Linear Dichroism Data Research Articles

Simulation of XANES spectra for protein-bound metal centers: analysis of linear dichroism data

For protein-bound transition metals, the structure of the metal site (geometric arrangement of the nuclei) and the electronic structure (oxidations state and orbital occupancy) can be investigated by x-ray absorption spectroscopy. While the extended x-ray absorption fine-structure (EXAFS) is theoretically well understood and the advantages of EXAFS spectroscopy on protein-bound metal centers have been repeatedly demonstrated, quantitative analysis of the near-edge structure XANES is more demanding. However, by now XANES simulations, for which a number of codes are available, may be useful to understand geometric and electronic structure effects.For a simplified model of the manganese complex in photosystem II we simulate polarization-dependent XANES spectra using the FEFF 8.2 code [Ankudinov et al, Phys. Rev. B 12 (1998)], which includes self-consistent muffin-tin potentials and polarization-dependent full multiple-scattering calculations. We derive a scheme to analyze the polarization dependence of XANES data that facilitates a treatment of partially uni-directionally oriented samples. Reasonably good agreement between simulations and experiments is obtained for the chosen model of the photosystem II manganese complex and its orientation with respect to the protein-carrying membrane.

Time-Resolved Linear Dichroism and Linear Birefringence of Bacteriorhodopsin at Alkaline pH: Identification of Two N Substates with Different Orientations of the Transition Dipole Moment

Transient linear dichroism and linear birefringence changes in the photocycle of bacteriorhodopsin at alkaline pH were measured with magnetically oriented purple membrane samples using the method of isotropic excitation (Borucki, B.; Otto, H.; Heyn, M. P. J. Phys. Chem. B 1999, 103, 6371−6383). At pH 10.4, the accumulation of the O intermediate is negligible, and N is the only intermediate that is relevant in the M decay and the recovery of the bR ground state. We introduced a new analytical approach that is model-independent and makes use of the transient linear dichroism in combination with isotropic absorbance changes. SVD analysis reveals that only one species (spectral component), namely, the N intermediate, is involved in the M decay at pH 10.4. The spectrum of this intermediate and its average anisotropy are determined from an eigenvalue equation. The transient linear dichroism data suggest a transition between two substates of the N intermediate with different anisotropies (i.e., with different orientations of the electronic transition dipole moment). Assuming that the polar angle of the transition dipole moment with respect to the membrane normal is 70° in the bR ground state, we get 66.3° (upper limit) for the first and 67.9° (lower limit) for the second N substate. The reorientation of the chromophore in the N1 → N2 transition is probably associated with the movement of the protonated Schiff base away from Asp96, suggesting that it serves as a reprotonation switch for Asp96 by stabilizing the protonation state of the Schiff base. In contrast to measurements at neutral pH, the linear birefringence changes at alkaline pH contain a wavelength-independent component that is not due to the transient absorption changes and whose time dependence is correlated with the kinetics of the N intermediate. This result is attributed to an electro-optical effect caused by the large electric field generated by the transient negative charge on Asp96 in the N intermediate. Alternatively this change in Δn may be due to the major conformational change in the cytoplasmic region of the membrane during N.

Magnetoelectricity inV2O3

Motivated by the recent theoretical discussions on the implications of x-ray resonant scattering and linear dichroism data, we have measured the magnetoelectric effect in ${\mathrm{V}}_{2}{\mathrm{O}}_{3}.$ We were not able to detect any effect and could fix an upper limit for the magnetoelectric susceptibility $\ensuremath{\alpha}<~0.01\mathrm{p}\mathrm{s}/\mathrm{m}.$ Moreover, we could verify that it is impossible to perform a magnetoelectric annealing on the system at the transition temperature, because of its small electrical resisitivity. This finding has precise implications on the ground-state properties of the system.

Revealing the Orientation of Nystatin and Amphotericin B in Lipidic Multilayers by UV−Vis Linear Dichroism

Amphotericin B UV−Vis absorption linear dichroism data was combined with Nystatin steady-state fluorescence linear dichroism data to calculate their orientational probability density functions in m...

