Quantitation of protein orientation in flow-oriented unilamellar liposomes by linear dichroism

The linear dichroism of the visible wavelength transitions of retinal have been used to analyse linear dichroism spectra to determine the orientation of aromatic and peptide structural motifs of Bacteriorhodopsin incorporated into unilamellar soy bean liposomes. The results are consistent with the available X-ray data. This proves that visible light absorbing chromophores can be used to analyse linear dichroism data to give the orientation of membrane proteins in membrane mimicking environments. The work has been extended by screening a wide range of hydrophobic molecules with high extinction coefficients in transitions above 300 nm to find molecules that could be used as independent probes of liposome orientation for experiments involving proteins incorporated into liposomes. Three probes were found to have potential for future work: bis-(1,3-dibutylbarbituric acid)pentamethine oxonol (DiBAC₄), retinol and rhodamine B. All three can be used to determine the orientation of the porphyrin of cytochrome c, the aromatic residues of gramicidin and the helices of both proteins. The orientation parameter, S, for the liposomes varied from batch to batch of unilamellar liposomes prepared by extruding through a 100 nm membrane. The value and variation in S was 0.030 ± 0.010. Repeat experiments with the same batch of liposomes showed less variation. Film LD data were measured for DiBAC₄ and rhodamine B to determine the polarisations of their long wavelength transitions.     

Infrared dichroism of polyethylene crystallized by orientation and pressure in a capillary viscometer

Polarized infrared absorption spectra have been obtained by Fourier-transform spectroscopy for several crystalline and noncrystalline absorption bands of polyethylene crystallized by orientation and pressure in capillary viscometer. An analysis of data obtained at room temperature yielded degrees of crystallinity which are in good accord with values obtained from calorimetry and density measurements. The dichroism of the infrared absorption bands for the crystalline region revealed an extreme degree of orientation consistent with previous x-ray studies and also demonstrated that the degree of orientation is a good or better than that obtained from drawn polyethylene films with extension ratios of 20. Dichroism of bands from the amorphous phases revealed that the noncrystalline chain segments are in a comparatively relaxed state compared with results for drawn films having extension ratios of about 2 to 7. This is 1/10 to 1/3 the extension ratio of drawn polyethylene which shows maximum crystalline orientation. The results also indicated that the ratio of the GTG′ to GG segment conformations in the amorphous regions is larger than that of amorphous portions in unoriented polyethylene. The vinyl endgroups were shown to be highly oriented, while the main bulk of the amorphous polymer was fairly relaxed, i.e., of low orientation. It is concluded that the amorphous polyethylene state is strongly dependent on the nature of the crystalline–amorphous interface.     

Orientational dependence of linear dichroism exemplified by dyed spherulites

D-sorbitol forms so-called spherulites from under-cooled melts. These polycrystalline formations have optically uniaxial radii. Melts pressed between glasses crystallize as plane sections of spheres. Dyes that are soluble in molten sorbitol become oriented as the crystallization front passes through the melt so as to form disks with large linear dichroism in the absorption bands of the dyes. The dyeing of spherulites is thus a general method of solute alignment. The linear optical properties of sorbitol spherulites containing the azo dye amaranth were analyzed in detail so as to correct a persistent confusion in the literature regarding the orientational dependence of linear dichroism. In cases involving thin film dichroism of multilayered samples requiring many corrections of intensity data in non-normal incidence, some authors have taken transmittance and others absorbance as having a cosine-squared angular dependence on the plane of the electric vector of linearly polarized light. Plane sections of doped spherulites present all orientations of an electric dipole oscillator in spatially localized region in normal incidence. As such, the samples described herein are ideally suited to resolving this confusion. Images of transmittance of dyed spherulites in polarized light were recorded with a CCD camera and simulated under the assumption that both absorbance and transmittance show a cosine-squared angular dependence but with respect to different angles. Transmittance with a cosine-squared dependence follows azimuthal rotations of the spherulite radii around the wave vector, while absorbance with a cosine-squared dependence follows rotations about axes perpendicular to the wave vector, natural consequences of the properties of the optical indicatrix that are often overlooked. Spherulites obviate the substantial experimental complexities that are engendered in non-normal incidence by sample reorientation. Thus, the principles of anisotropic absorption are given in a complete and intuitive fashion.     

