Role of isotropic lipid phase in the fusion of photosystem II membranes.

It has been thoroughly documented, by using 31P-NMR spectroscopy, that plant thylakoid membranes (TMs), in addition to the bilayer (or lamellar, L) phase, contain at least two isotropic (I) lipid phases and an inverted hexagonal (HII) phase. However, our knowledge concerning the structural and functional roles of the non-bilayer phases is still rudimentary. The objective of the present study is to elucidate the origin of I phases which have been hypothesized to arise, in part, from the fusion of TMs (Garab et al. 2022 Progr Lipid Res 101,163). We take advantage of the selectivity of wheat germ lipase (WGL) in eliminating the I phases of TMs (Dlouhý et al. 2022 Cells 11: 2681), and the tendency of the so-called BBY particles, stacked photosystem II (PSII) enriched membrane pairs of 300-500 nm in diameter, to form large laterally fused sheets (Dunahay et al. 1984 BBA 764: 179). Our 31P-NMR spectroscopy data show that BBY membranes contain L and I phases. Similar to TMs, WGL selectively eliminated the I phases, which at the same time exerted no effect on the molecular organization and functional activity of PSII membranes. As revealed by sucrose-density centrifugation, magnetic linear dichroism spectroscopy and scanning electron microscopy, WGL disassembled the large laterally fused sheets. These data provide direct experimental evidence on the involvement of I phase(s) in the fusion of stacked PSII membrane pairs, and strongly suggest the role of non-bilayer lipids in the self-assembly of the TM system.

Advantages of a synchrotron light source for fluorescence-detected linear dichroism.

Fluorescence-detected linear dichroism (FD-LD) enables one to collect linear dichroism spectra for oriented fluorophores in the presence of other absorbing species and light scattering. The experiment proceeds by scanning the excitation wavelength and using a filter to collect only emitted photons from the fluorophore. Thus, it has the potential to give data with enhanced selectivity and quality. By using a synchrotron radiation light source and fluorescence-detection, we show data for a range of fluorophores in different orienting environments. Film and flow-oriented FD-LD spectra were collected down to 170 nm. Even for flow-oriented liposomes, we have data collected down to 210 nm. For strongly scattering samples, for example, liposomes, FD-LD has the clear advantage that scattering is absent for the longer wavelength fluorescence photons. The collimated and smaller beam size of the synchrotron radiation also gives rise to sharper and more well-defined features in the spectra.

Linear dichroism reveals the perpendicular orientation of DNA bases in the RecA and Rad51 recombinase filaments: A possible mechanism for the strand exchange reaction.

Linear dichroism spectroscopy is used to investigate the structure of RecA family recombinase filaments (RecA and Rad51 proteins) with DNA for clarifying the molecular mechanism of DNA strand exchange promoted by these proteins and its activation. The measurements show that the recombinases promote the perpendicular base orientation of single-stranded DNA only in the presence of activators, indicating the importance of base orientation in the reaction. We summarize the results and discuss the role of DNA base orientation.

X-ray linear dichroic ptychography.

Biominerals such as seashells, coral skeletons, bone, and tooth enamel are optically anisotropic crystalline materials with unique nanoscale and microscale organization that translates into exceptional macroscopic mechanical properties, providing inspiration for engineering new and superior biomimetic structures. Using Seriatopora aculeata coral skeleton as a model, here, we experimentally demonstrate X-ray linear dichroic ptychography and map the c-axis orientations of the aragonite (CaCO3) crystals. Linear dichroic phase imaging at the oxygen K-edge energy shows strong polarization-dependent contrast and reveals the presence of both narrow (<35°) and wide (>35°) c-axis angular spread in the coral samples. These X-ray ptychography results are corroborated by four-dimensional (4D) scanning transmission electron microscopy (STEM) on the same samples. Evidence of co-oriented, but disconnected, corallite subdomains indicates jagged crystal boundaries consistent with formation by amorphous nanoparticle attachment. We expect that the combination of X-ray linear dichroic ptychography and 4D STEM could be an important multimodal tool to study nano-crystallites, interfaces, nucleation, and mineral growth of optically anisotropic materials at multiple length scales.