Electronic states of the phenoxyl radical

The phenoxyl radical and two of its isotopomers were investigated by UV-VIS and IR polarization spectroscopy of molecular samples immobilized in cryogenic argon matrices. Analysis of the combined electronic and infrared linear dichroism data led to determination of absolute transition moment directions and symmetry assignments for four low-lying excited electronic states. The bands observed at 16 000, 25 200, 33 900, and 41 800 cm−1 were assigned to A12, B12, A12, and B12 π–π* states, respectively. A very weak transition observed in the near-infrared close to 8900 cm−1 was assigned to an optically forbidden B22 n–π* state. The electronic transitions predicted by time dependent density functional theory (TD-UB3LYP/cc-pVTZ) were in good agreement with the observed transitions.

Long range supra-organisation of the bacterial photosynthetic unit: archetype or artefact ?

The hypothesis that the small hydrophobic protein Puf X induces the formation of arrays of core complexes in Rhodobacter sphaeroides (Frese et al. 2000) was advanced on the basis of linear dichroism (LD) data from a mutant of Rb. sphaeroides (LH2-LH1-RC-X-) complemented with plasmid-borne genes for the Light-Harvesting 1 complex and the Reaction Centre, with and without puf X. The use of a multi-copy plasmid raises the possibility of an excess of core complexes, with respect to the other components of the respiratory chain, being present in the intracytoplasmic membrane. This system differs markedly from the wild type where there is only one copy of the puf operon and which also has the puc operon present. To test our hypothesis further we have examined the LD properties of membranes from a mutant, DBCW G, that has only a single genomic copy of the puf operon (LH2-LH1+RC+X+). We have also compared true WT membranes with `pseudo? WT membranes, generated by complementing the puf deletion mutant, DPF2R (LH2+LH1-RC-X-), with the plasmid-borne puf operon. The properties of these membranes are reported.

Infrared linear dichroism study of a hydrolytically degraded poly(ester urethane)

Static and dynamic infrared linear dichroism data have been used to supply additional insight into changes in tensile properties as a consequence of hydrolytic degradation of a segmented poly(ester urethane). Unaged material responds to tensile deformation with the soft (polyester) segments supplying the elasticity and the hard (polyurethane) segments supplying strength. Upon hydrolytic degradation, the static and dynamic data indicate altered orientational responses at the molecular-level, which are interpreted as resulting from cleavage of the soft segment chains and altered hydrogen-bonding interactions for both segments.

Organization of the pigment molecules in the chlorophyll a/b/c containing alga Mantoniella squamata (Prasinophyceae) studied by means of absorption, circular and linear dichroism spectroscopy

In order to obtain information on the organization of the pigment molecules in chlorophyll (Chl) a/b/c-containing organisms, we have carried out circular dichroism (CD), linear dichroism (LD) and absorption spectroscopic measurements on intact cells, isolated thylakoids and purified light-harvesting complexes (LHCs) of the prasinophycean alga Mantoniella squamata. The CD spectra of the intact cells and isolated thylakoids were predominated by the excitonic bands of the Chl a/b/c LHC. However, some anomalous bands indicated the existence of chiral macrodomains, which could be correlated with the multilayered membrane system in the intact cells. In the red, the thylakoid membranes and the LHC exhibited a well-discernible CD band originating from Chl c, but otherwise the CD spectra were similar to that of non-aggregated LHC II, the main Chl a/b LHC in higher plants. In the Soret region, however, an unusually intense (+) 441 nm band was observed, which was accompanied by negative bands between 465 and 510 nm. It is proposed that these bands originate from intense excitonic interactions between Chl a and carotenoid molecules. LD measurements revealed that the Q Y dipoles of Chl a in Mantoniella thylakoids are preferentially oriented in the plane of the membrane, with orientation angles tilting out more at shorter than at longer wavelengths (9° at 677 nm, 20° at 670 nm and 26° at 662 nm); the Q Y dipole of Chl c was found to be oriented at 29° with respect to the membrane plane. These data and the LD spectrum of the LHC, apart from the presence of Chl c, suggest an orientation pattern of dipoles similar to those of higher plant thylakoids and LHC II. However, the tendency of the Q Y dipoles of Chl b to lie preferentially in the plane of the membrane (23° at 653 nm and 30° at 646 nm) is markedly different from the orientation pattern in higher plant membranes and LHC II. Hence, our CD and LD data show that the molecular organization of the Chl a/b/c LHC, despite evident similarities, differs significantly from that of LHC II.

