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Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure–rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides. Significance Circular dichroism (CD) spectroscopy is widely used for protein secondary structure analysis. However, quantitative estimation for β-sheet–containing proteins is problematic due to the huge morphological and spectral diversity of β-structures. We show that parallel/antiparallel orientation and twisting of β-sheets account for the observed spectral diversity. Taking into account the twist of β-structures, our method accurately estimates the secondary structure for a broad range of protein folds, particularly for β-sheet–rich proteins and amyloid fibrils. Moreover, the method can predict the protein fold down to the topology level following the CATH classification. We provide a general tool for a quick and reliable structure analysis using conventional or synchrotron radiation CD spectroscopy, which is especially useful when X-ray or NMR techniques fail.

A two-dimensional honeycomb lattice harbours a pair of inequivalent valleys in the k -space electronic structure, in the vicinities of the vertices of a hexagonal Brillouin zone, K ± . It is particularly appealing to exploit this emergent degree of freedom of charge carriers, in what is termed 'valleytronics'. The physics of valleys mimics that of spin, and will make possible devices, analogous to spintronics, such as valley filter and valve, and optoelectronic Hall devices, all very promising for next-generation electronics. The key challenge lies with achieving valley polarization, of which a convincing demonstration in a two-dimensional honeycomb structure remains evasive. Here we show, using first principles calculations, that monolayer molybdenum disulphide is an ideal material for valleytronics, for which valley polarization is achievable via valley-selective circular dichroism arising from its unique symmetry. We also provide experimental evidence by measuring the circularly polarized photoluminescence on monolayer molybdenum disulphide, which shows up to 50% polarization. The monolayer transition-metal dichalcogenide molybdenum disulphide has recently attracted attention owing to its distinctive electronic properties. Cao and co-workers present numerical evidence suggesting that circularly polarized light can preferentially excite a single valley in the band structure of this system.

Graphene layers can be placed on top of each other with accurate twisting angles and show a remarkably high circular dichroism. Chiral materials possess left- and right-handed counterparts linked by mirror symmetry. These materials are useful for advanced applications in polarization optics 1 , 2 , stereochemistry 3 , 4 and spintronics 5 , 6 . In particular, the realization of spatially uniform chiral films with atomic-scale control of their handedness could provide a powerful means for developing nanodevices with novel chiral properties. However, previous approaches based on natural or grown films 1 , 2 , 7 , 8 , or arrays of fabricated building blocks 9 , 10 , 11 , could not offer a direct means to program intrinsic chiral properties of the film on the atomic scale. Here, we report a chiral stacking approach, where two-dimensional materials are positioned layer-by-layer with precise control of the interlayer rotation ( θ ) and polarity, resulting in tunable chiral properties of the final stack. Using this method, we produce left- and right-handed bilayer graphene, that is, a two-atom-thick chiral film. The film displays one of the highest intrinsic ellipticity values (6.5 deg μm –1 ) ever reported, and a remarkably strong circular dichroism (CD) with the peak energy and sign tuned by θ and polarity. We show that these chiral properties originate from the large in-plane magnetic moment associated with the interlayer optical transition. Furthermore, we show that we can program the chiral properties of atomically thin films layer-by-layer by producing three-layer graphene films with structurally controlled CD spectra.

Oxidative stress can lead to various derivatives of the tyrosine residue in peptides and proteins. A typical product is 3-nitro-L-tyrosine residue (Nit), which can affect protein behavior during neurodegenerative processes, such as those associated with Alzheimer's and Parkinson's diseases. Surface enhanced Raman spectroscopy (SERS) is a technique with potential for detecting peptides and their metabolic products at very low concentrations. To explore the applicability to Nit, we use SERS to monitor tyrosine nitration in Met-Enkephalin, rev-Prion protein, and α-synuclein models. Useful nitration indicators were the intensity ratio of two tyrosine marker bands at 825 and 870 cm−1 and a bending vibration of the nitro group. During the SERS measurement, a conversion of nitrotyrosine to azobenzene containing peptides was observed. The interpretation of the spectra has been based on density functional theory (DFT) simulations. The CAM-B3LYP and ωB97XD functionals were found to be most suitable for modeling the measured data. The secondary structure of the α-synuclein models was monitored by electronic and vibrational circular dichroism (ECD and VCD) spectroscopies and modeled by molecular dynamics (MD) simulations. The results suggest that the nitration in these peptides has a limited effect on the secondary structure, but may trigger their aggregation.

