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Light can effectively interrogate biological systems providing control over complex cellular processes. Particularly advantageous features of photo-induced processes are reversibility, physiological compatibility, and spatiotemporal precision. Understanding the underlying biophysics of light-triggered changes in bio-systems is crucial for cell viability and optimizing clinical applications of photo-induced processes in biotechnology, optogenetics and photopharmacology. Employing membranes doped with the photolipid azobenzene-phosphatidylcholine (azo-PC), we provide a holistic picture of light-triggered changes in membrane morphology, mechanics and dynamics. We combine microscopy of giant vesicles as minimal cell models, Langmuir monolayers, and molecular dynamics simulations. We employ giant vesicle elelctrodeformation as a facile and accurate approach to quantify the magnitude, reversibility and kinetics of light-induced area expansion/shrinkage as a result of azo-PC photoisomerization and content. Area increase as high as ~25% and a 10-fold decrease in the membrane bending rigidity is observed upontrans-to-cisazo-PC isomerization. These results are in excellent agreement with simulations data and monolayers. Simulations also show thattrans-to-cisisomerization of azo-PC decreases the membrane leaflet coupling. We demonstrate that light can be used to finely manipulate the shape and mechanics of photolipid-doped minimal cell models and liposomal drug carriers, thus, presenting a promising therapeutic alternative for the repair of cellular disorders.

A de novo designed class of peptide-based fluoropolymers composed of fluorinated aliphatic amino acids as main components is reported. Structural characterization provided insights into fluorine-induced alterations on β-strand to α-helix transition upon an increase in SDS content and revealed the unique formation of PPII structures for trifluorinated fluoropeptides. A combination of circular dichroism, fluorescence-based leaking assays and surface enhanced infrared absorption spectroscopy served to examine the insertion and folding processes into unilamellar vesicles. While partitioning into lipid bilayers, the degree of fluorination conducts a decrease in α-helical content. Furthermore, this study comprises a report on the proteolytic stability of peptides exclusively built up by fluorinated amino acids and proved all sequences to be enzymatically degradable despite the degree of fluorination. Herein presented fluoropeptides as well as the distinctive properties of these artificial and polyfluorinated foldamers with enzyme-degradable features will play a crucial role in the future development of fluorinated peptide-based biomaterials.

Cytochrome c oxidase (CcO) is a transmembrane heme-copper metalloenzyme that catalyzes the reduction of O2 to H2O at the reducing end of the respiratory electron transport chain. To understand this reaction, we followed the conversion of CcO from Rhodobacter sphaeroides between several active-ready and carbon monoxide (CO) inhibited states via attenuated total reflection Fourier-transform infrared (ATR FTIR) difference spectroscopy. Utilizing a novel gas-titration setup, we prepared the mixed-valence, CO-inhibited R2CO state as well as the fully-reduced R4 and R4CO states and induced the “active ready” oxidized state OH. These experiments are performed in the dark yielding FTIR difference spectra exclusively triggered by exposure to O2, the natural substrate of CcO. Our data demonstrate that the presence of CO at heme a3 does not impair the catalytic oxidation of CcO when the cycle starts from the fully-reduced states. Interestingly, when starting from the R2CO state, the release of the CO ligand upon purging with inert N2 gas results in a product that is indistinguishable from photolysis-induced states. The observed changes at heme a3 in the catalytic binuclear center (BNC) result from the loss of CO and are unrelated to electronic excitation upon illumination. Based on our experiments, we re-evaluate the assignment of marker bands that appear in time-resolved photolysis and perfusion-induced experiments on CcO.

The [4Fe-4S] cluster containing scaffold complex HypCD is the central construction site for the assembly of the [Fe](CN)2CO cofactor precursor of [NiFe]-hydrogenase. While the importance of the HypCD complex is well established, not much is known about the mechanism by which the CN– and CO ligands are transferred and attached to the iron ion. We developed an efficient protocol for the production and isolation of the functional HypCD complex that facilitated detailed spectroscopic investigations. The results obtained by UV/Vis-, electron paramagnetic Resonance (EPR)-, Resonance Raman-, Fourier-transform infrared (FTIR), and Mössbauer spectroscopy provide comprehensive evidence for an electron inventory fit to drive multi-electron redox reactions. We demonstrate the redox activity of the HypCD complex reporting the interconversion of the [4Fe-4S]2+/+ couple. Additionally, we observed a reversible redox conversion between the [4Fe-4S]2+ and a [3Fe-4S]+ cluster. MicroScale thermophoresis indicated preferable binding between the HypCD complex and its interaction partner HypEF under reducing conditions. Together, these results suggest a redox cascade involving the [4Fe-4S] cluster and a conserved disulfide bond of HypD that may facilitate the synthesis of the [Fe](CN)2CO cofactor precursor on the HypCD scaffold complex.

