Dichroism Spectral Changes Research Articles

Quadruplex Structure of Polyriboinosinic Acid: Dependence on Alkali Metal Ion Concentration, pH and Temperature

The vibrational infrared (IR) absorption and vibrational circular dichroism (VCD) spectral changes of polyinosinic acid (polyI) as a function of alkali metal ion concentration, temperature and pH have been investigated to establish how changes in spectral features relate to the structural modifications of polyI. A single positive VCD couplet associated with the carbonyl absorption band is considered to be the signature of quadruplex structure for polyI. The disruption of the quadruplex structure with temperature increase or pH increase at low alkali metal ion concentration is evidenced by the disappearance of this positive VCD couplet. The absence of any VCD signal upon quadruplex disruption indicates that the newly formed structure lacks helical chirality and is likely to be disordered. In the presence of 1 M NaCl or 0.1 M NaCl, the heat-induced quadruplex disruption is completely reversible. A mildly alkaline environment, in the presence of 0.1 M NaCl, is not sufficient to support the quadruplex structure of polyI. Trehalose-assisted polyI film at room temperature exhibits the same quadruplex spectral signature as that seen for solution at room temperature, but the quadruplex spectral signature in the film state remains at higher temperature, unlike in solution. This indicates that the quadruplex structure of polyI in the film state resists heat-induced disruptions.

Uncharged water-soluble porphyrin tweezers as a supramolecular sensor forα-amino acids

The binding between uncharged cobalt porphyrin tweezers and L-amino acids in aqueoussolutions is studied by means of UV–vis and circular dichroism spectroscopy.By varying the length of the aliphatic bridge between the two porphyrin units,the number of cobalt ions in the porphyrin cores and the pH of the solution,the chirality induction phenomenon has been investigated. The binding of theamino acid to the porphyrin seems to occur via a coordination mechanism betweenthe metal and the nitrogen of the amino group; the steric, hydrophobic andπ–π interactions operate to stabilize the complexes. The chirogenesis displays an oppositebehaviour in the presence of aromatic guests with respect to the non-aromatic ones.Moreover, the UV–vis and the induced circular dichroism spectral changes suggest that theamino acid arrangement in the tweezers is determined by many factors, so that, unlike inorganic solvent, the porphyrin tweezers in aqueous solution allow for two differentarrangements of the same aromatic amino acid. The experimental findings indicate that theporphyrins tweezers reported in the paper are promising in opening perspectives towardtheir application as a selective molecular sensor in aqueous solutions directly.

Potential propelling and rotating functions of propeller-type complexes. III. Detection of the propelling motion in fac-tris(S-2,3-diaminopropionato)cobalt(III) in an aqueous solution upon IR irradiation

Circular dichroism spectra of the fac and mer isomers of tris-cobalt(III) complexes of S-2,3-Hdap (Hdap = diaminopropionic acid); fac and mer-[Co(S-dap)3] (Λ or Δ), and [Co(en)3]3+ (Λ or Δ, en = ethylenediamine) in an aqueous solution without and upon IR irradiation were measured. The detection of the propelling motion that corresponds to circular dichroism spectral changes of the propeller-type complex, fac-[Co(S-dap)3] in an aqueous solution upon IR irradiation gave good agreement with the computer-simulation result, that is, the propelling (translation and rotation) motion occurs in propeller-type metal complexes in aqueous solution as a consequence of an appropriate energy supply, which had been obtained by theoretical study based on molecular dynamics (MD) simulations by the use of AMBER 6 program.