Background: The present study aimed to fabricate surface-modified chitosan nanoparticles with two mucoadhesive polymers (sodium alginate and polyethylene glycol) to optimize their protein encapsulation efficiency, improve their mucoadhesion properties, and increase their stability in biological fluids. Method: Ionotropic gelation was employed to formulate chitosan nanoparticles and surface modification was performed at five different concentrations (0.05, 0.1, 0.2, 0.3, 0.4% w/v) of sodium alginate (ALG) and polyethylene glycol (PEG), with ovalbumin (OVA) used as a model protein antigen. The functional characteristics were examined by dynamic light scattering (DLS), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and scanning electron microscopy (SEM)/scanning transmission electron microscopy (STEM). Stability was examined in the presence of simulated gastric and intestinal fluids, while mucoadhesive properties were evaluated by in vitro mucin binding and ex vivo adhesion on pig oral mucosa tissue. The impact of the formulation and dissolution process on the OVA structure was investigated by sodium dodecyl-polyacrylamide gel electrophoresis (SDS-PAGE) and circular dichroism (CD). Results: The nanoparticles showed a uniform spherical morphology with a maximum protein encapsulation efficiency of 81%, size after OVA loading of between 200 and 400 nm and zeta potential from 10 to 29 mV. An in vitro drug release study suggested successful nanoparticle surface modification by ALG and PEG, showing gastric fluid stability (4 h) and a 96 h sustained OVA release in intestinal fluid, with the nanoparticles maintaining their conformational stability (SDS-PAGE and CD analyses) after release in the intestinal fluid. An in vitro mucin binding study indicated a significant increase in mucin binding from 41 to 63% in ALG-modified nanoparticles and a 27–49% increase in PEG-modified nanoparticles. The ex vivo mucoadhesion showed that the powdered particles adhered to the pig oral mucosa. Conclusion: The ALG and PEG surface modification of chitosan nanoparticles improved the particle stability in both simulated gastric and intestinal fluids and improved the mucoadhesive properties, therefore constituting a potential nanocarrier platform for mucosal protein vaccine delivery.

Proline is a unique amino acid in that its side-chain is cyclised to the backbone, thus giving proline an exceptional rigidity and a considerably restricted conformational space. Polyproline forms two well-characterized helical structures: a left-handed polyproline helix (PPII) and a right-handed polyproline helix (PPI). Usually, sequences made only of prolyl residues are in PPII conformation, but even sequences not rich in proline but which are rich in glycine, lysine, glutamate, or aspartate have also a tendency to form PPII helices. Currently, the only way to study unambiguously PPII structure in solution is to use spectroscopies based on optical activity such as circular dichroism, vibrational circular dichroism and Raman optical activity. The importance of the PPII structure is emphasized by its ubiquitous presence in different organisms from yeast to human beings where proline-rich motifs and their binding domains are believed to be involved in vital biological processes. Some of the domains that are bound by proline-rich motifs include SH3 domains, WW domains, GYF domains and UEV domains, etc. The PPII structure has been demonstrated to be essential to biological activities such as signal transduction, transcription, cell motility, and immune response.

Circular dichroism (CD) has long been used to trace chiral molecular states and changes of protein configurations. In recent years, chiral plasmonic nanostructures have shown potential for applications ranging from pathogen sensing to novel optical materials. The plasmonic coupling of the individual elements of such metallic structures is a crucial prerequisite to obtain sizeable CD signals. We here identify and implement various coupling entities—chiral and achiral—to demonstrate chiral transfer over distances close to 100 nm. The coupling is realized by an achiral nanosphere situated between a pair of gold nanorods that are arranged far apart but in a chiral fashion using DNA origami. The transmitter particle causes a strong enhancement of the CD response, the emergence of an additional chiral feature at the resonance frequency of the nanosphere, and a redshift of the longitudinal plasmonic resonance frequency of the nanorods. Matching numerical simulations elucidate the intricate chiral optical fields in complex architectures. Here, the authors experimentally demonstrate chiral transfer over large distances up to 100 nm. They realise the coupling with an achiral nanosphere situated between a pair of distant gold nanorods arranged in a chiral fashion using DNA origami, and observe enhanced circular dichroism signals.