Synthetic multichromophore systems are of great importance in artificial light harvesting devices, organic optoelectronics, tumor imaging and therapy. Here, we introduce a promising strategy for the construction of self-assembled peptide templated dye stacks based on coupling of a de novo designed pH sensitive peptide with a cyanine dye Cy5 at its N-terminus. Microscopic techniques, in particular cryogenic TEM (cryo-TEM) and cryo-electron tomography technique (cryo-ET), reveal two types of highly ordered three-dimensional assembly structures on the micrometer scale. Unbranched compact layered rods are observed at pH 7.4 and two-dimensional membrane-like assemblies at pH 3.4, both species displaying spectral features of H-aggregates. Molecular dynamics simulations reveal that the coupling of Cy5 moieties promotes the formation of both ultrastructures, whereas the protonation states of acidic and basic amino acid side chains dictates their ultimate three-dimensional organization.

In biological photoreceptors, the energy stored in early transient species is a key feature to drive the photocycle or a chain of reactions. Time-resolved photoacoustics (PA) can explore the energy landscape of transient species formed within few ns after photoexcitation, as well as volumetric changes (ΔV) of these intermediates with respect to the parental state. In this work, PA identified these important parameters for several channelrhodopsins, namely CaChR1 from Chlamydomonas augustae and CrChR2 from Chlamydomonas reinhardtii and various variants. PA has access to the sub-ns formation of the early photoproduct P1 and to its relaxation, provided that this latter process occurs within a few μs. We found that ΔVP1 for CaChR1 is ca. 12 mL/mol, while it is much smaller for CrChR2 (4.7 mL/mol) and for H. salinarum bacteriorhodopsin (HsBR, ΔVK = 2.8 mL/mol). PA experiments on variants strongly indicate that part of this large ΔVP1 value for CaChR1 is caused by the protonation dynamics of the Schiff base counterion complex involving E169 and D299. PA data further show that the energy level of P1 is higher in CrChR2 (ca. 96 kJ/mol) than in CaChr1 (ca. 46 kJ/mol), comparable to the energy level of the K state of HsBR (60 kJ/mol). Instrumental to gain these molecular values from the raw PA data was the estimation of the quantum yield (Φ) for P1 formation via transient spectroscopy; for both channelrhodopsins, ΦP2 was evaluated as ca. 0.4. Graphical Abstract

Cytochrome c oxidase (CcO) in its as-isolated form is known to exist in a slow and fast form, which differ drastically in their ability to bind oxygen and other ligands. While preparation methods h...

Phosphotyrosine residues are essential functional switches in health and disease. Thus, phosphotyrosine biomimetics are crucial for the development of chemical tools and drug molecules. We report here the discovery and investigation of pentafluorophosphato amino acids as novel phosphotyrosine biomimetics. A mild acidic pentafluorination protocol was developed and two PF5-amino acids were prepared and employed in peptide synthesis. Their structures, reactivities, and fluorine-specific interactions were studied by NMR and IR spectroscopy, X-ray diffraction, and in bioactivity assays. The mono-anionic PF5 motif displayed an amphiphilic character binding to hydrophobic surfaces, to water molecules, and to protein-binding sites, exploiting charge and H−F-bonding interactions. The novel motifs bind 25- to 30-fold stronger to the phosphotyrosine binding site of the protein tyrosine phosphatase PTP1B than the best current biomimetics, as rationalized by computational methods, including molecular dynamics simulations.

