Helix sense of copoly(ethyl-l-aspartate-benzyl-l-aspartate)

Copoly(ethyl-L-aspartate-benzyl-L-aspartate)s with various compositions were prepared by ethylation of poly (β-benzyl-L-aspartate). Helix sense of copolyaspartates in chloroform solution was examined by optical rotatory dispersion and circular dichroism methods as a function of a degree of ethylation and temperature. Copolyaspartates of ethylation less than 35% exhibited the same left handed helix as that of poly (β-benzyl-L-aspartate), while copolymer of ethylation more than 70% assumed the right handed α-helical conformation like poly (β-ethyl-L-aspartate). Copolymers with the intermediate ethyl content of 35–70% indicated the reversal in helix sense from a right handed to a left handed helix with increasing temperature from ?20° to 60°C. The transition of reversal was reversibly observed and transition temperature rose with the increase of ethylation. In these intermediate copolymers, the mechanism of the reversal in helix sense was examined by circular dichroism and dielectric measurements. Three possibilities were postulated here for the conformation which should arise at the transition temperature of the reversal; First is the random conformation, second is the equimolar mixture of left and right handed α-helices in a chain, and the third is the equimolar mixture of left and right handed α helix chains. No observational circular dichroism spectra characteristic to random coil conformation and no remarkable change in residue dipole moment strongly suggested the third possibility.     

Optical rotatory dispersion and circular dichroism studies of copolyaspartates with long alkyl side chain

Copoly(hexyl-l-aspartate-benzyl-l-aspartate), copoly(nonyl-l-aspartate-benzyl-l-aspartate) and copoly(dodecyl-l-aspartate-benzyl-l-aspartate) with various compositions were prepared by ester exchange reaction of poly(β-benzyl-l-aspartate). Copolyaspartates of low degree of alkylation were found to take a left handed α helix, similar to poly(β-benzyl-l-aspartate), and those of high degree of alkylation changed to a right handed α helix. Copoly(hexyl-l-aspartate-benzyl-l-aspartate) and copoly(dodecyl-l-aspartate-benzyl-l-aspartate) changed helix sense from left to right at 50% hexylation and 10% dodecylation, respectively. A small induced circular dichroism trough appeared around 230nm for these two copolyaspartates above 75% alkylation, indicative of a certain ordering of the carbonyl group due to the formation of an ordered structure of a long alkyl side chain. However, copoly(nonyl-l-aspartate-benzyl-l-aspartate) of 13% nonylation exhibited the induced circular dichroism spectrum and took a left handed α helix. Copoly(nonyl-l-aspartate-benzyl-l-aspartate) caused the reversal in helix sense above 70% nonylation according to a stabilizing effect of the ordered structure of the side chain.     

Preparation and properties of pure crystalline perovskite CeFeO3 thin films with vanadium doping

Cerium ferrite (CeFeO₃) thin films doped with vanadium (V:CeFeO₃) were grown on SiO₂ quartz glass and <100>‐oriented SrTiO₃ (STO) crystal substrates by the radio‐frequency magnetron sputtering method in this study. The effects of crystallization, substrate, and V‐doping on the quality, the magnetic property and the magneto‐optical property of as‐prepared films are investigated. V:CeFeO₃ film grown on STO substrate has better crystallinity and has better lattice integrity due to the higher lattice matching between substrate and film. The magnetic hysteresis loop and the magnetic circular dichroism spectra show that the magnetization strength and the magneto‐optical properties of V:CeFeO₃ films have the significant anisotropy. Moreover, V‐doping and the stress lead to the change in easy magnetization direction of film. It shows that the perovskite B‐site doping with transition‐metal ion has significant influence on the magnetic and the magneto‐optical properties of CeFeO₃ thin films.     

Nanosecond T-Jump Experiment in Poly(glutamic acid): A Circular Dichroism Study

Poly(glutamic acid) has been studied with a nanosecond T-jump experiment. A new experimental set-up based on the frequency-quadrupling of an 82 MHz Titanium-Sapphire laser allows rapid CD measurements to be performed. Combining time-resolved absorption and circular dichroism at 204 and 220 nm, we are able to measure precisely the unfolding relaxation time as well as the helical fraction evolution. We show that only CD at 220 nm is relevant to observe the unfolding of an alpha helix whereas no change is observed for CD at 204 nm. Conversely, both absorptions yield information on the dynamics of the process.     

