Application of optical rotatory dispersion and circular dichrosim to the study of biopolymers

MEMS-actuated terahertz metamaterials driven by phase-transition materials

The non-ionizing and penetrative characteristics of terahertz (THz) radiation have recently led to its adoption across a variety of applications. To effectively utilize THz radiation, modulators with precise control are imperative. While most recent THz modulators manipulate the amplitude, frequency, or phase of incident THz radiation, considerably less progress has been made toward THz polarization modulation. Conventional methods for polarization control suffer from high driving voltages, restricted modulation depth, and narrow band capabilities, which hinder device performance and broader applications. Consequently, an ideal THz modulator that offers high modulation depth along with ease of processing and operation is required. In this paper, we propose and realize a THz metamaterial comprised of microelectromechanical systems (MEMS) actuated by the phase-transition material vanadium dioxide (VO2). Simulation and experimental results of the three-dimensional metamaterials show that by leveraging the unique phase-transition attributes of VO2, our THz polarization modulator offers notable advancements over existing designs, including broad operation spectrum, high modulation depth, ease of fabrication, ease of operation condition, and continuous modulation capabilities. These enhanced features make the system a viable candidate for a range of THz applications, including telecommunications, imaging, and radar systems.

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.

Protein nitration induced by Hemin/NO: A complementary mechanism through the catalytic functions of hemin and NO-scavenging

Hemin and heme-peroxidases have been considered essential catalysts for the nitrite/hydrogen peroxide (H₂O₂)-mediated protein nitration in vitro, understood as one of the main pathways for protein modification in biological systems. However, the role of nitric oxide (^●NO) in the heme/hemin-induced protein nitration has not been studied in-depth. This is despite its reductive nitrosylating effects following binding to hemin and the possible involvement of the reactive nitrogen species in the nitration of various functional proteins. Here, the ^●NO-binding affinity of hemin has been studied along with the influence of ^●NO on the internalization of hemin into MDA-MB-231 cells and the accompanying changes in the profile of intracellular nitrated proteins. Moreover, to further understand the mechanism involved, bovine serum albumin (BSA) nitration was studied after treatment with hemin and ^●NO, with an investigation of the effects of pH of the reaction medium, generation of H₂O₂, and the oxidation of the tyrosine residues as the primary sites for the nitration. We demonstrated that hemin nitrosylation enhanced its cellular uptake and induced the one-electron oxidation and nitration of different intracellular proteins along with its ^●NO-scavenging efficiency. Moreover, the hemin/NO-mediated BSA nitration was proved to be dependent on the concentration of ^●NO and the pH of the reaction medium, with a vital role being played by the scavenging effects of protein for the free hemin molecules. Collectively, our results reaffirm the involvement of hemin and ^●NO in the nitration mechanism, where the nitrosylation products can induce protein nitration while promoting the effects of the components of the nitrite/H₂O₂-mediated pathway.

Electrical access to critical coupling of circularly polarized waves in graphene chiral metamaterials

Active control of polarization states of electromagnetic waves is highly desirable because of its diverse applications in information processing, telecommunications, and spectroscopy. However, despite the recent advances using artificial materials, most active polarization control schemes require optical stimuli necessitating complex optical setups. We experimentally demonstrate an alternative-direct electrical tuning of the polarization state of terahertz waves. Combining a chiral metamaterial with a gated single-layer sheet of graphene, we show that transmission of a terahertz wave with one circular polarization can be electrically controlled without affecting that of the other circular polarization, leading to large-intensity modulation depths (>99%) with a low gate voltage. This effective control of polarization is made possible by the full accessibility of three coupling regimes, that is, underdamped, critically damped, and overdamped regimes by electrical control of the graphene properties.