On the Spatial Organization of Hemes and Chlorophyll in Cytochrome b6f: A LINEAR AND CIRCULAR DICHROISM STUDY

The organization of chromophores in the cytochrome b(6) f from Chlamydomonas reinhardtii has been studied spectroscopically. Linear dichroism (LD) measurements, performed on the complex co-reconstituted into vesicles with photosynthetic reaction centers as an internal standard, allow the determination of the orientations of the chromophore with respect to the membrane plane. The orientations of the b(H)- and b(L)-hemes are comparable to those determined crystallographically on the cytochrome bc(1). The excitonic CD signal, resulting from the interaction between b-hemes, is similar to that reported for the cytochrome bc(1). LD and CD data are consistent with the differences between the b(6) f and bc(1) leaving the orientation of the b-hemes unaffected. By contrast, the LD data yield a different orientation for the heme f as compared either to the heme c(1) in the crystallographic structures or to the heme f as studied by electron paramagnetic resonance. This difference could either result from incorrect assumptions regarding the orientations of the electronic transitions of the f-heme or may point to the possibility of a redox-dependent movement of cytochrome f. The chlorophyll a was observed in a well defined orientation, further corroborating a specific binding site for it in the b(6) f complex.

DNA structure control by polycationic species: polyamine, cobalt ammines, and di-metallo transition metal chelates.

Many polycationic species bind to DNA and induce structural changes. The work reported here is the first phase of a program whose long-term aim is to create a class of simple and inexpensive sequence-selective compounds that will enable enhanced DNA structure control for a wide range of applications. Three classes of molecule have been included in this work: the polyamine spermine (charge: 4(+)) and spermidine (charge: 3(+)) (which are known to induce a wide range of DNA conformational changes but whose binding modes are still not well understood); cobalt (III) amine transition metal complexes as potential polyamine mimics and [Fe(H(2)O)(6)](3+); and the first member of a new class of di-metallo tris-chelated cylinders of helical structure (charge 4(+)). Temperature-dependent absorption, circular dichroism, linear dichroism, gel electrophoresis, and molecular modeling data are presented. The cobalt amines prove to be effective polyamine mimics, although their binding appears to be restricted to backbone and major groove. All the ligands stabilize the DNA, but the 4(+) di-iron tris-chelate does so comparatively weakly and seems to have a preference for single-stranded DNA. All the molecules studied bend the DNA, with the di-iron tris-chelate having a particularly dramatic effect even at very low drug load.

DNA Binding of ∧-and Δ-cis-β-[Ru(RR-picchxn)(phen)]2+ Studied by NMR and Flow Linear Dichroism Spectroscopy

Two novel substitutionally-inert diastereomeric ruthenium(II) cations of the form ∧-and Δ-cis-β-[Ru(RR-picchxn)(phen)]2+, where RR-picchxn is N,N'-dimethyl-/N,/N'-di(2-picolyl)-1R,2R-diaminocyclohexane and phen is 1,10-phenanthroline, have been studied with respect to their interactions with duplex DNA. NMR investigations show that both diastereomers bind to the oligonucleotide [d(CGCGATCGCG)]2 in the fast exchange regime and that binding predominantly takes place in the minor groove of the oligonucleotide, but that the governing interactions are significantly different for the two Δ and ∧ forms. Linear dichroism data support the latter interpretation, in that the relative orientations of cis-β-[Ru(RR-pic-chxn)(phen)]2+ to calf thymus DNA also are observed to differ for the Δ and ∧ diastereomers. Interpretation of these data indicates the ∧ form to be bound with the planar phen ligand closely parallel to the DNA base-pairs, but the average orientation of the phen ligand in the Δ form deviates significantly from a parallel alignment.