Optical Effect Modulation in Polarized Raman Spectroscopy of Transparent Layered α-MoO3.

Optical anisotropy, which is quantified by birefringence (Δn) and linear dichroism (Δk), can significantly modulate the angle-resolved polarized Raman spectroscopy (ARPRS) response of anisotropic layered materials (ALMs) by external interference. This work studies the separate modulation of birefringence on the ARPRS response and the intrinsic response by selecting transparent birefringent crystal α-MoO3 as an excellent platform. It is found that there are several anomalous ARPRS responses in α-MoO3 that cannot be reproduced by the real Raman tensor widely used in non-absorbing materials; however, they can be well explained by considering the birefringence-induced Raman selection rules. Moreover, the systematic thickness-dependent study indicates that birefringence modulates the ARPRS response to render an interference pattern; however, the amplitude of modulation is considerably lower than that by linear dichroism as occurred in black phosphorous. This weak modulation brings convenience to the crystal orientation determination of transparent ALMs. Combining the atomic vibrational pattern and bond polarizability model, the intrinsic ARPRS response of α-MoO3 is analyzed, giving the physical origins of the Raman anisotropy. This study employs α-MoO3 as an example, although it is generally applicable to all transparent birefringent ALMs.

Can we still measure circular dichroism with circular dichroism spectrometers: The dangers of anisotropic artifacts.

Chiral materials with strong linear anisotropies are difficult to accurately characterize with circular dichroism (CD) because of artifactual contributions to their spectra from linear dichroism (LD) and birefringence (LB). Historically, researchers have used a second-order Taylor series expansion on the Mueller matrix to model the LDLB interaction effects on the spectra in conventional materials, but this approach may no longer be sufficient to account for the artifactual CD signals in emergent materials. In this work, we present an expression to model the measured CD using a third-order expansion, which introduces "pairwise interference" terms that, unlike the LDLB terms, cannot be averaged out of the signal. We find that the third-order pairwise interference terms can make noticeable contributions to the simulated CD spectra. Using numerical simulations of the measured CD across a broad range of linear and chiral anisotropy parameters, the LDLB interactions are most prominent in samples that have strong linear anisotropies (LD, LB) but negligible chiral anisotropies, where the measured CD strays from the chirality-induced CD by factors greater than 103 . Additionally, the pairwise interactions are most significant in systems with moderate-to-strong chiral and linear anisotropies, where the measured CD is inflated twofold, a figure that grows as linear anisotropies approach their maximum. In summary, media with moderate-to-strong linear anisotropy are in great danger of having their CD altered by these effects in subtle manners. This work highlights the significance of considering distortions in CD measurements through higher-order pairwise interference effects in highly anisotropic nanomaterials.

Characterization of membrane-interaction mechanisms of proteins using vacuum-ultraviolet circular dichroism spectroscopy.

Protein-membrane interactions play an important role in various biological phenomena, such as material transport, demyelinating diseases, and antimicrobial activity. We combined vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy with theoretical (e.g., molecular dynamics and neural networks) and polarization experimental (e.g., linear dichroism and fluorescence anisotropy) methods to characterize the membrane interaction mechanisms of three soluble proteins (or peptides). α1 -Acid glycoprotein has the drug-binding ability, but the combination of VUVCD and neural-network method revealed that the membrane interaction causes the extension of helix in the N-terminal region, which reduces the binding ability. Myelin basic protein (MBP) is an essential component of the myelin sheath with a multi-layered structure. Molecular dynamics simulations using a VUVCD-guided system showed that MBP forms two amphiphilic and three non-amphiphilic helices as membrane interaction sites. These multivalent interactions may allow MBP to interact with two opposing membrane leaflets, contributing to the formation of a multi-layered myelin structure. The antimicrobial peptide magainin 2 interacts with the bacterial membrane, causing damage to its structure. VUVCD analysis revealed that the M2 peptides assemble in the membrane and turn into oligomers with a ß-strand structure. Linear dichroism and fluorescence anisotropy suggested that the oligomers are inserted into the hydrophobic core of the membrane, disrupting the bacterial membrane. Overall, our findings demonstrate that VUVCD and its combination with theoretical and polarization experimental methods pave the way for unraveling the molecular mechanisms of biological phenomena related to protein-membrane interactions.