The structural characterization of non-covalent complexes between nucleic acids and small molecules (ligands) is of a paramount significance to bioorganic research. Highly informative methods about nucleic acid/ligand complexes such as single crystal X-ray diffraction or NMR spectroscopy cannot be performed under biologically compatible conditions and are extensively time consuming. Therefore, in search for faster methods which can be applied to conditions that are at least similar to the naturally occurring ones, a set of polarization spectroscopy methods has shown highly promising results. Electronic circular dichroism (ECD) is the most commonly used method for the characterization of the helical structure of DNA and RNA and their complexes with ligands. Less common but complementary to ECD, is flow-oriented linear dichroism (LD). Other methods such as vibrational CD (VCD) and emission-based methods (FDCD, CPL), can also be used for suitable samples. Despite the popularity of polarization spectroscopy in biophysics, aside several highly focused reviews on the application of these methods to DNA/RNA research, there is no systematic tutorial covering all mentioned methods as a tool for the characterization of adducts between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably.

In our study, the effects of high-power (400 W) and low-frequency (20 kHz) ultrasound pretreatment applied for different durations (5, 10, and 20 min) and proteases (alcalase and flavourzyme) on the physicochemical, structural, and antioxidant properties of lupin protein hydrolysates (LPH) were examined. Changes in structural characteristics of the isolates and the resulting hydrolysates were measured using circular dichroism (CD), Fourier-transform infrared (FTIR), and UV–Vis spectroscopic techniques. Antioxidant activities of the LPH were assessed using 2,2-diphenyl-1picrylhydrazyl (DPPH) and 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) assays. Physicochemical properties including the yield of hydrolysate, relative crystallinity, and surface charge were also evaluated. FTIR analysis revealed that ultrasound pretreatment altered the secondary structure of the proteins as indicated by the movement of absorption peaks to higher wavelength. Also, CD studies showed a reduction in α-helix and increase in the β-sheet component of LPH samples after ultrasound pre-treatment except hydrolysates prepared using flavourzyme. The particle size, zeta potential, and relative crystallinity of the hydrolysates were significantly affected by ultrasonication time and enzyme type. Also, ultrasonication had a noticeable impact on the antioxidant activity as maximum DPPH activity was recorded after 10 min sonication in hydrolysates prepared using alcalase and flavourzyme. In addition, yield of hydrolysate increased significantly ( p  < 0.05) after ultrasonication pretreatment. Principal component analysis also produced a two-principal component model that explained 65.33% of total data variation. It may be suggested that application of ultrasound treatment to lupin protein could enhance the various characteristics including physicochemical and antioxidant activities of its hydrolysate.

Life on Earth employs chiral amino acids in stereochemical l -form, but the cause of molecular symmetry breaking remains unknown. Chiroptical properties of amino acids – expressed in circular dichroism (CD) – have been previously investigated in solid and solution phase. However, both environments distort the intrinsic charge distribution associated with CD transitions. Here we report on CD and anisotropy spectra of amino acids recorded in the gas phase, where any asymmetry is solely determined by the genuine electromagnetic transition moments. Using a pressure- and temperature-controlled gas cell coupled to a synchrotron radiation CD spectropolarimeter, we found CD active transitions and anisotropies in the 130–280 nm range, which are rationalized by ab initio calculation. As gas phase glycine was found in a cometary coma, our data may provide insights into gas phase asymmetric photochemical reactions in the life cycle of interstellar gas and dust, at the origin of the enantiomeric selection of life’s l -amino acids. Chiroptical properties of amino acids are challenging to investigate in the gas phase due to the low vapor pressure of these molecules. Here the authors succeed in measuring circular dichroism active transitions and anisotropies in the ultraviolet range for several gas-phase amino acids, shedding light on the interactions between molecules and circularly polarized light that lead to chiral symmetry breaking.