Reorientation of the Retinylidene Chromophore in the K, L, and M Intermediates of Bacteriorhodopsin from Time-Resolved Linear Dichroism: Resolving Kinetically and Spectrally Overlapping Intermediates of Chromoproteins

We determined the change in orientation of the electronic transition dipole moment with respect to the membrane normal in the K, L, and M intermediates of bacteriorhodopsin using transient linear dichroism. Purple membranes were oriented in a 14 T magnetic field and immobilized in a gel. The oriented purple membranes were excited isotropically and the transient absorbance changes were detected with the sample between two parallel polarizers. The absorbance changes were measured as a function of wavelength, time, and angle between the orientation axis and polarizer direction. In this way, the transient changes in isotropic absorbance, linear dichroism, and linear birefringence were determined with high accuracy. The Kramers−Kronig transform of the transient linear dichroism was in excellent agreement with the transient linear birefringence and this served as a useful control on the reliability of the linear dichroism data. We developed a novel formalism to extract the anisotropies, spectra and time courses...

Excited States of the Photosynthetic Reaction Center of Rhodopseudomonas viridis: SAC−CI Study

The excitation spectrum of the photosynthetic reaction center (PSRC) of Rhodopseudomonas (Rps.) viridis is assigned by using the SAC(symmetry adapted cluster)−CI(configuration interaction) method. All the chromophores included in the PSRC, bacteriochlorophyll b dimer (special pair, P), bacteriochlorophyll b in L- and M-branches (BL and BM), bacteriopheophytin b in L- and M-branches (HL and HM), menaquinone (MQ), ubiquinone (UQ), and four different hemes, c-552, c-554, c-556, and c-559 in c-type cytochrome subunit, were calculated within the environment of proteins, waters, and the other chromophores which were dealt with by the point-charge electrostatic model. We have assigned successfully all the peaks in the experimental spectrum in the energy range from 1.2 to 2.5 eV. The assignment was done by comparing the SAC−CI theoretical spectrum with the experimental one in excitation energy, oscillator strength, linear dichroism data (angle of transition moment), and other experimental information available. Almost all the peaks were red shifted due to the effect of proteins. The present assignment of the spectrum would give a basis for future photoexperimental studies of the PSRC.

Orientation and excitonic interactions of the Fenna—Matthews—Olson bacteriochlorophyll a protein in membranes of the green sulfur bacterium Chlorobium tepidum

Linear and circular dichroism spectra of isolated bacteriochlorophyll a proteins (FMO proteins) and membrane vesicles containing FMO protein from the green sulfur bacterium Chlorobium tepidum were measured at room temperature and 77 K. The orientation of membranes and isolated FMO protein was obtained by gel squeezing. Linear dichroism (LD) data indicate that isolated FMO protein and membrane vesicles associated with the FMO protein are oriented in a similar way in a squeezed polyacrylamide gel. Both samples show a characteristic negative LD band around 814 nm with flanking positive bands at 802 and 824 nm ascribed to the Qy excitonic transitions of BChl a of the FMO protein. This confirms that the C3 symmetry axis of the trimer is perpendicular to the membrane plane, which is supported by the model of the disc-like structure of FMO protein trimers of Cb. tepidum [Li Yi-Fen, Zhou W, Blankenship RE, and Allen JP (1997) J Mol Biol 272: 456–471]. The LD data are consistent with either BChl 3 or 6, but not 7 as the principal contributor to the low temperature band at 825 nm. The low temperature linear and circular dichroism spectra of FMO protein trimers from Chlorobium tepidum show significant differences from the low temperature LD and CD spectra of FMO protein trimers from Prosthecochloris aestuarii. The data are interpreted in terms of somewhat different pigment-protein and pigment-pigment interactions in the two complexes.

Binding of Hoechst 33258 to the TAR RNA of HIV-1. Recognition of a pyrimidine bulge-dependent structure.