Conformational transition state is responsible for assembly of microtubule-binding domain of tau protein

In the brains of Alzheimer’s disease patients, the tau protein dissociates from the axonal microtubule and abnormally aggregates to form a paired helical filament (PHF). One of the priorities in Alzheimer research is to clarify the mechanism of PHF formation. Although several reports on the regulation of tau assembly have been published, it is not yet clear whether in vivo PHFs are composed of β-structures or α-helices. Since the four-repeat microtubule-binding domain (4RMBD) of the tau protein has been considered to play an essential role in PHF formation, its heparin-induced assembly propensity was investigated by the thioflavin fluorescence method to clarify what conformation is most preferred for the assembly. We analyzed the assembly propensity of 4RMBD in Tris–HCl buffer with different trifluoroethanol (TFE) contents, because TFE reversibly induces the transition of the random structure to the α-helical structure in an aqueous solution. Consequently, it was observed that the 4RMBD assembly is most significantly favored to proceed in the 10–30% TFE solution, the concentration of which corresponds to the activated transition state of 4RMBD from a random structure to an α-helical structure, as determined from the circular dichroism (CD) spectral changes. Since such an assembly does not occur in a buffer containing TFE of <10% or >40%, the intermediate conformation between the random and α-helical structures could be most responsible for the PHF formation of 4RMBD. This is the first report to clarify that the non-native α-helical intermediate in transition from random coil is directly associated with filament formation at the start of PHF formation.

Effect of Metal Binding on the Structural Stability of Pigeon Liver Malic Enzyme

The cytosolic malic enzyme from the pigeon liver is sensitive to chemical denaturant urea. When monitored by protein intrinsic fluorescence or circular dichroism spectral changes, an unfolding of the enzyme in urea at 25 degrees C and pH 7.4 revealed a biphasic phenomenon with an intermediate state detected at 4-5 m urea. The enzyme activity was activated by urea up to 1 m but was completely lost before the intermediate state was detected. This suggests that the active site region of the enzyme was more sensitive to chemical denaturant than other structural scaffolds. In the presence of 4 mm Mn(2+), the urea denaturation pattern of malic enzyme changed to monophasic. Mn(2+) helped the enzyme to resist phase I urea denaturation. The [urea](0.5) for the enzyme inactivation shifted from 2.2 to 3.8 m. Molecular weight determined by the analytical ultracentrifuge indicated that the tetrameric enzyme was dissociated to dimers in the early stage of phase I denaturation. In the intermediate state at 4-5 m urea, the enzyme showed polymerization. However, the polymer forms were dissociated to unfolded monomers at a urea concentration greater than 6 m. Mn(2+) retarded the polymerization of the malic enzyme. Three mutants of the enzyme with a defective metal ligand (E234Q, D235N, E234Q/D235N) were cloned and purified to homogeneity. These mutant malic enzymes showed a biphasic urea denaturation pattern in the absence or presence of Mn(2+). These results indicate that the Mn(2+) has dual roles in the malic enzyme. The metal ion not only plays a catalytic role in stabilization of the reaction intermediate, enol-pyruvate, but also stabilizes the overall tetrameric protein architecture.

A Redox Switch Based on Dihydro[5]helicene: Drastic Chiroptical Response Induced by Reversible C-C Bond Making/Breaking upon Electron Transfer.

Helicity and axial chirality are reversibly interconverted in the novel redox pair 1 and 22+ ; the compounds exhibit drastic UV/Vis and circular dichroism spectral changes as well as dynamic structural changes upon electron transfer, thus furnishing an unprecedented multi-output response system with high bistability. X=S or O.

Deflavination of flavo-oxidases by nucleophilic reagents

Using spectroscopic techniques we studied the effect of the nucleophilic reagents cyanide, cyanate and thiocyanate on three flavo-oxidases namely alcohol oxidase (AO), glucose oxidase (GOX) and D-amino acid oxidase (DAOX). All three ions, added at concentrations in the mM range, caused release of the flavin adenine dinucleotide (FAD) co-factors from the enzyme molecules. In the case of AO this was accompanied by significant conformational perturbations, which was not observed for GOX and DAOX. As suggested from fluorescence, absorption and circular dichroism spectral changes at least one phenolic hydroxyl group became ionized upon FAD release from AO and a new class of Trp residues, fluorescent only in apo-AO protein, was demasked.

Kinetic effect of zinc(II) and cadmium(II) ions on configurational inversion of deltaLLL-fac(S)-tris(L-cysteinato-N,S)cobalt(III) complex.

