence of the two types of straight flagella seems to be proved.     

Joint molecule formation following conjugation in wild type and mutant Escherichia coli recipients

The sedimentation coefficients of closed circular Simian virus (SV40) DNA, phage PM2 DNA and animal mitochondrial DNAs in alkaline NaCl and alkaline CsCl were found to decrease by about 5% as the initial superhelix densities decreased from 0.0 to ?0.10, corresponding to a decrease in the degree of strand interwinding from 1.0 to 0.9 net turns per ten base pairs. The small dependence of the appropriately normalized sedimentation coefficients on the degree of strand interwinding is taken to indicate that fully titrated and denatured closed circular DNA is highly supercoiled in a positive sense. This supercoiling results from the spontaneous decrease in the number of secondary turns in the no longer ordered pairs of polynucleotide strands.The measured sedimentation coefficients form a smoothly connected monotonie curve when plotted along with the sedimentation coefficients in alkali (Sebring et al., 1971) of parental closed circles derived from closed circular SV40 DNA replicating intermediates. These DNAs have degrees of strand interwinding that range from 0.6 to 0.15.The possibility raised by Paoletti &; LePecq (1971) that closed circular duplex DNAs contain positive supercoils, i.e. have degrees of strand interwinding greater than 1.0, has been ruled out in a series of ethidium bromide titrations of partially replicated mitochondrial DNA before and after removal of the progeny strand. More ethidium bromide was required in the latter case for relaxation, a result which shows that intercalated ethidium and a displacing strand act on the duplex in the same way, and that both unwind the duplex. This result requires the supercoils of naturally closed circular DNAs to be negative.     

Conformational stabilities of the rat α- and β-parvalbumins

It is widely believed that β-parvalbumin (PV) isoforms are intrinsically less stable than α-parvalbumins, due to greater electrostatic repulsion and an abbreviated C-terminal helix. However, when examined by differential scanning calorimetry, the apo-form of the rat β-PV (i.e. oncomodulin) actually displays greater thermal stability than the α-PV. Whereas the melting temperature of the α isoform is 45.8°C at physiological pH and ionic strength, the T_m for the β isoform is more than 7° higher (53.6°C). This result suggests that factors besides net charge and C-terminal helix length strongly influence parvalbumin conformational stability. Extension of the F helix in the β-PV, by insertion of Ser-109, has a modest stabilizing effect, raising the T_m by 1.1°. Truncation of the α-PV F helix, by removal of Glu-108, has a more profound impact, lowering the T_m by 4.0°.     

NMR studies on thermal stability of α‐helix conformation of melittin in pure ethanol and ethanol–water mixture solvents

Thermal stability of the α‐helix conformation of melittin in pure ethanol and ethanol–water mixture solvents has been investigated by using NMR spectroscopy. With increase in water concentration of the mixture solvents (from 0 wt% to ~71.5 wt%) as well as temperature (from room temperature to 60 °C), the intramolecular hydrogen bonds formed in melittin are destabilized and the α‐helix is partially uncoiled. Further, the hydrogen bonds are found to be more thermally stable in pure ethanol than in pure methanol, suggesting that their stability is enhanced with increase in the size of the alkyl groups of alcohol molecules. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Molecular structure and biological activity: A Symposium on Biologically Active Molecules Buffalo,NY, U.S.A., 26 to 28 August 1981

Analysis of the pattern of residue to residue contacts at the interface of 50 helix to helix packings observed in ten proteins of known structure supports a model for helix to helix packing in which the ridges and grooves on the helix surface intercalate. These ridges are formed by rows of residues whose separation in sequence is usually four, occasionally three and rarely one. The model explains the observed predominance of packings whose interhelical angle is ~ ?50 °. Of the 50 packings, 38 agree with the model and the general features of another ten packings are described by an extension to the model in which ridges can pack across each other if a small side-chain occurs at the place where they cross.     

DNA bifunctional intercalators. I. Synthesis and conformational properties of an ethidium homodimer and of an acridine ethidium heterodimer.