Chiral copolymers of (R)‐N‐(1‐phenylethyl) methacrylamide and 2‐hydroxyethyl methacrylate: copolymerization characteristics and chiroptical properties

The aim of this investigation was the copolymerization of a chiral monomer, (R)‐N‐(1‐phenylethyl) methacrylamide, with an achiral monomer, 2‐hydroxyethyl methacrylate (HEMA). The copolymerization characteristics as well as the chiroptical properties (optical rotation and circular dichroism) and their variation with copolymer composition and temperature are discussed. The copolymers are statistical and enriched in HEMA. The monomer reactivity ratio of the chiral monomer (r₁) is 0.133 whereas that of HEMA (r₂) is 1.042 based on the Kelen–Tudos method. The sequence of consecutive chiral monomer units predominates for a feed composition between 0.5 and 0.9 (mole fraction). On the other hand, the sequence of HEMA is uniform and it predominates for a feed composition of around 0.5 (mole fraction). The chiroptical properties of the copolymers do not vary linearly with the content of chiral units in the copolymers. The optical rotation and circular dichroism attain optimum values above 30–40 mol% of chiral monomer units in the copolymers. However, the circular dichroism of the copolymers varies linearly with the temperature. The chiral monomer being a more bulky structure is less reactive than HEMA. The nonlinear variation of chiroptical properties of the copolymers with the content of chiral units may be due to the secondary interaction in the copolymers associated with the hydrogen bonding involving the amide linkage (CONH) present in the pendant chromophore of the chiral monomer as well as the hydroxyl pendant group of HEMA and also the aromatic π–π interaction. Copyright © 2009 Society of Chemical Industry     

The Bacterial Extracellular Matrix Protein TapA Is a Two-Domain Partially Disordered Protein

Biofilms are aggregates of microbial cells that form on surfaces and at interfaces, and are encased in an extracellular matrix. In biofilms made by the soil bacterium Bacillus subtilis, the protein TapA mediates the assembly of the functional amyloid protein TasA into extracellular fibers, and it anchors these fibers to the cell surface. We used circular dichroism and NMR spectroscopy to show that, unlike the structured TasA, TapA is disordered. In addition, TapA is composed of two weakly interacting domains: a disordered C-terminal domain and a more structured N-terminal domain. These two domains also exhibited different structural changes in response to changes in external conditions, such as increased temperatures and the presence of lipid vesicles. Although the two TapA domains weakly interacted in solution, their cooperative interaction with lipid vesicles prevented disruption of the vesicles. These findings therefore suggest that the two-domain composition of TapA is important in its interaction with single or multiple partners in the extracellular matrix in biofilms.     

A Holistic Approach to Determining Stereochemistry of Potential Pharmaceuticals by Circular Dichroism with β-Lactams as Test Cases

This paper’s main objective is to show that many different factors must be considered when solving stereochemical problems to avoid misleading conclusions and obtain conclusive results from the analysis of spectroscopic properties. Particularly in determining the absolute configuration, the use of chiroptical methods is crucial, especially when other techniques, including X-ray crystallography, fail, are not applicable, or give inconclusive results. Based on various β-lactam derivatives as models, we show how to reliably determine their absolute configuration (AC) and preferred conformation from circular dichroism (CD) spectra. Comprehensive CD analysis, employing both approaches, i.e., traditional with their sector and helicity rules, and state-of-the-art supported by quantum chemistry (QC) calculations along with solvation models for both electronic (ECD) and vibrational (VCD) circular dichroism ranges, allows confident defining stereochemistry of the β-lactams studied. Based on an in-depth analysis of the results, we have shown that choosing a proper chiroptical method/s strictly depends on the specific case and certain structural features.     