Infrared (IR) absorption spectroscopy detects the state and chemical composition of biomolecules solely by their inherent vibrational fingerprints. Major disadvantages like the lack of spatial resolution and sensitivity have lately been overcome by the use of pointed probes as local sensors enabling the detection of quantities as few as hundreds of proteins with nanometer precision. However, the strong absorption of infrared radiation by liquid water still prevents simple access to the measured quantity: the light scattered at the probing atomic force microscope tip. Here we report on the local IR response of biological membranes immersed in aqueous bulk solution. We make use of a silicon solid immersion lens as the substrate and focusing optics to achieve detection efficiencies sufficient to yield IR near-field maps of purple membranes. Finally, we suggest a means to improve the imaging quality by tracing the tip by a laser-scanning approach.

Chloride transport by microbial rhodopsins is an essential process for which molecular details such as the mechanisms that convert light energy to drive ion pumping and ensure the unidirectionality of the transport have remained elusive. We combined time-resolved serial crystallography with time-resolved spectroscopy and multiscale simulations to elucidate the molecular mechanism of a chloride-pumping rhodopsin and the structural dynamics throughout the transport cycle. We traced transient anion-binding sites, obtained evidence for how light energy is used in the pumping mechanism, and identified steric and electrostatic molecular gates ensuring unidirectional transport. An interaction with the π-electron system of the retinal supports transient chloride ion binding across a major bottleneck in the transport pathway. These results allow us to propose key mechanistic features enabling finely controlled chloride transport across the cell membrane in this light-powered chloride ion pump. ISSN:0036-8075 ISSN:1095-9203

Mid-IR spectroscopy is a powerful and label-free technique to investigate protein reactions. In this study, we use quantum-cascade-laser-based dual-comb spectroscopy to probe protein conformational changes and protonation events by a single-shot experiment. By using a well-characterized membrane protein, bacteriorhodopsin, we provide a comparison between dual-comb spectroscopy and our homebuilt tunable quantum cascade laser (QCL)-based scanning spectrometer as tools to monitor irreversible reactions with high time resolution. In conclusion, QCL-based infrared spectroscopy is demonstrated to be feasible for tracing functionally relevant protein structural changes and proton translocations by single-shot experiments. Thus, we envisage a bright future for applications of this technology for monitoring the kinetics of irreversible reactions as in (bio-)chemical transformations.

Microbial rhodopsins have recently been discovered in pathogenic fungi and have been postulated to be involved in signaling during the course of an infection. Here, we report on the spectroscopic characterization of a light-driven proton pump rhodopsin (

The pH low insertion peptide (pHLIP) is a pH-sensitive cell penetrating peptide that transforms from an unstructured coil on the membrane surface at pH 7, to a transmembrane (TM) α-helix at pH 5. By exploiting this unique property, pHLIP attracts interest as a potential tool for drug delivery and visualisation of acidic tissues produced by various maladies such as cancer, inflammation, hypoxia etc. Even though the structures of initial and end states of pHLIP insertion have been widely accepted, the intermediate structures in between these two states are less clear. Here, we have applied in situ Surface-Enhanced Infrared Absorption spectroscopy to examine the pH-induced insertion and folding processes of pHLIP into a solid-supported lipid bilayer. We show that formation of partially helical structure already takes place at pH only slightly below 7.0, but with the helical axis parallel to the membrane surface. The peptide starts to reorientate its helix from horizontal to vertical direction, accompanied by the insertion into the TM region at pH 6.2. Further insertion into the TM region of the peptide results in an increase of inherent α-helical structure and complete secondary structure formation at pH 5.3. Analysis of the changes of the carboxylate vibrational bands upon pH titration shows two distinctive groups of aspartates and glutamates with pK

We demonstrate ultra-rapid electro-optic sampling (EOS) of octave-spanning mid-infrared pulses centered at 9 μm, implemented by mechanically scanning a mirror with a sonotrode resonating at 19 kHz (forward and backward acquisition at 38 kHz). The instrument records the infrared waveform with a spectral intensity dynamic range of 1.6 × 105 for a single scan over a 1.6-ps delay range, acquired within 26 μs. The purely reflective nature of the delay scanning technique is compatible with broad optical bandwidths, short pulse durations (16 fs, centered at 1030 nm) and high average powers (Watt-level). Interferometric tracking of the sonotrode motion in combination with a predictor-corrector algorithm allows for delay-axis determination with down to single-digit attosecond precision. Ultra-rapid mid-infrared EOS will advance applications such as molecular fingerprinting of static samples as well as tracking of biological processes and chemical reactions and is likely to find new fields of application such as infrared-spectroscopic flow cytometry.