Circular dichroism effect for linear molecules induced by a resonant circularly polarized pumping optical field

In this paper we propose and discuss the laser-induced circular dichroism (LICD) effect, which is expected to occur in linear molecules pumped by a strong circular resonant light beam. The effect is to be detected via the absorption of a weak circularly polarized probe beam on another transition. Analogous to the external magnetic field in magnetic circular dichroism the resonant circular polarized pumping optical field can induce the nonzero antisymmetric rotational polarizabilities of a linear molecule, and cause the LICD effect. LICD contains three distinct contributions from M-dependent splittings of the sublevels mid R:JM due to the ac Stark effect, from the differences of Boltzmann statistical distributions among the ground state sublevels mid R:JM due to the ac Stark splittings, and from the changes of occupation probability in rotational sublevels mid R:JM due to the pumping effect. The fundamental formulas for the above three terms of LICD have been deduced by the density matrix method. As an example, the LICD for CO molecules have been calculated. The results indicate that in comparison with the rotationally resolved magnetic vibrational circular dichroism experiment, LICD may be measurable and form a basis of a different kind of CD spectroscopy.     

Circular and linear dichroism of proteins

Circular dichroism (CD) is an important technique in the structural characterisation of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the so-called matrix method, with an accuracy which is almost quantitative for helical proteins. Thus, for proteins of unknown structure, CD calculations and experimental data can be used in conjunction to aid structure analysis. Linear dichroism (LD) can be calculated using analogous methodology and has been used to establish the relative orientations of subunits in proteins and protein orientation in an environment such as a membrane. However, simple analysis of LD data is not possible, due to overlapping transitions. So coupling the calculations and experiment is an important strategy. In this paper, the use of LD for the determination of protein orientation and how these data can be interpreted with the aid of calculations, are discussed. We review methods for the calculation of CD spectra, focusing on semiempirical and ab initio parameter sets used in the matrix method. Lastly, a new web interface for online CD and LD calculation is presented.     

Segmental orientation and chain relaxation of polymers by fourier transform infrared dichroism

Fourier transform infrared dichroism has been used to investigate molecular orientation in polymeric materials. It is first applied to characterize network behavior in some elastomeric systems such as model networks of poly(dimethylsiloxane). The strain dependence of segmental orientation is analyzed through networks of known degree of cross-linking and experimental results are compared with calculation predictions based on the rotational isomeric state formalism. Infrared dichroism spectroscopy has also been used to analyze orientational relaxation in binary blends of long and short polystyrene chains. The effect of short deuterated chains (M_w = 3000 to 72000) on the orientational relaxation of long entangled chains (Mw = 2 000 000) is examined in the bidisperse melts uniaxially deformed above the glass transition temperature. While the long chain relaxation is found to be dependent on the short-chain concentration, the local orientational order of the latter is molecular weight dependent in agreement with the classical relaxation theories.     

Binding of methyl green to deoxyribonucleic acid analyzed by linear dichroism

From linear dichroism data a distinct structure of the strongest complex between the methyl green (MG) dication and the B-form DNA is concluded. MG is not intercalated but binds (probably to hydrophobic surfaces in the major groove) with its x and z axes at an angle to the local helix axis of 48° and 90°, respectively. At higher occupation density, exciton coupling between transition dipoles of adjacent molecules is visualized in the linear and circular dichroism spectra. The final spectra may be understood in terms of a right-handed (MG)_N helix in the major groove of the double helix.     