An ethidium homodimer and an acridine ethidium heterodimer have been synthesized. The ethidium and the acridine chromophore were introduced in such bifunctional intercalators in order to allow the fluorometric study of the interaction of such molecules with DNA, which is reported in the companion paper (Gaugain, B., Barbet, J., Capelle, N., Roques, B.P., & Le Pecq, J.B.(1978) Biochemistry 17 (following paper in this issue)). In the preparation of the acridine-ethidium dimer, we report the use of acetyl groups as new protecting agents in the phenanthridine series. Conformational studies of these molecules by visible absorption and NMR spectroscopy indicate that these dimers exist in equilibrium between folded and unfolded conformations and that this equilibrium is pH and temperature dependent. Models for the geometry of the folded forms are proposed.     

Packing interactions of aib-containing helices: Molecular modeling of parallel dimers of simple hydrophobic helices and of alamethicin

α-Aminoisobutyric acid (Aib) is a helicogenic α,α-dimethyl amino acid found in channel-forming peptaibols such as alamethicin. Possible effects of Aib on helix–helix packing are analyzed. Simulated annealing via restrained molecular dynamics is used to generate ensembles of approximately parallel helix dimers. Analysis of variations in geometrical and energetic parameters within ensembles defines how tightly a pair of helices interact. Simple hydrophobic helix dimers are compared: Ala₂₀, Leu₂₀, Aib₂₀, and P20, the latter a simple channel-forming peptide [G. Menestrina, K. P. Voges, G, Jung, and G. Boheim (1986) Journal of Membrane Biology, Vol. 93, pp. 111–132]. Ala₂₀ and Leu₂₀ dimers exhibit well-defined ridges-in-grooves packing with helix crossing angles (Ω) of the order of +20°. Aib₂₀ α-helix dimers are much more loosely packed, as evidenced by a wide range of Ω values and small helix-helix interaction energies. However, when in a 3₁₀ conformation Aib₂₀ helices pack in three well-defined parallel modes, with Ω ca. ?15°, +5°, and 10°. Comparison of helix–helix interaction energies suggests that dimerization may favor the 3₁₀ conformation. P20, with 8 Aib residues, also shows looser packing of α-helices. The results of these studies of hydrophobic helix dimers are analyzed in the context of the ridges-in-grooves packing model. Simulations are extended to dimers of alamethicin, and of an alamethicin derivative in which all Aib residues are replaced by Leu. This substitution has little effect on helix–helix packing. Rather, such interactions appear to be sensitive to interactions between polar side chains. Overall, the results suggest that Aib may modulate the packing of simple hydrophobic helices, in favor of looser interactions. For more complex amphipathic helices, interactions between polar side chains may be more critical. © 1995 John Wiley & Sons, Inc.     

Theoretical π-π* circular dichroic spectra of helical poly(glycine) and poly(L-alanine) as functions of backbone torsion angles

Circular dichroic spectra and oscillator strengths of the π-π transition near 190 nm are calculated for helical (Gly)₆ and (Ala)₆ at 30° intervals of the backbone torsion angles (?,ψ) over the range -180° ≤ ? ≤ -60°, ?60° ≤ ψ ≤ 180°, using the partially dispersive normal mode treatment of the dipole interaction model. Polarizabilities of atoms and the NC′O group are those determined semiempirically in previous studies. Calculations for (Ala)₆ at (?,ψ) angles corresponding to the α-helix, the poly(Pro) II helix, a collagen single helix, a poly-(MeAla) helix, and single β-helices are found to agree well with most of the available experimental data.     

Stability of the helical conformation of random L-alanine-L-lysine copolymers in aqueous solution

The potentiometric titration of random copolymers of L -lysine and L -alanine containing 0–35% alanine was carried out. The standard free-energy change for the transition of coil to helix was calculated from the titration curve, and was treated by taking account of first-neighbor interactions. For uncharged lysine ΔG° = ?140 cal/mole, and for alanine ΔG° = ?50 cal/mole in 0.06M NaBr at 25°C, indicating that the alanine helix is thermodynamically less stable than the lysine helix. The randomness in co-polymerization was confirmed by trypsin treatment.     