We investigate light-induced irreversible structuring of surface topographies in poly(3-sulfopropyl methacrylate/potassium salt) (PSPMK) brushes on flat solid substrates prepared by surface-initiated atom transfer radical polymerization. The brushes have been loaded with azobenzene-based surfactant comprised of positively charged headgroups and hydrophobic tail. The surfactant exhibits photoresponsive properties through photoisomerization from the trans to cis states leading to significant changes in physicochemical properties of grafted polymer chains. The azobenzene surfactant enables photoresponsive behavior without introducing irreversible changes to chemical composition of the parent polymer brush. Exposing these photosensitive brushes to irradiation with UV interference beams causes the polymer brush to form surface relief grating (SRG) patterns. The cationic surfactant penetrates only similar to 25% of the upper portion of the PSPMK brush, resulting in the formation of two sections within the brush: a photoresponsive upper layer and nonfunctional buried layer, which is not affected by the UV irradiation. Using nano-FTIR spectroscopy, we characterize locally the chemical composition of the polymer brush and confirm partial penetration of the surfactant within the film. Strong optomechanical stresses take place only within the upper layer of the brush that is impregnated with the surfactants and causes surface topography alternation due to a local rupture of grafted polymer chains. The cleaved polymer chains are then removed from the surface by using a good solvent, leaving behind topographical grating on top of the nonfunctional brush layer. We demonstrate that photostructured polymer brush can be used for reversible switching of brush topography by varying external humidity.

Surface-enhanced vibrational spectroscopy strongly increases the cross section of Raman scattering and infrared absorption, overcoming the limited sensitivity and resolution of these two powerful analytic tools. While surface-enhanced setups with maximum enhancement have been studied widely in recent years, substrates with reproducible, uniform enhancement have received less attention although they are required in many applications. Here, we show that plasmonic supercrystals are an excellent platform for enhanced spectroscopy because they possess a high density of hotspots in the electric field. We describe the near field inside the supercrystal within the framework of plasmon polaritons that form due to strong light-matter interaction. From the polariton resonances we predict resonances in the far-field enhancement for Raman scattering and infrared absorption. We verify our predictions by measuring the vibrations of polystyrene molecules embedded in supercrystals of gold nanoparticles. The intensity of surface-enhanced Raman scattering is uniform within 10% across the crystal with a peak integrated enhancement of up to 300 and a peak hotspot enhancement of 105. The supercrystal polaritons induce pairs of incoming and outgoing resonances in the enhanced cross section as we demonstrate experimentally by measuring surface-enhanced Raman scattering with multiple laser wavelengths across the polariton resonance. The infrared absorption of polystyrene is likewise enhanced inside the supercrystals with a maximum enhancement of 400%. We show with a coupled oscillator model that the increase originates from the combined effects of hotspot formation and the excitation of standing polariton waves. Our work clearly relates the structural and optical properties of plasmonic supercrystals and shows that such crystals are excellent hosts and substrates for the uniform and predictable enhancement of vibrational spectra.

To shed light on recently explored long-range surface forces generated by subsurface-confined water, the structural characteristics of water molecules penetrating into nanoporous homogeneous and nanograded siloxane plasma polymer films (PPFs) over the time scale of 24 hours are studied by surface-enhanced IR spectroscopy (SEIRAS). Chemically graded PPFs, with embedded hydrophobic-to-hydrophilic gradient, are found to significantly change the average interfacial water orientation due to a unique nanoporous morphology and silanol group coordination. Diffusion of water through the hydrophobic SiO:CH matrix creates an evolution of the coordination of matrix silanol groups, which are eventually deprotonated as soon as the hydration network connects to the aqueous environment. This occurs after ~6 hours of water immersion and coincides with the change of average interfacial water orientation. Both effects are present on hydrophobic samples, but are significantly amplified by the presence of the subsurface vertical amphiphilic gradient (Vgrad), whereas enhanced water uptake in oxygen-plasma modified graded PPFs is covering such effects.