Infrared dichroism and polymer orientation in attenuated total reflection. Theoretical considerations

The orientation of molecular chains in polymers cannot be easily extracted from ATR spectra measurements. One can infer the orientation parameters by using plausible models that describe the type of the statistical distribution of the molecular chains in the sample. In this work, we are interested in the case of weakly aligned polymers. Therefore, we first adjusted the partial axial orientation model usually applied for strongly oriented polymers to the samples under our investigations and second, related the parameters describing the orientation configuration to the dichroic ratios in four particular molecular chain distributions: randomly, totally, partially, and elliptically oriented. A new method that leads to the determination of these dichroic ratios from ATR spectra is presented. This method is based only on the use of three distinct polarizations of the beam. Thus, all the practical difficulties usually encountered in the other methods are eliminated. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35 : 1361–1372, 1997     

Micelle studies by high-sensitivity linear dichroism. Benzene solubilization in rod-shaped micelles of cetyltrimethylammoniumbromide in water

A high-sensitivity linear dichroism (LD) technique has been employed in studying the indirect orientation of benzene by solubilization in rod-shaped micelles in a system of cetyltrimethylammoniumbromide (CTAB): water, oriented by flow in a couvette device. The dependence of the LD signal due to the π-π^* transitions in the benzene plane on the temperature, on the shear gradient and on the benzene concentration, has been investigated. The net positive LD, observed from the benzene chromophore, derives from benzene orientation at the surface of the rod-shaped micelles. The orientation of the micelle rods is very high and the system is suggested for use as a standard matrix for studying solubilized molecules in polarized spectroscopy.     

A two-chromophore model for two-photon circular dichroism

A discussion of two-photon circular dichroism due to dissymmetrically placed chromophores is presented. Using quantum electrodynamics, expressions are derived for the differential rates or absorption associated with an electronic transition which is electric dipole forbidden to a one-photon interaction. A complex field formulation enables effective interaction operators to be derived which are formally equivalent to those arising in the theory of induced circular dichroism. For non-equivalent chromophores, it is shown that a coupling mechanism provides the necessary chiral discrimination, whilst for equivalent chromophores there is an additional contribution from an interference term which becomes more important as the chromophore separation is decreased.     

All-trans 2,7-dialkylperhydrophenanthrene as a solvent for measurements of helical twisting power and linear dichroism

The values of twisting power of a chiral bridged binaphthyl and (+)-trans-stilbene oxide in a rigid hydrocarbon perhydrophenanthrene nematic are much smaller than in conformationally flexible nematics, indicating the importance of the solvent structure for cholesteric induction. The perhydrophenanthrene phase constitutes an excellent solvent for linear dichroism measurements of anthracene but it is unable to orient 9,9'-spirobifluorene.     

用衰减全反射红外二向色性表征聚环氧乙烷薄膜的表面取向

应用衰减全反射二向色性表征聚合物的表面取向,可不必测定样品的折光率使大多数实验简化.以聚环氧乙烷为例.用衰减全反射偏振红外光谱测定了它的表面二向色性比和计算了相应的取向函数.     

All-trans 2,7-dialkylperhydrophenanthrene as a solvent for measurements of helical twisting power and linear dichroism

Abstract

The values of twisting power of a chiral bridged binaphthyl and (+)-trans-stilbene oxide in a rigid hydrocarbon perhydrophenanthrene nematic are much smaller than in conformationally flexible nematics, indicating the importance of the solvent structure for cholesteric induction. The perhydrophenanthrene phase constitutes an excellent solvent for linear dichroism measurements of anthracene but it is unable to orient 9,9′-spirobifluorene.     