Effect of superhelical structure on the secondary structure of DNA rings

A quantity, called the linking number, is defined, which specifies the total number of twists in a circular helix. The linking number is invariant under continuous deformations of the ring and therefore enables one to calculate the influence of superhelical structures on the secondary helix of a circular molecule. The linking number can be determined by projecting the helix into a plane and counting strand crosses in the projection as described. For example, it has been shown that for each 180° twist in a left-handed superhelix, a right-handed 360° twist is removed from the secondary helix, thus allowing local unwinding.     

The part of a long beta hairpin from the scrapie form of the human prion protein is reconstructed in the synthetic CC36 protein

Mechanisms of beta sheet formation by the human prion protein are not clear yet. In this work, we clarified the role of the region containing C‐half of the second helix and N‐half of the third helix of that protein in the process of alpha helix to beta sheet transition. Solid phase automatic synthesis of the original peptide (CC36: Cys179–Cys214) failed because of the beta hairpin formation in the region 206‐MERVVEQMC‐214 with a high beta strand potential. Using Met206Arg and Val210Arg substitutions, we increased the probability of alpha helix formation by that sequence. After that modification, the complete CC36 peptide with disulfide bond has been synthesized. Modified peptide has been studied by circular dichroism (CD) and fluorescence spectrography. According to the CD spectra analysis, the CC36 peptide contains 37% of residues in beta sheet and just 15% in helix. Thermal analysis under the control of CD shows that the secondary structure content of the peptide is stable from 5°C to 80°C. Dissociation of oligomers of the CC36 peptide finishes at 37°C according to the fluorescence analysis. The CC36 peptide is able to bind Mn²⁺ cations, which causes small temperature‐associated structural shifts at concentrations of 2 – 10·10^?6 M. Predicted beta hairpin of the CC36 peptide (two beta strands are: 184‐IKQHTVT‐190 and 197‐TETDVKM‐205) should be the part of a longer beta hairpin from the scrapie form of the prion protein (PrPSc). Analogs of the CC36 peptide may be considered as antigens for the future development of a vaccine against PrPSc. Proteins 2016; 84:1462–1479. © 2016 Wiley Periodicals, Inc.     

Effect of aqueous ethanol on the triple helical structure of collagen

Collagen, the most abundant protein in mammals, is widely used for making biomaterials. Recently, organic solvents have been used to fabricate collagen-based biomaterials for biological applications. It is therefore necessary to understand the behavior of collagen in the presence of organic solvents at low (≤50 %, v/v) and high (≥90 %, v/v) concentrations. This study was conducted to examine how collagen reacts when exposed to low and high concentrations of ethanol, one of the solvents used to make collagen-based biomaterials. Solubility testing indicated that collagen remains in solution at low concentrations (≤50 %, v/v) of ethanol but precipitates (gel-like) thereafter, irrespective of the method of addition of ethanol (single shot or gradual addition); this behavior is different from that observed recently with acetonitrile. Collagen retains its triple helix in the presence of ethanol but becomes thermodynamically unstable, with substantially reduced melting temperature, with increasing concentration of ethanol. It was also found that the CD ellipticity at 222 nm, characteristic of the triple-helical structure, does not correlate with the thermal stability of collagen. Time-dependent experiments reveal that the collagen triple helix is kinetically stable in the presence of 0–40 % (v/v) ethanol at low temperature (5 °C) but highly unstable in the presence of ethanol at elevated temperature (~34 °C). These results indicate that when ethanol is used to process collagen-based biomaterials, such factors as temperature and duration should be done taking into account, to prevent extensive damage to the triple-helical structure of collagen .     

Response of the Praying Mantis,Sphodromantis Viridis,to Target Change in Size and to Target Visual Occlusion

Mantises (Mantodea, Mantidae) visually detect insect prey and capture it by a ballistic strike of their specialized forelegs. We tested predatory responses of female mantis, Sphodromantis viridis, to computer generated visual stimuli, to determine the effects of (i) target size and velocity (ii) discrete changes in target size and (iii) visual occlusion. Maximal predatory responses were elicited by stimuli that (i) subtended ~20°–23° horizontally and ~16°–19° vertically, at the eye, and moved across the screen at angular velocities of ~46°–119°/s, (ii) increased in size in a stepwise manner, with step duration ≥0.8 s, while stimuli decreasing in size elicited only peering movements, (iii) Stimuli disappearing gradually behind a virtual occlusion elicited one or more head saccades but not actual interception.