Disentangling the Orientations of Spectrally Overlapping Transition Dipoles in Dense Dye Layers.

The transition dipole orientations of dye assemblies in heterostructures have a crucial impact on the efficiency of novel optoelectronic devices such as organic thin-film transistors and light-emitting diodes. These devices are frequently based on heterojunctions and tandem structures featuring multiple optical transitions. Precise knowledge of preferred orientations, spatial order, and spatial variations is highly relevant. We present a fast and universal large-area screening method to determine the transition dipole orientations in dye assemblies with diffraction-limited spatial resolution. Moreover, our hyperspectral imaging approach disentangles the orientations of different chromophores. As a demonstration, we apply our technique to dye monolayers with two optical transitions sandwiched between two ultrathin silicate nanosheets. A comprehensive model for dipole orientation distributions in monolayers reveals a long-range orientational order and a strong correlation between the two transitions.

Linear Dichroism Measurements for the Study of Protein-DNA Interactions.

Linear dichroism (LD) is a differential polarized light absorption spectroscopy used for studying filamentous molecules such as DNA and protein filaments. In this study, we review the applications of LD for the analysis of DNA-protein interactions. LD signals can be measured in a solution by aligning the sample using flow-induced shear force or a strong electric field. The signal generated is related to the local orientation of chromophores, such as DNA bases, relative to the filament axis. LD can thus assess the tilt and roll of DNA bases and distinguish intercalating from groove-binding ligands. The intensity of the LD signal depends upon the degree of macroscopic orientation. Therefore, DNA shortening and bending can be detected by a decrease in LD signal intensity. As examples of LD applications, we present a kinetic study of DNA digestion by restriction enzymes and structural analyses of homologous recombination intermediates, i.e., RecA and Rad51 recombinase complexes with single-stranded DNA. LD shows that the DNA bases in these complexes are preferentially oriented perpendicular to the filament axis only in the presence of activators, suggesting the importance of organized base orientation for the reaction. LD measurements detect DNA bending by the CRP transcription activator protein, as well as by the UvrB DNA repair protein. LD can thus provide information about the structures of protein-DNA complexes under various conditions and in real time.

Stress-Induced Inversion of Linear Dichroism by 4,4'-Bipyridine Rotation in a Superelastic Organic Single Crystal.

The molecular crystals that manifest unusual mechanical properties have attracted growing attention. Herein, we prepared an organic single crystal that shows bidirectional superelastic transformation in response to shear stress. Single-crystal X-ray diffractions revealed this crystal-twinning related shape change is owed to a stress-controlled 90° rotation of 4,4'-bipyridine around the hydrogen bonds of a chiral organic trimer. As a consequence of the 90° shift in the aromatic plane, an interconversion of crystallographic a-, b-axes (a→b' and b→a') was detected. The molecular rotations changed the anisotropic absorption of linearly polarized light. Therefore, a stress-induced inversion of linear dichroism spectra was demonstrated for the first time. This study reveals the superior mechanical flexibilities of single crystals can be realized by harnessing the molecular rotations and this superelastic crystal may find applications in optical switching and communications.

Direct Observation of the Linear Dichroism Transition in Two-Dimensional Palladium Diselenide.