Infrared optical activity: electric field approaches in time domain

Vibrational circular dichroism (VCD) spectroscopy provides detailed information about the absolute configurations of chiral molecules including biomolecules and synthetic drugs. This method is the infrared (IR) analogue of the more popular electronic CD spectroscopy that uses the ultraviolet and visible ranges of the electromagnetic spectrum. Because conventional electronic CD spectroscopy measures the difference in signal intensity, problems such as weak signal and low time-resolution can limit its utility. To overcome the difficulties associated with that approach, we have recently developed femtosecond IR optical activity (IOA) spectrometry, which directly measures the IOA free-induction-decay (FID), the impulsive chiroptical IR response that occurs over time. In this Account, we review the time-domain electric field measurement and calculation methods used to simultaneously characterize VCD and related vibrational optical rotatory dispersion (VORD) spectra. Although conventional methods measure the electric field intensity, this vibrational technique is based on a direct phase-and-amplitude measurement of the electric field of the chiroptical signal over time. This method uses a cross-polarization analyzer to carry out heterodyned spectral interferometry. The cross-polarization scheme enables us to selectively remove the achiral background signal, which is the dominant noise component present in differential intensity measurement techniques. Because we can detect the IOA FID signal in a phase-amplitude-sensitive manner, we can directly characterize the time-dependent electric dipole/magnetic dipole response function and the complex chiral susceptibility that contain information about the angular oscillations of charged particles. These parameters yield information about the VCD and VORD spectra. In parallel with such experimental developments, we have also calculated the IOA FID signal and the resulting VCD spectrum. These simulations use a quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) method and calculate the electric dipole/magnetic dipole cross-correlation function in the time domain. Although many quantum chemistry calculation approaches can only consider a limited number of geometry-optimized conformations of chiral molecules in a gas phase, this computational method includes the solute-solvent interactions and the inhomogeneous distributions of solute conformers in condensed phases. A subsequent Fourier transformation of the chiral response function produced a theoretical VCD spectrum in the entire mid-IR frequency range. Directly comparing theory and experiment, we demonstrate quantitative agreement between frequency-tunable femtosecond IOA measurements and QM/MM MD simulations of (1S)-β-pinene in CCl(4) solution. We anticipate that these direct IOA measurement and calculation methods will be applied to the studies of equilibrium chiroptical properties and structure determinations. These methods provide tools to investigate ultrafast structural dynamics of chiral systems with unprecedented time resolution.     

Early Events, Kinetic Intermediates and the Mechanism of Protein Folding in Cytochrome c

Kinetic studies of the early events in cytochrome c folding are reviewed with a focus on the evidence for folding intermediates on the submillisecond timescale. Evidence from time-resolved absorption, circular dichroism, magnetic circular dichroism, fluorescence energy and electron transfer, small-angle X-ray scattering and amide hydrogen exchange studies on the t ≤ 1 ms timescale reveals a picture of cytochrome c folding that starts with the ~ 1-μs conformational diffusion dynamics of the unfolded chains. A fractional population of the unfolded chains collapses on the 1 – 100 μs timescale to a compact intermediate I_C containing some native-like secondary structure. Although the existence and nature of I_C as a discrete folding intermediate remains controversial, there is extensive high time-resolution kinetic evidence for the rapid formation of I_C as a true intermediate, i.e., a metastable state separated from the unfolded state by a discrete free energy barrier. Final folding to the native state takes place on millisecond and longer timescales, depending on the presence of kinetic traps such as heme misligation and proline mis-isomerization. The high folding rates observed in equilibrium molten globule models suggest that I_C may be a productive folding intermediate. Whether it is an obligatory step on the pathway to the high free energy barrier associated with millisecond timescale folding to the native state, however, remains to be determined.     

Structural,Thermal and Magnetic Properties of Thin Metal Films and Adsorbate–Substrate Systems Studied by XAFS and XMCD

Thin metal films often exhibit interesting properties that are essentially different from the bulk ones. XAFS (X-ray absorption fine structure) and XMCD (X-ray magnetic circular dichroism) techniques are quite suitable to investigate structural, thermal and magnetic properties of thin metal films. In this proceeding, we will present following two topics concerning structural and magnetic properties of adsorbates on thin metal films. The first one is the adsorption geometry of SO₂ on a 1-monolayer (ML) Pd thin film grown on a Ni(111) single crystal. It was found by S K-edge XAFS that SO₂ is lying flat on 1-ML Pd/Ni(111). This result is not similar to the bulk Pd surface but to the bulk Ni one. This finding indicates significant modification of the electronic structure of the 1-ML Pd film compared to the bulk one. The second topic is the magnetic moment induced on CO adsorbed on Ni epitaxial films grown on Cu(001). The O K-edge XMCD results revealed that in the perpendicularly magnetized 10-ML Ni film the orbital moment of CO is parallel to the substrate Ni magnetization, while it is antiparallel in the in-planar magnetized 6-ML and thick (>100 ML) films. The origin of the induced orbital moment at CO is discussed.     