The transactivation response region (TAR) RNA is an essential component in transcriptional regulation of the human immunodeficiency virus type-1 (HIV-1) genome. We have examined the interaction between TAR RNA and the bisbenzimidazole derivative Hoechst 33258. Previous studies have shown that this drug, which is well known as an AT-selective DNA minor groove binder, can also interact with GC-rich sequences in DNA as well as with RNA, possibly by intercalation. Absorption spectroscopy, circular dichroism and electric linear dichroism, as well as RNase A footprinting, were employed to compare binding of Hoechst 33258 to wild-type RNA and its analogue lacking the pyrimidine bulge. The uridine bulge, which is an important contributor to the structural stability of TAR, plays an essential role in drug binding. Deletion of the bulge destabilizes both free and drug-bound forms of TAR and markedly affects the orientation of the drug chromophore complexed with the RNA. According to the linear dichroism data, the bisbenzimidazole is oriented more or less perpendicular to the RNA helix axis. The data are compatible with a model in which the bisbenzimidazole chromophore is inserted into the existing cavity created by the pyrimidine bulge. The footprinting experiments, showing that the drug binds to a unique site opposite the unpaired uridine residues, also support this model. The binding of Hoechst 33258 to the sequence 5'-GCUCU, which delimits the cavity, reflects the greater accessibility of that region compared with other sites in the RNA molecule. The identification of a binding site for small molecules in TAR offers promising perspectives for developing drugs that would block the access of TAR RNA to proteins and therefore for the design of anti-HIV agents.

Chromophore structural changes in rhodopsin from nanoseconds to microseconds following pigment photolysis.

Rhodopsin is a prototypical G protein-coupled receptor that is activated by photoisomerization of its 11-cis-retinal chromophore. Mutant forms of rhodopsin were prepared in which the carboxylic acid counterion was moved relative to the positively charged chromophore Schiff base. Nanosecond time-resolved laser photolysis measurements of wild-type recombinant rhodopsin and two mutant pigments then were used to determine reaction schemes and spectra of their early photolysis intermediates. These results, together with linear dichroism data, yielded detailed structural information concerning chromophore movements during the first microsecond after photolysis. These chromophore structural changes provide a basis for understanding the relative movement of rhodopsin's transmembrane helices 3 and 6 required for activation of rhodopsin. Thus, early structural changes following isomerization of retinal are linked to the activation of this G protein-coupled receptor. Such rapid structural changes lie at the heart of the pharmacologically important signal transduction mechanisms in a large variety of receptors, which use extrinsic activators, but are impossible to study in receptors using diffusible agonist ligands.

Modulation of nucleic acid structure by ligand binding: induction of a DNA·RNA·DNA hybrid triplex by DAPI intercalation

The aromatic diamidine, DAPI (4′,6-diamidino-2-phenylindole), is used as an important biological and cytological tool since it forms highly fluorescent complexes with nucleic acid duplexes via minor groove-directed/intercalative modes of interaction. In this study, we find that DAPI binding can induce the formation of an RNA-DNA hybrid triplex that would not otherwise form. More specifically, through application of a broad range of spectroscopic, viscometric, and molecular modeling techniques, we demonstrate that DAPI intercalation induces the formation of the poly(dT)·poly(rA)·poly(dT) hybrid triple helix, a structure which does not form in the absence of the ligand. Using UV mixing studies, we demonstrate that, in the presence of DAPI, the poly(rA)·poly(dT) duplex and the poly(dT) single strand form a 1:1 complex (a triplex) that does not form in the absence of DAPI. Through temperature-dependent absorbance measurements, we show that the poly(dT)·poly(rA)·poly(dT) triplex melts via two distinct transitions: initial conversion of the triplex to the duplex state, with the DAPI remaining bound, followed by denaturation of the duplex-DAPI complex to its component single strands and free DAPI. Using optical melting profiles, we show that DAPI binding enhances the thermal stability of the poly(dT)·poly(rA)·poly(dT) triplex, an observation consistent with the preferential binding of the ligand to the triplex versus the duplex and single-stranded states. Our differential scanning calorimetric measurements reveal melting of the DAPI-saturated poly(dT)·poly(rA)·poly(dT) triplex to be associated with a lower enthalpy but greater cooperativity than melting of the corresponding DAPI-saturated poly(rA)·poly(dT) duplex. Our flow linear dichroism and viscometric data are consistent with an intercalative mode of binding when DAPI interacts with both the poly(dT)·poly(rA)·poly(dT) triplex and the poly(rA)·poly(dT) duplex. Finally, computer modeling studies suggest that a combination of both stacking and electrostatic interactions between the intercalated ligand and the host nucleic acid play important roles in the DAPI-induced stabilization of the poly(dT)·poly(rA)·poly(dT) triplex. In the aggregate, our results demonstrate that ligand binding can be used to induce the formation of triplex structures that do not form in the absence of the ligand. This triplex-inducing capacity has potentially important implications in the design of novel antisense, antigene, antiviral, and diagnostic strategies.