Interactions between carbonic anhydrase and its inhibitors revealed by gel electrophoresis and circular dichroism

Structural properties, and especially the differential stability, of complexes between carbonic anhydrase (CA) and three sulfonamide inhibitors, acetazolamide, dorzolamide and methazolamide, were investigated by spectroscopic and electrophoretic techniques. These included denaturant gradient gel electrophoresis either across a urea or a steady-state transverse sodium dodecyl sulfate (SDS) gradient. Acetazolamide, the smallest and most hydrophilic of the sulfonamides, forms the most stable complex in the presence of urea, whereas dorzolamide, with a bulky and hydrophobic structure, is most stable against the effects of SDS. At pH 7.4, complexes with dorzolamide show minimal changes in mobility across the SDS gradient, as if unaffected by the detergent, both in the presence and in the absence of excess ligand in the gel. When bound to both acetazolamide and methazolamide, on the other hand, CA displays an increase in mobility above 0.05% SDS, lower in the presence than in the absence of excess ligand. The finding of a distinct pattern for the unliganded enzyme, however, suggests the complexes can still retain the ligand, although binding of the surfactant changes their charge density. Under saturating conditions and in the presence of SDS, the surface charge of all complexes is much lower than for unliganded, denatured CA. Circular dichroism (CD) spectra clearly indicate that the increase in secondary structure and the decrease in tertiary structure brought about in CA by the presence of low concentrations of SDS are largely prevented by complexing with the inhibitors. These observations point out peculiar properties of each CA inhibitor, of potential value in the definition of their biological activities and also in the potential development of novel antagonist molecules.     

Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model

An increased circular dichroism (CD) signal of large molecular aggregates formed upon DNA condensation was observed a long time ago, and is often referred to as psi-CD. The effort to understand this phenomenon is further motivated by the latest DNA packing studies and advances in macromolecular chemistry. In the present work, the transition dipole coupling model describing interactions of molecules with light has been extended to handle systems of arbitrary size. The analytical formulae obtained retain the simplicity and computational speed of the standard approach. The origin of the psi-effect was investigated on several model systems. The results suggest that the CD enhancement is primarily caused by delocalized phonon-like excitations in nucleic acid strands. The size of the system exhibiting the effect thus does not need to be comparable with or greater than the wavelength of the absorbed light. Small structural irregularities still allow for the enhancement while a larger disorder breaks it. The modeling is consistent with previous experimental electronic and vibrational CD studies, and makes it possible to correlate the enhancement with the geometry of the nucleic acid systems.     

Application of linear dichroism measurements to highly symmetric chromophores

The linear dichroic spectrum of fluoranthene in stretched polyethylene film was analyzed and compared with the previously reported results.     

Spectroscopic linear dichroism FT-IR studies of synthetic spider silk

This work deals with the analysis of the orientation behavior of different segments of synthetic spider silk samples containing hard and soft segments. Two different types of spider silk were examined, one with an aliphatic hard segment (hexamethylene-diisocyanate) and an amorphous soft segment (polytetramethylene oxide) (A40) and the other with an aromatic hard segment (4,4′-methylene bisphenyl diisocyanate) and a semicrystalline soft segment (polyethylene oxide-polypropylene oxide- polyethylene oxide) (A143). In order to observe the orientation behavior of the hard and the soft segments it was necessary to define marker bands. While for both samples the chosen marker bands for the hard segments were the same, the marker bands for the soft segments were different. FT-IR spectra were recorded while strain was applied to the material at the same time. Two parameters, the dichroic ratio R and the order Parameter f were used to evaluate the behavior of these materials under conditions of strain. It was found that sample A143 broke at a strain level of 37,5 %, while sample A40 showed a high dynamic range up to a strain level of 307 %.     

Humidity-dependent dynamic infrared linear dichroism study of a poly(ester urethane)

Fourier transform infrared techniques, infrared difference spectroscopy and dynamic infrared linear dichroism (DIRLD), have been utilized to explore the effects of humidity and water absorption on a poly(ester urethane). An environmental infrared microbalance cell was used to measure the infrared spectra as a function of humidity and accompanying weight change for the absorption-desorption processes. The infrared difference data indicate that exposure to humidity affects the hydrogen-bonding interactions in the polymer. Dynamic infrared linear dichroism studies in tensile deformation mode as a function of humidity demonstrate how changes in water content affect the orientational response of functional groups. Complex behavior as a function of humidity for functional groups involved in hydrogen bonding indicates that water absorbed by the polymer affects the micro-environments near these functional groups.