The linear dichroism (LD) transition within anisotropic photonic materials displays promising prospects for applications in polarization-wavelength-selective detectors, optical switching, and optical communication. In conventional two-dimensional (2D) anisotropic materials, the LD is predominantly uniaxial over a broad spectrum of wavelengths and arises principally from the reduced symmetry of the materials. However, the LD transition behavior in crystalline 2D materials remains elusive. Here, we demonstrate the observation of a unique LD conversion phenomenon at a wavelength of 472 nm in palladium diselenide (PdSe2) using polarization-resolved absorption spectroscopy. This material exhibits prominent anisotropic responses and a high absorption ratio of αy/αx ≈ 1.11 at 364 nm, 1.15 at 532 nm, and 0.84 at 633 nm. We propose that this abnormal LD conversion behavior originates from the forceful localization rules at different parallel energy bands that exist within this material. Furthermore, the robust periodicity of Ag and B1g modes in polarization-resolved Raman spectroscopy is in good agreement with the theoretical structure symmetry analysis. This indicates the strong intrinsic LD effect in the anisotropic nature of PdSe2, which offers a macrolevel determination of crystal orientations. Such unique LD conversion features, in combination with strong LD effects, enable the air-stable PdSe2 to be a potential candidate for technological innovations in multispectral imaging, sensing, and polarization-sensitive and wavelength-controllable photoelectronic applications.

Membrane Association Modes of Natural Anticancer Peptides: Mechanistic Details on Helicity, Orientation, and Surface Coverage.

Anticancer peptides (ACPs) could potentially offer many advantages over other cancer therapies. ACPs often target cell membranes, where their surface mechanism is coupled to a conformational change into helical structures. However, details on their binding are still unclear, which would be crucial to reach progress in connecting structural aspects to ACP action and to therapeutic developments. Here we investigated natural helical ACPs, Lasioglossin LL-III, Macropin 1, Temporin-La, FK-16, and LL-37, on model liposomes, and also on extracellular vesicles (EVs), with an outer leaflet composition similar to cancer cells. The combined simulations and experiments identified three distinct binding modes to the membranes. Firstly, a highly helical structure, lying mainly on the membrane surface; secondly, a similar, yet only partially helical structure with disordered regions; and thirdly, a helical monomeric form with a non-inserted perpendicular orientation relative to the membrane surface. The latter allows large swings of the helix while the N-terminal is anchored to the headgroup region. These results indicate that subtle differences in sequence and charge can result in altered binding modes. The first two modes could be part of the well-known carpet model mechanism, whereas the newly identified third mode could be an intermediate state, existing prior to membrane insertion.

Differential Polarization Imaging of Plant Cells. Mapping the Anisotropy of Cell Walls and Chloroplasts.

Modern light microscopy imaging techniques have substantially advanced our knowledge about the ultrastructure of plant cells and their organelles. Laser-scanning microscopy and digital light microscopy imaging techniques, in general-in addition to their high sensitivity, fast data acquisition, and great versatility of 2D-4D image analyses-also opened the technical possibilities to combine microscopy imaging with spectroscopic measurements. In this review, we focus our attention on differential polarization (DP) imaging techniques and on their applications on plant cell walls and chloroplasts, and show how these techniques provided unique and quantitative information on the anisotropic molecular organization of plant cell constituents: (i) We briefly describe how laser-scanning microscopes (LSMs) and the enhanced-resolution Re-scan Confocal Microscope (RCM of Confocal.nl Ltd. Amsterdam, Netherlands) can be equipped with DP attachments-making them capable of measuring different polarization spectroscopy parameters, parallel with the 'conventional' intensity imaging. (ii) We show examples of different faces of the strong anisotropic molecular organization of chloroplast thylakoid membranes. (iii) We illustrate the use of DP imaging of cell walls from a variety of wood samples and demonstrate the use of quantitative analysis. (iv) Finally, we outline the perspectives of further technical developments of micro-spectropolarimetry imaging and its use in plant cell studies.

Limitations of Linear Dichroism Spectroscopy for Elucidating Structural Issues of Light-Harvesting Aggregates in Chlorosomes.