Structural studies of E. coli ribosomes by spectroscopic techniques: a specialized review

We present a review on our interdisciplinary line of research based on strategies of molecular biology and biophysics. These have been applied to the study of the prokaryotic ribosome of the bacterium Escherichia coli. Our investigations on this organelle have continued for more than a decade and we have adopted different spectroscopic biophysical techniques such as: dielectric and fluorescence spectroscopy as well as light scattering (photon correlation spectroscopy). Here we report studies on the whole 70S ribosomes and on the separated subunits 30S and 50S. Our results evidence intrinsic structural features of the subunits: the small shows a more "floppy" structure, while the large one appears to be more rigid. Also, an inner "kernel" formed by the RNA/protein association is found within the ribosome. This kernel is surrounded by a ribonucleoprotein complex more exposed to the solvent. Initial analyses were done on the so called Kaldtschmit-Wittmann ribosome: more recently we have extended the studies to the "tight couple" ribosome known for its better functional performance in vitro. Data evidence a phenomenological correlation between the differential biological activity and the intrinsic structural properties of the two-ribosome species. Finally, investigations were also conducted on particles treated at sub-denaturing temperatures and on ribosomes partially deproteinized by salt treatment (ribosomal cores). Results suggest that the thermal treatment and the selective removal of proteins cause analogous structural alterations.

Characterization of DNA structures by circular dichroism

Circular dichroism (CD) of nucleic acids is commonly used to provide a signature for a given secondary structure. CD is particularly powerful for monitoring structural changes resulting from changes in environmental conditions such as temperature, ionic strength, and pH. A number of commercially available instruments are available for the measurement of CD spectra. Since the details of instrumental operation differ for each machine, this unit provides a descriptive guide, rather than a strict protocol. It describes considerations that the experimentalist will face when attempting to examine nucleic acid structures by CD spectropolarimetry. Specific details are also given for cell filling and cleaning, and for instrumental calibration. Finally, several examples of CD spectra are given to provide useful reference points for a variety of nucleic acid structures, ranging from single-stranded to triplex and quadruplex forms.

The biochemistry and medical significance of the flavonoids

Flavonoids are plant pigments that are synthesised from phenylalanine, generally display marvelous colors known from flower petals, mostly emit brilliant fluorescence when they are excited by UV light, and are ubiquitous to green plant cells. The flavonoids are used by botanists for taxonomical classification. They regulate plant growth by inhibition of the exocytosis of the auxin indolyl acetic acid, as well as by induction of gene expression, and they influence other biological cells in numerous ways. Flavonoids inhibit or kill many bacterial strains, inhibit important viral enzymes, such as reverse transcriptase and protease, and destroy some pathogenic protozoans. Yet, their toxicity to animal cells is low. Flavonoids are major functional components of many herbal and insect preparations for medical use, e.g., propolis (bee's glue) and honey, which have been used since ancient times. The daily intake of flavonoids with normal food, especially fruit and vegetables, is 1-2 g. Modern authorised physicians are increasing their use of pure flavonoids to treat many important common diseases, due to their proven ability to inhibit specific enzymes, to simulate some hormones and neurotransmitters, and to scavenge free radicals.

Probing the details of the HIV-1 Rev-Rev-responsive element interaction: effects of modified nucleotides on protein affinity and conformational changes during complex formation

The solution structure of the human immunodeficiency virus type 1 (HIV-1) Rev-responsive element (RRE) has been investigated by enzymic and chemical structural probing of a 71 nt RRE transcript. The minimum sequence information required to maintain recognition by the Rev protein has previously been mapped to a 29 nt stem-loop structure, known as minSLIIB. The key recognition target is a single-stranded RNA bubble at the base of the RNA stem. The fine details of RNA recognition have been probed using chemically synthesized minSLIIBs containing variant base or sugar residues at sites within the bubble. These have been analysed by gel retardation assays and their relative affinities for Rev protein determined. Complex formation between the wild-type minSLIIB RRE and Rev protein was also monitored using CD spectroscopy, which suggests a change in RNA conformation upon Rev binding. The spectral change is consistent with localized melting of RNA, leading to a decrease in the level of base stacking and/or a change in base tilting, during formation of the complex. Deoxynucleotide substitutions on just one side, the 5' side, of the bubble inhibit the conformational change detected by CD. The data are consistent with a dynamic interaction between Rev and its target site. The contact points between Rev and the RRE were probed directly using photo-cross-linking with either ribo-5-bromouridine- or ribo-4-thiouridine-substituted minSLIIBs. The data are consistent with protein-RNA contacts at the bottom of the bubble.