The interplay of fluorination and structure of alkane self-assembled monolayers and how these affect hydrophobicity are explored via molecular dynamics simulations, contact angle goniometry, and surface-enhanced infrared absorption spectroscopy. Wetting coefficients are found to grow linearly in the monolayer density for both alkane and perfluoroalkane monolayers. The larger contact angles of monolayers of perfluorinated alkanes are shown to be primarily caused by their larger molecular volume, which leads to a larger nearest-neighbor grafting distance and smaller tilt angle. Increasing the Lennard-Jones force cutoff in simulations is found to increase hydrophilicity. Specifically, wetting coefficients scale like the inverse square of the cutoff, and when extrapolated to the infinite cutoff limit, they yield contact angles that compare favorably to experimental values. Nanoscale roughness is also found to reliably increase monolayer hydrophobicity, mostly via the reduction of the entropic part of the work of adhesion. Analysis of depletion lengths shows that droplets on nanorough surfaces partially penetrate the surface, intermediate between Wenzel and Cassie-Baxter states.

We present a nanospectroscopic device platform allowing simple and spatially resolved thermoelectric detection of molecular fingerprints of soft materials. Our technique makes use of a locally generated thermal gradient converted into a thermoelectric photocurrent that is read out in the underlying device. The thermal gradient is generated by an illuminated atomic force microscope tip that localizes power absorption onto the sample surface. The detection principle is illustrated using a concept device that contains a nanostructured strip of polymethyl methacrylate (PMMA) defined by electron beam lithography. The platform’s capabilities are demonstrated through a comparison between the spectrum obtained by on-chip thermoelectric nanospectroscopy with a nano-FTIR spectrum recorded by scattering-type scanning near-field optical microscopy at the same position. The subwavelength spatial resolution is demonstrated by a spectral line scan across the edge of the PMMA layer., info:eu-repo/semantics/published

Although the outward-directed proton transport across biological membranes is well studied and its importance for bioenergetics is clearly understood, inward-directed light-driven proton pumping by microbial rhodopsins has remained a mystery both physiologically and mechanistically. A new family of Antarctic rhodopsins, which is a subgroup within a novel class of schizorhodopsins reported recently, includes a member, denoted as AntR, which proved amenable to extensive characterization with experiments and computation. Phylogenetic analyses identify AntR as distinct from the well-studied microbial rhodopsins that function as outward-directed ion pumps, and bioinformatics sequence analyses reveal amino acid substitutions at conserved sites essential for outward proton pumping. Modeling and numerical simulations of AntR, combined with advanced analyses using the graph theory and centrality measures from social sciences, identify the dynamic three-dimensional network of hydrogen-bonded water molecules and amino acid residues that function as communication hubs in AntR. This network undergoes major rearrangement upon retinal isomerization, showing important changes in the connectivity of the active center, retinal Schiff base, to the opposing sides of the membrane, as required for proton transport. Numerical simulations and experimental studies of the photochemical cycle of AntR by spectroscopy and site-directed mutagenesis allowed us to identify pathways that could conduct protons in the direction opposite to that commonly known for outward-directed pumps.

Infrared (IR) absorption spectroscopy detects state and chemical composition of biomolecules solely by their inherent vibrational fingerprints. Major disadvantages like the lack of spatial resolution and sensitivity were compensated lately by the use of pointed probes as local sensors enabling the detection of quantities as few as hundreds of proteins with nanometer precision. This makes infrared scattering-type scanning near-field optical microscopy a very powerful tool in life science. The strong absorption of infrared radiation of liquid water, however, still prevents to simply access the measured quantity – light scattered at the probing atomic force microscope tip. Here we report on the local IR response of biological membranes immersed in aqueous bulk solution. We make use of a silicon solid immersion lens as substrate and focusing optics to achieve detection efficiencies sufficient to yield IR near-field maps of purple membranes. We scrutinized our experimental findings by applying theoretical models. Finally, we suggest a means to improve the imaging quality by laser scanning assisted scattering-type scanning near-field optical microscopy. We believe that IR scattering-type scanning near-field optical microscopy will resolve biological structures in their native environments at nm resolution without the need for labeling.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Antiferromagnets offer spintronic device characteristics unparalleled in ferromagnets owing to their lack of stray fields, THz spin dynamics, and rich materials landscape. Microscopic imaging of antiferromagnetic domains is one of the key prerequisites for understanding physical principles of the device operation. However, adapting common magnetometry techniques to the dipolar-field-free antiferromagnets has been a major challenge. Here we demonstrate in a collinear antiferromagnet a thermoelectric detection method by combining the magneto-Seebeck effect with local heat gradients generated by scanning far-field or near-field techniques. In a 20-nm epilayer of uniaxial CuMnAs we observe reversible 180∘ switching of the Neel vector via domain wall displacement, controlled by the polarity of the current pulses. We also image polarity-dependent 90∘ switching of the Neel vector in a thicker biaxial film, and domain shattering induced at higher pulse amplitudes. The antiferromagnetic domain maps obtained by our laboratory technique are compared to measurements by the established synchrotron-based technique of x-ray photoemission electron microscopy using x-ray magnetic linear dichroism.