It has been confirmed from circular dichroism (CD) spectral changes of aqueous solutions of deltaLLL-fac(S)-[Co(L-cys-N,S)3]3- that the absolute configurational inversion to the ALLL isomer is remarkably accelerated by zinc(II), while it is retarded by cadmium(II). In the diluted solutions of these metal ions containing excess deltaLLL-fac(S)-[Co(L-cys-N,S)3]3-, the observed inversion rate constant linearly depends on the zinc(II) concentration with an intercept, while it is not affected by the cadmium(II) concentration. The kinetic behavior has been explained by difference between zinc(II)- and cadmium(II)-interactions with lone pairs on sulfur donor atoms of fac(S)-[Co(L-cys-N,S)3]3-. It has also been proposed that concentrations of zinc(II) and cadmium(II) can be simultaneously determined by the kinetic measurements.

Efficient photocleavage of DNA by cationic porphyrin-acridine hybrids with the effective length of diamino alkyl linkage.

Positively charged porphyrins bearing an acridine with various lengths of diamino alkyl linkage, 5-[4-[(6-chloro-2-methoxy-9-acridyl)aminoalkylaminocarbonyl]phenyl]-10,15,20-tris(4-N-methylpyridiniumyl)porphine triiodide, alkyl=ethyl, butyl, hexyl, or octyl, were synthesized. They exhibited more enhanced photocleavage activity of pUC18 plasmid DNA than TMPyP, meso-tetrakis(4-N-methylpyridiniumyl)porphine, which is well known to bind to DNA tightly and to cleave DNA effectively; the hybrid linked with the hexamethylene chain showed particularly high activity. An equilibrium dialysis experiment demonstrated that the binding ability of the hybrids to calf thymus (CT) DNA correlated quantitatively with the photocleavage activity. The lack of the substantial red-shift of the Soret maxima of the hybrids through the titration with CTDNA denied the intercalative binding of the porphyrin part. In their circular dichroism (CD) spectral change on binding to CTDNA, two negative peaks appeared at 275 nm and at 285-290 nm in the UV range. The latter negative peak was observed for hybrids, but not for TMPyP, and thus we assigned it to induced CD (ICD) derived from intercalation of acridine chromophore. In the visible range, the hybrids showed only a positive peak around their Soret maxima, and this feature suggested the porphyrin moiety lay in the DNA groove. In addition, the length of the linker markedly influenced the ellipticity of their visible ICD, suggesting that the proximity of the porphyrin moiety to DNA was greatly affected by the linker.

Changes of tyrosine and tryptophan residues in human hemoglobin by oxygen binding: near- and far-UV circular dichroism of isolated chains and recombined hemoglobin

In order to assign the circular dichroism (CD) spectral change in the region between 280 and 300 nm of human adult hemoglobin (Hb A) upon the quaternary structure transition induced by oxygen binding, the near- and far-UV CD spectra of the isolated chains and the recombined hemoglobin were examined. Deoxygenation made the negative CD band at 290 nm of oxy-α chain deeper. On the other hand, positive CD bands of oxy-β chain at the 280∼300 nm became negative upon deoxygenation. These changes were interpreted as being due to environmental alterations of tyrosine (Tyr) and/or tryptophan (Trp) perturbed by tertiary structural changes from the oxy to deoxy form in isolated chains, referring to the CD spectra of model compounds. From the difference between CD bands of the arithmetic mean of deoxy isolated chains and the CD band of deoxyHb tetramer, the contribution of tertiary structural change to the negative CD band of deoxyHb A at 287 nm was estimated to be 50%. This finding has revealed that the net contribution of quaternary structure transition to the negative band is 50%. In far-UV CD spectra, the environmental changes of aromatic residues upon the quaternary structure transition were also detected as a negative band at 225 nm.