The induced circular dichroism of bilirubin complexed with the alpha-helix form of poly(L-lysine)

Binding of bilirubin by the alpha-helix conformation of poly(L-lysine) in water induces optical activity. The bisignate circular dichroism spectrum exhibits exciton bands centred at 444 nm, negative, and at 525 nm, positive. The magnitude of the induced circular dichroism depends on the concentration of total bilirubin and total lysine residues, the molar ratio of total lysine residues-to-total bilirubin molecules, the pH and the degree of polymerization of poly(L-lysine). Although bilirubin binds to the random coil conformation of poly(L-lysine), as evidence by the absorption spectrum, the complex is optically inactive. The results suggest that bilirubin binds to the poly(L-lysine) in the form of dimers and oligomers.

Underlying assumptions in the estimation of secondary structure content in proteins by circular dichroism spectroscopy--a critical review

Recombinant DNA technology has made possible the large-scale production of proteins for pharmaceutical applications. As a result, there has been a renaissance in methodology which can provide information on the structural stability and character of these materials. Circular dichroism (CD) spectroscopy, with its sensitivity to the secondary structure adopted by the polypeptide chain, is a powerful tool in this regard. Quantitative analysis of the CD spectra of proteins is now wide-spread, aided by the availability of such algorithms on commercial instrumentation. However, there are basic assumptions made when conducting these calculations, many of which have not been addressed or summarized. Some of these assumptions are independent of the selection of basis spectra and the algorithm employed. These assumptions are listed and the available data concerning their validity is presented and discussed.

Analysis of the near-ultraviolet circular dichroic spectra of staphylococcal enterotoxins A, B and C

The near-ultraviolet CD spectra from 260 to 300 nm of staphylococcal enterotoxins A, B and C were resolved empirically into Gaussian curves. Each spectrum contained the same six components with maximum ellipticities at virtually identical wavelengths. The rotatory strength of the bands of enterotoxin A, however, differed significantly from that of enterotoxins B and C. Each Gaussian curve was identified as corresponding to a prominent CD transition of an aromatic chromophore: two phenylalanine bands from its 1Lb transition (0-0 and 0 + 930 cm-1); four tyrosine bands from its 1Lb transition (the 800 cm-1 primary vibronic progression) with the weakest of these overlapping a phenylalanine band; and one 1Lb tryptophan band. At alkaline pH, tyrosylate CD bands arose, centered at 247-249 nm and at 295-298 nm. The intensity of the 295-298 nm bands indicated that most of the tyrosine CD in the neutral enterotoxins was contributed by buried residues. The tryptophan contribution to the CD of enterotoxin A was positive, while that of B and C was negative. Also indicative of a different milieu was the ready oxidation of the A toxin by N-bromosuccinimide and the unavailability of the single tryptophan residue in the other two toxins to this reagent. The environment of the disulfide bond was markedly diverse in the three enterotoxins. Enterotoxin C was refractory to reduction by mercaptoethanol under conditions where enterotoxins B and A were readily reduced. The contribution of the disulfide of enterotoxin B to its CD spectrum was positive with an intensity of about 9000 deg . cm2 . dmol-1 and was centered near 273 nm. The difference spectrum between native and reduced enterotoxin A was much smaller and appeared to be conformational in origin.

Spectral analysis of allophycocyanin I, II, III and B from Nostoc sp. phycobilisomes

Low temperature (-196C) and room temperature (25C) absorption spectra of a family of allophycocyanin spectral forms isolated from Nostoc sp. phycobilisomes as well as of the phycobilisomes themselves have been analyzed by Gaussian curve-fitting. Allophycocyanin I and B share long wavelength components at 668 and 679 nm, bands that are absent from allophycocyanin II and III. These long wavelength absorption components are apparently responsible for the 20 nm difference between the 680 nm fluorescence emission maximum of allophycocyanin I and B and the 660 nm maximum of II and III. This indicates that allophycocyanin I and B are the final acceptors of excitation energy in the phycobilisome and the excitation energy transfer bridge linking the phycobilisome with the chlorophyll-containing thylakoid membranes. These Gaussian components are also found in resolved spectra of phycobilisomes, are arguing against this family of allophycocyanin molecules being artifactual products of protein purification procedures.