Linear dichroism (LD) spectroscopy is a widely used technique for studying the mutual orientation of the transition-dipole moments of the electronically excited states of molecular aggregates. Often the method is applied to aggregates where detailed information about the geometrical arrangement of the monomers is lacking. However, for complex molecular assemblies where the monomers are assembled hierarchically in tiers of supramolecular structural elements, the method cannot extract well-founded information about the monomer arrangement. Here we discuss this difficulty on the example of chlorosomes, which are the light-harvesting aggregates of photosynthetic green-(non) sulfur bacteria. Chlorosomes consist of hundreds of thousands of bacteriochlorophyll molecules that self-assemble into secondary structural elements of curved lamellar or cylindrical morphology. We exploit data from polarization-resolved fluorescence-excitation spectroscopy performed on single chlorosomes for reconstructing the corresponding LD spectra. This reveals that LD spectroscopy is not suited for benchmarking structural models in particular for complex hierarchically organized molecular supramolecular assemblies.

X-ray absorption linear dichroism at the Ti K-edge of rutile (001) TiO2 single crystal.

X-ray absorption linear dichroism of rutile TiO2 at the Ti K-edge provides information about the electronic states involved in the pre-edge transitions. Here, linear dichroism with high energy resolution is analyzed in combination with ab initio finite difference method calculations and spherical tensor analysis. It provides an assignment of the three pre-edge peaks beyond the octahedral crystal field splitting approximation and estimates the spatial extension of the corresponding final states. It is then discussed for the first time the X-ray absorption (XAS) of pentacoordinated titanium atoms due to oxygen vacancies and it is found that, similarly to anatase TiO2, rutile is expected to exhibit a transition on the low-energy side of peak A3. Its apparent absence in the experiment is related to the degree of p-d orbital mixing which is small in rutile due to its centrosymmetric point group. A recent XAS linear dichroism study on anatase TiO2 single crystals has shown that peak A2 has an intrinsic origin and is due to a quadrupolar transition to the 3d energy levels. In rutile, due to its centrosymmetric point group, the corresponding peak A2 has a small dipole moment explaining the weak transition. The results are confronted with recent picosecond X-ray absorption spectroscopy on rutile TiO2 nanoparticles.

Experimental and Theoretical Investigation of the 3sp(d) Rydberg States of Fenchone by Polarized Laser Resonance-Enhanced-Multiphoton-Ionization and Fourier Transform VUV Absorption Spectroscopy.

The VUV absorption spectrum of fenchone is re-examined using synchrotron radiation Fourier transform spectrometry, revealing new vibrational structure. Picosecond laser (2+1) resonance enhanced multiphoton ionization (REMPI) spectroscopy complements this, providing an alternative view of the 3spd Rydberg excitation region. These spectra display broadly similar appearance, with minor differences that are largely explained by referring to calculated one- and two-photon electronic excitation cross-sections. Both show good agreement with Franck-Condon simulations of the relevant vibrational structures. Parent ion REMPI ionization yields with both femtosecond and picosecond excitation laser pulses are studied as a function of laser polarization and intensity, the latter providing insight into the relative two-photon excitation and one-photon ionization rates. The experimental circular-linear dichroism observed in the parent ion yields varies strongly between the 3s and 3p Rydberg states, in good overall agreement with the calculated two-photon excitation circular-linear dichroism, while corroborating other evidence that the 3pz sub-state plays no more than a very minor role in the (2+1) REMPI spectrum. Vibrationally resolved photoelectron spectra are recorded with picosecond pulse duration (2+1) REMPI at selected intermediate vibrational excitations. The 3s intermediate state displays a very strong Δv=0 propensity on ionization, but the 3p intermediate evidences more complex vibronic dynamics, and we infer some 3p→3s internal conversion prior to ionization.

Circular Dichroism Measurement of Single Metal Nanoparticles Using Photothermal Imaging.