Strategy and Effects of Polyproline Peptide Stapling by Copper(I)-Catalyzed Alkyne–Azide Cycloaddition Reaction

Polyproline is a unique type of peptide that has a stable, robust, and well-defined helical structure in an aqueous environment. These features have allowed polyproline to be used as a nanosized scaffold for applications in chemical biology and related fields. To understand its structural properties and to expand the applications, this secondary structure was tested systematically by stapling the peptide at different locations with staples of various lengths. Using the efficient copper(I)-catalyzed alkyne–azide cycloaddition (CuAAC), we successfully prepared stapled polyproline and investigated the impact of this peptide macrocyclization through circular dichroism analysis. Whereas the stapling seems to have no significant effect on polyproline helix II (PPII) conformation in water, the location and the length of the staple affect the transformation of conformation in n-propanol. These results provide valuable information for future research using peptide stapling to manipulate polyproline conformation for various applications.     

ε-Fe2O3 nanoparticles embedded in silica xerogel – Magnetic metamaterial

A novel method for synthesizing a new metamaterial based on ε-Fe₂O₃ nanoparticles immobilized in the xerogel matrix was proposed. Samples with different contents of ε-Fe₂O₃ nanoparticles dispersed in silica xerogel were synthesized by impregnation of as prepared hydrogel with iron (II) salts with the subsequent calcination. The structure and magnetic properties of the prepared composites were studied by transmission electron microscopy, X-ray diffraction, Mössbauer spectroscopy, and static magnetic measurements. The absence of other iron oxide polymorphs, controllable particle size distribution, and high ε-Fe₂O₃ nanoparticle concentration in combination with the weak interparticle magnetic interactions ensured the preservation of the unique magnetic properties of individual ε-Fe₂O₃ nanoparticles and allowed us to obtain a novel metamaterial. The high optical transparency and homogeneity of the prepared composites made it possible to detect the magnetic circular dichroism (MCD) of the magnetic silica xerogel, which is typical of the ε-Fe₂O₃-based systems.     

Flow Alignment of Extracellular Vesicles: Structure and Orientation of Membrane‐Associated Bio‐macromolecules Studied with Polarized Light

Extracellular vesicles (EVs) are currently in scientific focus, as they have great potential to revolutionize the diagnosis and therapy of various diseases. However, numerous aspects of these species are still poorly understood, and thus, additional insight into their molecular‐level properties, membrane–protein interactions, and membrane rigidity is still needed. We here demonstrate the use of red‐blood‐cell‐derived EVs (REVs) that polarized light spectroscopy techniques, linear and circular dichroism, can provide molecular‐level structural information on these systems. Flow‐linear dichroism (flow‐LD) measurements show that EVs can be oriented by shear force and indicate that hemoglobin molecules are associated to the lipid bilayer in freshly released REVs. During storage, this interaction ceases; this is coupled to major protein conformational changes relative to the initial state. Further on, the degree of orientation gives insight into vesicle rigidity, which decreases in time parallel to changes in protein conformation. Overall, we propose that both linear dichroism and circular dichroism spectroscopy can provide simple, rapid, yet efficient ways to track changes in the membrane–protein interactions of EV components at the molecular level, which may also give insight into processes occurring during vesiculation.     

Synthesis and conformational study of poly(l-β-3,4-dihydroxyphenyl-α-alanine)

High molecular weight poly(l-β-3,4-dihydroxyphenyl-α-alanine) has been synthesized. Both optical rotatory dispersion and circular dichroism spectra of the polypeptide are anomalous and give little information about its conformation. From the total results obtained by a study of the optical rotation, nuclear magnetic resonance and infra-red absorption, poly(l-β-3,4-dihydroxyphenyl-α-alanine) is most probably right-handed helical in trimethyl phosphate, methanol or water/trimethyl phosphate ($\text{1:1}\text{v}\text{v}$) mixed solvents below pH 10.4. It is in the random coil structure in dimethyl sulphoxide or water/trimethyl phosphate mixed solvents above pH 11. The transition midpoint is pH 10.6 in water/trimethyl phosphate mixed solvents. The results were compared with those of poly(l-tyrosine).     