Sugar ‘Chirality’ Sensing Using a ‘Prochiral’ Salen–Co(II) Complex

A prochiral salen–Co(II) complex ( 6) bearing two boronic acid groups was synthesized. The saccharide-binding event was conveniently monitored by a circular dichroism (CD) spectral change. The exciton-coupling-type CD spectra thus obtained were compared with those of chiral salen–Co(II) complexes, ( R)- 4 and ( R)- 5. Very interestingly, monosaccharides which are selectively bound to ( R)- 4 and ( R)- 5 with P helicity generate the P helicity CD spectra in prochiral 6. This means that the two boronic acid groups in ( R)- 4 and ( R)- 5 are chirally preorganized suitable to the binding of these monosaccharides. Reflecting the short distance between the two boronic acid groups, 6 shows the very high selectivity for talose which has all OH groups arranged on the same side of the pyranose ring. These results indicate that 6 is useful for sugar ‘chirality’ sensing at visible wavelength region and prediction of d/ l selectivity for ( R)- 4 and ( R)- 5.

Photochromism of Diarylethene Diammonium Derivative in the Cyclodextrin Cavity

The effect on the quantum yield for the cyclization reaction and the circular dichroism (CD) spectral change by the addition of β-cyclodextrin (β-CDx) to an aqueous solution of 2,2′-dimethyl-3,3′-(perfluorocyclopentene-1,2-diyl)bis-(benzo[b]thiophene-6-ammonium)iodide (1a) were studied. The quantum yield for the cyclization reaction was increased because of the increase of the ratio of the photoactive anti-parallel conformation. The CD spectral change upon irradiation with 313 nm light was also studied. The induced CD spectrum of an aqueous mixture of 1 and β-CDx changed from negative to positive by 313 nm light irradiation and the CD spectral change was photoreversible.

Photochromism of Dithienylethenes Included in Cyclodextrins

The effect of inclusion of diarylethenes in cyclodextrin cavities on cyclization quantum yields and on circular dichroism (CD) spectral changes by photoirradiation was studied. The addition of β- and γ-cyclodextrins to an aqueous solution of the open-ring form of 2,2‘-dimethyl-3,3‘-(perfluorocyclopentene-1,2-diyl)bis(benzo[b]thiophene-6-sulfonate) (1a) increased the ratio of the antiparallel conformation. The enrichment of antiparallel conformation caused an increase in the photocyclization quantum yield of 1a. The CD spectral intensity of the mixtures of 1a or 2,2‘,4,4‘-tetramethyl-3,3‘-(perfluorocyclopentene-1,2-diyl)bis(thiophen-5-yl-(phenyl-4-sulfonate)) (2a) and cyclodextrins in aqueous solution increased with the increasing concentration of cyclodextrins. The induced CD spectrum of 1 in β-cyclodextrin reversibly changed from negative to positive by UV irradiation. The spectral change was attributed to the change in the direction of transition moment of 1 in the cavity.

Escherichia coli purine repressor: key residues for the allosteric transition between active and inactive conformations and for interdomain signaling.

The Escherichia coli purine repressor, PurR, exists in an equilibrium between open and closed conformations. Binding of a corepressor, hypoxanthine or guanine, shifts the allosteric equilibrium in favor of the closed conformation and increases the operator DNA binding affinity by 40-fold compared to aporepressor. Glu70 and Trp147 PurR mutations were isolated which perturb the allosteric equilibrium. Three lines of evidence indicate that the allosteric equilibrium of E70A and W147A aporepressors was shifted toward the closed conformation. First, compared to wild-type PurR, these mutant repressors had a 10-30-fold higher corepressor binding affinity. Second, the mutant aporepressors bound to operator DNA with an affinity that is characteristic of the wild-type PurR holorepressor. Third, binding of guanine to wild-type PurR resulted in a near-UV circular dichroism spectral change at 297-305 nm that is attributed to the closed conformation. The circular dichroism spectrum of the E70A aporepressor at 297-305 nm was that expected for the closed conformation, and it was not appreciably altered by corepressor binding. Mutational analysis was used to identify an Arg115-Ser46' interdomain intersubunit hydrogen bond that is necessary for transmitting the allosteric transition in the corepressor binding domain to the DNA binding domain. R115A and S46G PurR mutants were defective in DNA binding in vitro and repressor function in vivo although corepressor binding was identical to the wild type. These results establish that the hydrogen bond between the side chain NH2 of Arg115 and the main chain CO of Ser46' plays a critical role in interdomain signaling.