Circular dichroism (CD) spectroscopy is a powerful optical technique for the study of chiral materials and molecules. It gives access to an enantioselective signal based on the differential absorption of right and left circularly polarized light, usually obtained through polarization analysis of the light transmitted through a sample of interest. CD is routinely used to determine the secondary structure of proteins and their conformational state. However, CD signals are weak, limiting the use of this powerful technique to ensembles of many molecules. Here, we experimentally realize the concept of photothermal circular dichroism, a technique that combines the enantioselective signal from circular dichroism with the high sensitivity of photothermal microscopy, achieving a superior signal-to-noise ratio to detect chiral nano-objects. As a proof of principle, we studied the chiral response of single plasmonic nanostructures with CD in the visible range, demonstrating a signal-to-noise ratio better than 40 with only 30 ms integration time for these nanostructures. The high signal-to-noise ratio allows us to quantify the CD signal for individual nanoparticles. We show that we can distinguish relative absorption differences for right circularly and left circularly polarized light as small as gmin = 4 × 10-3 for a 30 ms integration time with our current experimental settings. The enhanced sensitivity of our technique extends CD studies to individual nano-objects and opens CD spectroscopy to numbers of molecules much lower than those in conventional experiments.

Homo-FRET in π-Conjugated Polygons: Intermediate-Strength Dipole-Dipole Coupling Makes Energy Transfer Reversible.

The concept of homo-FRET is often used to describe energy transfer between like chromophores of molecular aggregates such as in π-conjugated polymers. Homo-FRET is revealed by a dynamic depolarization in fluorescence but strictly only applies to the limit of weak dipole-dipole coupling, where energy transfer occurs on time scales much longer than those of nuclear relaxation. By considering the polarization anisotropy of photoluminescence emission and excitation of model multichromophoric aggregates on the single-molecule level, we demonstrate the transition of energy-transfer dynamics from the case of weak coupling to that of strong coupling, revealing the elusive regime of intermediate-strength coupling where energy transfer between degenerate donor and acceptor chromophores becomes reversible so that information on the excitation route of the emitting chromophore is lost.

Fluorescence-detected linear dichroism imaging in a re-scan confocal microscope equipped with differential polarization attachment.

Confocal laser scanning microscopy is probably the most widely used and one of the most powerful techniques in basic biology, medicine and material sciences that is employed to elucidate the architecture of complex cellular structures and molecular macro-assemblies. It has recently been shown that the information content, signal-to-noise ratio and resolution of such microscopes (LSMs) can be improved significantly by adding different attachments or modifying their design, while retaining their user-friendly features and relatively moderate costs. Differential polarization (DP) attachments, using high-frequency modulation/demodulation circuits, have made LSMs capable of high-precision 2D and 3D mapping of the anisotropy of microscopic samples-without interfering with their 'conventional' fluorescence or transmission imaging (Steinbach et al. in Methods Appl Fluoresc 2:015005, 2014). The resolution and the quality of fluorescence imaging have been enhanced in the recently constructed Re-scan confocal microscopy (RCM) (De Luca et al. in Biomed Opt Express 4:2644-2656, 2013). In this work, we developed the RCM technique further, by adding a DP-attachment modulating the exciting laser beam via a liquid crystal (LC) retarder synchronized with the data acquisition system; by this means, and with the aid of a software, fluorescence-detected linear dichroism (FDLD), characteristic of the anisotropic molecular organization of the sample, could be recorded in parallel with the confocal fluorescence imaging. For demonstration, we show FDLD images of a plant cell wall (Ginkgo biloba) stained with Etzold's staining solution.

Measurement of Circular Dichroism Spectra without Control of a Phase Modulator using Retardation Domain Analysis.

This study investigated the measurement of circular dichroism (CD) spectra without controlling a phase modulator. In a conventional CD system, the peak retardation of the phase modulator must remain constant over the observed wavelength range. Thus, the phase modulator must be controlled to maintain an appropriate modulation degree at an observed wavelength. In contrast, CD obtained using retardation domain analysis is not affected by peak retardation. Consequently, CD spectra can be measured without control of the phase modulator, which was experimentally demonstrated in this study. Additionally, linear dichroism spectra were obtained using retardation domain analysis.