Hydrogenases are among the fastest H2 evolving catalysts known to date and have been extensively studied under in vitro conditions. Here, we report the first mechanistic investigation of an [FeFe]-hydrogenase under in vivo conditions. Functional [FeFe]-hydrogenase from the green alga Chlamydomonas reinhardtii is generated in genetically modified Escherichia coli cells, by addition of a synthetic cofactor to the growth medium. The assembly and reactivity of the resulting semi-synthetic enzyme was monitored using whole-cell electron paramagnetic resonance as well as Fourier-transform infrared spectroscopy. Through a combination of gas treatments, pH titrations and isotope editing, we were able to corroborate the physiological relevance of a number of proposed catalytic intermediates, including reactive iron-hydride species. We demonstrate the formation of the so-called hydride state in vivo. Moreover, two previously uncharacterized redox species are reported herein, illustrating the complex metal hydride chemistry of [FeFe]-hydrogenase.

Hydrogenases are among the fastest H2 evolving catalysts known to date and have been extensively studied under in vitro conditions. Here, we report the first mechanistic investigation of an [FeFe]-hydrogenase under whole-cell conditions. Functional [FeFe]-hydrogenase from the green alga Chlamydomonas reinhardtii is generated in genetically modified Escherichia coli cells by addition of a synthetic cofactor to the growth medium. The assembly and reactivity of the resulting semi-synthetic enzyme was monitored using whole-cell electron paramagnetic resonance and Fourier-transform Infrared difference spectroscopy as well as scattering scanning near-field optical microscopy. Through a combination of gas treatments, pH titrations, and isotope editing we were able to corroborate the formation of a number of proposed catalytic intermediates in living cells, supporting their physiological relevance. Moreover, a previously incompletely characterized catalytic intermediate is reported herein, attributed to the formation of a protonated metal hydride species., The mechanism of hydrogen gas formation by [FeFe] hydrogenase is probed under whole cell conditions, revealing the formation of reactive metal hydride species under physiologically relevant conditions.

Channelrhodopsins (ChRs) are light-gated cation channels. In spite of their wide use to activate neurons with light, the photocurrents of ChRs rapidly decay in intensity under both continuous illum...

Infrared continuum bands that extend over a broad frequency range are a key spectral signature of protonated water clusters. They are observed for many membrane proteins that contain internal water molecules, but their microscopic mechanism has remained unclear. Here we compute infrared spectra for protonated and unprotonated water chains, discs, and droplets from ab initio molecular dynamics simulations. The continuum bands of the protonated clusters exhibit significant anisotropy for chains and discs, with increased absorption along the direction of maximal cluster extension. We show that the continuum band arises from the nuclei motion near the excess charge, with a long-ranged amplification due to the electronic polarizability. Our experimental, polarization-resolved light–dark difference spectrum of the light-driven proton pump bacteriorhodopsin exhibits a pronounced dichroic continuum band. Our results suggest that the protonated water cluster responsible for the continuum band of bacteriorhodopsin is oriented perpendicularly to the membrane normal., Protein-bound water clusters play a key role for proton transport and storage in molecular biology. Here, the authors show by simulations and experiments that the orientation of non-spherical protonated water clusters in bacteriorhodopsin is unveiled by polarization-resolved infrared spectroscopy.