Circular dichroism studies of the binding of mammalian and non-mammalian cytochromes c to cytochrome c oxidase, cytochrome c peroxidase, and polyanions

The effects of binding of Candida krusei, Drosophila melanogaster, horse, human, and rat cytochromes c to beef cytochrome c oxidase (ferrocytochrome c: oxygen oxidoreductase, EC 1.9.3.1) and yeast cytochrome c peroxidase (ferricytochrome c: hydrogen-peroxide oxidoreductase, EC 1.11.1.5) on their circular dichroism spectra were determined. The binding to cytochrome oxidase results in a positive increase in the ellipticities of the positive and negative Cotton effects at 404 nm and 417 nm of cytochrome c. The horse, human, and rat cytochromes c display less of an increase in the ellipticity of the positive Cotton effect at 404 nm, but more of a positive change in the negative Cotton effect at 417 nm than the C. krusei or D. melanogaster proteins. Interaction with yeast cytochrome c peroxidase elicits only a positive change in the ellipticity of the positive Cotton effect at 404 nm. No significant change is observed in the negative Cotton effect at 417 nm. Rat cytochrome c variants with a phenylalanine in place of tyrosine-67 and/or an alanine in place of proline-30 all display circular dichroism spectral changes upon binding to cytochrome c oxidase or cytochrome c peroxidase identical to those of the unaltered protein. The increase in ellipticity at 404 nm upon binding occurs even though replacement of tyrosine-67 results in the loss of the positive Cotton effect at this position. Polyglutamate and phosvitin complexes of cytochrome c show changes in the circular dichroism spectrum similar to those observed with cytochrome c peroxidase. However, the magnitudes of the spectral changes were considerably less. A model is proposed in which the main cause of the circular dichroism spectral changes observed upon complexation arise from the exclusion of solvent from the exposed front heme edge. According to this model, the exclusion of solvent changes the relative asymmetry of the environment of the electronic transitions of the heme prosthetic group of cytochrome c, resulting in observed circular dichroic effects.

Temperature and Solvent Effects on Reaction Centers from ChlorofLexus aurantiacus and Chromatium tepidum1

Temperature and solvent effects on reaction center structures were examined in two thermophilic photosynthetic bacteria, Chloroflexus aurantiacus and Chromatium tepidum, in order to gain insight into the interactions among the reaction center proteins and pigment systems. Thermal stability of the reaction centers was found to be proportional to the optimum growth temperature. Circular dichroism (CD) spectra in the 250-300 nm region indicated that thermal denaturation destroyed tertiary structures (helix-to-helix interactions or amino acid residue conformation) in the native reaction center, keeping helical structures intact. Absorption and circular dichroism spectral changes showed that alcohol denatured the so-called special pair and the accessory BChl a independently. The alcohol denaturation further indicates that the coordination between BChl a and amino acid residue in the protein is one of the important interactions maintaining the pigment organization of the reaction centers.

A photoreversible circular dichroism spectral change in oat phytochrome is suppressed by a monoclonal antibody that binds near its N-terminus and by chromophore modification [Erratum to document cited in CA107(9):73025z

A photoreversible circular dichroism spectral change in oat phytochrome is suppressed by a monoclonal antibody that binds near its N-terminus and by chromophore modification [Erratum to document cited in CA107(9):73025z

A photoreversible circular dichroism spectral change in oat phytochrome is suppressed by a monoclonal antibody that binds near its N-terminus and by chromophore modification.