Simulations of the overshoot in the build-up of orientation of long DNA during gel electrophoresis based on a distribution of oscillation times.

The periodic extension-contraction motion observed for long DNA molecules undergoing agarose gel electrophoresis in a constant field is believed to be important for the separation mechanism in pulsed field gel electrophoresis. These oscillations give rise to an overshoot and an undershoot in the ensemble orientation of DNA in the beginning of a field pulse, when the molecules oscillate coherently. After approximately one oscillation cycle, the coherence between the molecules is lost, and a constant, cycle-averaged orientation is reached. In this paper we simulate this build-up of the ensemble orientation of DNA by using a distribution of oscillation times (the time between two consecutive compressed conformations) determined by fluorescence microscopy for YOYO-stained DNA. Six different orientation profiles, describing the orientation during one oscillation cycle, were used. The simulated orientation responses are compared with an orientation response measured by linear dichroism (LD) under the same experimental conditions as in the microscopy study. We found that the choice of orientation profile during the oscillation is important. Best agreement between the simulated and the experimental orientation response was obtained for an orientation profile based on a theoretical model by Schurr and Smith (Biopolymers 1990, 29, 1161-1165). The influence of the distribution of oscillation times and its standard deviation on the orientation response was also investigated. Furthermore, simulations at different field strengths and DNA sizes were performed and found to agree quite well with the experimentally obtained LD data.

Use of electric linear dichroism and competition experiments with intercalating drugs to investigate the mode of binding of Hoechst 33258, berenil and DAPI to GC sequences.

The drugs Hoechst 33258, berenil and DAPI bind preferentially to the minor groove of AT sequences in DNA. Despite a strong selectivity for AT sites, they can interact with GC sequences by a mechanism which remains so far controversial. The 2-amino group of guanosine represents a steric hindrance to the entry of the drugs in the minor groove of GC sequences. Intercalation and major groove binding to GC sites of GC-rich DNA and polynucleotides have been proposed for these drugs. To investigate further the mode of binding of Hoechst 33258, berenil and DAPI to GC sequences, we studied by electric linear dichroism the mutual interference in the DNA binding reaction between these compounds and a classical intercalator, proflavine, or a DNA-threading intercalating drug, the amsacrine-4-carboxamide derivative SN16713. The results of the competition experiments show that the two acridine intercalators markedly affect the binding of Hoechst 33258, berenil and DAPI to GC polynucleotides but not to DNA containing AT/GC mixed sequences such as calf thymus DNA. Proflavine and SN16713 exert dissimilar effects on the binding of Hoechst 33258, berenil and DAPI to GC sites. The structural changes in DNA induced upon intercalation of the acridine drugs into GC sites are not identically perceived by the test compounds. The electric linear dichroism data support the hypothesis that Hoechst 33258, berenil and DAPI interact with GC sites via a non-classical intercalation process.

Cleavage of supercoiled plasmid DNA by autoantibody Fab fragment: application of the flow linear dichroism technique.

A highly effective method consisting of two affinity chromatography steps and ion-exchange and gel-filtration chromatography steps was developed for purification of autoantibodies from human sera with DNA-hydrolyzing activity. Antibody Fab fragment, which had been purified 130-fold, was shown to catalyze plasmid DNA cleavage. The flow linear dichroism technique was used for quantitative and qualitative studying of supercoiled plasmid DNA cleavage by these autoantibodies in comparison with DNase I and EcoRI restriction endonuclease. The DNA autoantibody Fab fragment was shown to hydrolyze plasmid DNA by Mg(2+)-dependent single-strand multiple nicking of the substrate. Kinetic properties of the DNA autoantibody Fab fragment were evaluated from the flow linear dichroism and agarose gel electrophoresis data and revealed a high affinity (Kobsm = 43 nM) and considerable catalytic efficiency (kappcat/Kobsm = 0.32 min-1.nM-1) of the reaction.