Accompanying the phototransformation of native 124-kilodalton (kDa) oat phytochrome from red-absorbing form (Pr) to far-red-absorbing form (Pfr), there is a photoreversible change in circular dichroism (CD) in the far-UV region indicative of a 3% increase in alpha-helical folding of apoprotein. To elucidate the conformational change involved in the phytochrome phototransformation, several monoclonal antibodies have been used as epitope-specific probes. Monoclonal antibody oat-25 suppressed the photoreversible CD spectral change using phytochrome with an A666/A280 as Pr of 1.13. Monoclonal antibodies oat-22, oat-13, and oat-31 did not significantly affect the CD spectral change of phytochrome. Oat-25 requires an epitope near the N-terminus of phytochrome. Oat-22, oat-13, and oat-31 recognize epitopes on the N-terminus, chromophore-containing half of phytochrome, albeit further removed from the N-terminus than that recognized by oat-25. Interestingly, oat-13 and oat-31 did, however, induce a time-dependent decrease in the far-UV CD, apparently due to aggregation of phytochrome (both Pr and Pfr forms). Monoclonal antibodies oat-26 and oat-28, which recognize epitopes on the C-terminus half of phytochrome, also did not suppress the photoreversible CD change, although oat-26 and oat-28 slightly inhibited it. The photoreversible CD spectral change can also be inhibited by sodium borohydride, which bleaches the chromophore by reducing it, and by tetranitromethane, which oxidizes the chromophore of phytochrome. Although explanations of these results based on indirect interactions between the chromophore and the N-terminus segment are possible, we propose that an additional alpha-helical folding of the Pfr form of the phytochrome may result from a photoreversible interaction between the Pfr form of the chromophore and the N-terminus segment.

Interaction of D-phenylalanine with Co(II)-substituted rabbit muscle pyruvate kinase: kinetic and optical properties.

The kinetic and optical properties of Co(II)-substituted pyruvate kinase in the presence of D-phenylalanine (D-Phe) were investigated. The results are discussed in comparison with the effects of its optical isomer L-phenylalanine (L-Phe) on the same enzyme. The catalytic effect of D-Phe on rabbit muscle pyruvate kinase depended upon the nature of the activating divalent metal ion used. It has stimulatory effect on Mg(II)-activated enzyme, but inhibitory effect on Co(II)-activated enzyme. Unlike the inhibitory effect of L-Phe, the inhibition of Co(II)-enzyme by D-Phe was not sensitive to the changes of pH and temperature, could not be reversed by L-alanine (L-Ala), displayed hyperbolic kinetics, and was noncompetitive with respect to phosphoenopyruvate saturation. D-Phe induced substantial visible circular dichroism (CD) spectral changes of Co(II)-enzyme similar to those induced by L-Phe. Although ultraviolet CD spectrum was not affected, D-Phe induced an ultraviolet difference absorption spectral change very similar to, but much smaller than, that induced by L-Phe. Our results support that D-Phe and other amino acids interact with the enzyme at two different sites: a common site, causing similar conformational changes which bear little direct kinetic relevance, and a kinetically relevant site, which is sterically dependent upon the side chain of the amino acids.

Circular dichroism and absorbance properties of nitrotyrosyl chromophores in staphylococcal nuclease and in a model diketopiperazine.

An active derivative of staphylococcal nuclease, in which only tyrosine residue 115 has been nitrated with use of tetranitromethane, has been characterized using absorbance, circular dichroism, and fluorescence spectroscopy. The results show that nitrotyrosine-115 nuclease is indistinguishable from native nuclease with regard to the average secondary structure of the folded polypeptide chain, the susceptibility of the enzyme to heat denaturation, and the local tertiary structure around tryptophan residue 140. Inasmuch as optical properties of nitrotyrosine-115 nuclease from 300 to 500 nm can be unambiguously assigned to nitrotyrosine residue 115 in the active site region, this modified enzyme presents a good model system for studying the circular dichroism properties of this aromatic amino acid in a protein. The spectral properties of nitrotyrosine-115 nuclease have been compared to those of the model compounds, cyclo-(-Gly-Tyr(3NO2)-) and Tyr(3NO2). Circular dichroism spectral changes in nitrotyrosine-115 nuclease due to the binding of deoxythymidine 3',5'-diphosphate and Ca-2+ have been compared to the corresponding nitrotyrosyl-115 absorption spectral changes. This comparison shows that the circular dichroism difference spectrum exhibits an over-all change in the intensity of the observed Cotton effects, whereas the absorption difference spectrum exhibits a blue shift. This finding supports the suggestion that perturbations of aromatic amino acid chromophores in proteins due to ligand binding result in red or blue shifts in absorption difference spectra, but in over-all changes of intensity in circular dichroism difference spectra.