O.r.d.-c.d. and protonation of amide-containing polymers in strong acid media: 1. The case of poly(−)1,2-diaminopropane sebacamide, an optically active nylon-type polyamide

Optical rotatory dispersion (o.r.d.) and circular dichroism (c.d.) of poly(−)1,2-diaminopropane sebacamide I and of its model compound, N-N′-didecanoyl(−)1,2-diaminopropane II, are investigated in trifluoroethanol-formic acid, -trifluoroacetic, -methanesulphonic and -sulphuric acid mixtures, with emphasis on the two latter solvent systems. It is shown that the optical activity of both compounds depends on the nature and the concentration of the acid. The stronger the acid, the larger the chiroptical changes observed for a given value of the acid/amide molar ratio τ. The drastic changes caused by small amounts of methanesulphonic and sulphuric acids are assigned to protonation of amide chromophores solely.     

Conformational Changes in DNA upon Ligand Binding Monitored by Circular Dichroism

Circular dichroism (CD) spectroscopy is an optical technique that measures the difference in the absorption of left and right circularly polarized light. This technique has been widely employed in the studies of nucleic acids structures and the use of it to monitor conformational polymorphism of DNA has grown tremendously in the past few decades. DNA may undergo conformational changes to B-form, A-form, Z-form, quadruplexes, triplexes and other structures as a result of the binding process to different compounds. Here we review the recent CD spectroscopic studies of the induction of DNA conformational changes by different ligands, which includes metal derivative complex of aureolic family drugs, actinomycin D, neomycin, cisplatin, and polyamine. It is clear that CD spectroscopy is extremely sensitive and relatively inexpensive, as compared with other techniques. These studies show that CD spectroscopy is a powerful technique to monitor DNA conformational changes resulting from drug binding and also shows its potential to be a drug-screening platform in the future.     

Circular Dichroism and Circular Polarized Luminescence from a Green Fluorescent Protein—Initial Research for Chiroptical Emission of Biological Materials

Optical properties of a green fluorescent protein (GFP) are examined using optical absorption, circular dichroism (CD), and circular polarized luminescence (CPL) spectroscopies. The GFP has chiroptical activity and exhibits green circular polarized emission, although the g _em-factor is small. Poly(vinyl alcohol) (PVA)/GFP composite films are prepared to attempt long-term preservation of the GFP emission activity. After five years, the transparent PVA/GFP composite film still exhibits stable fluorescence that appears similar to the emission from the Aequorea jellyfish.     

Site-selective substitution and resulting magnetism in arc-melted perovskite ATiO3-δ (A = Ca,Sr, Ba)

Magnetic properties in perovskite titanates ATiO_3-δ (A = Ca, Sr, Ba) were investigated before and after arc melting. Crystal structure analysis was conducted by powder synchrotron X-ray diffraction with Rietveld refinements. Quantitative chemical element analysis was carried out by X-ray photoelectron spectroscopy. Magnetic measurements were conducted by vibrating sample magnetometer and X-ray magnetic circular dichroism (XMCD). The magnetic properties are found to be affected by impurities of 3d elements such as Fe, Co, and Ni. Depending on the composition and crystal structure, the occupation of the magnetic ions in perovskite titanates is selectively varied, which is interpreted to be the origin of the different magnetic behaviors in arc-melted perovskite titanates ATiO_3-δ (A = Ca, Sr, Ba). In addition, both formation of oxygen vacancies and the reduction of Ti⁴⁺ to Ti³⁺ during arc-melting also play a role as proven by XMCD. Nevertheless, preferential site occupation of magnetic impurities is dominant in the magnetic properties of arc-melted perovskite ATiO_3-δ (A = Ca, Sr, Ba).     

Optical activity measurements in solids 7. Polylactides and poly(β-hydroxybutyrates)

The optical activities of poly-(R)-lactide, poly-(S)-lactide, poly(β-hydroxybutyrate) and two β-hydroxyvalerate copolymers were measured in solution, as solid powders in suspension, and where possible, as films. Poly-(+)-3-methyl-1-pentene was also reinvestigated. In some cases the specific rotation values of powder samples showed significant differences from the values of the solution measurements. The discrepancies of the data observed seem to reflect the local environment of the polymer chains in supermolecular assemblies and consequently the solid state structure(morphology)of the polymers. The circular dichroism (CD) spectra of the polymers were also measured in solution and in the form of their films. For comparison, the CD spectra of the naturally occurring protein casein and of the synthetic polypeptide poly-(L)-proline were also measured.     

利用体积排阻色谱法进行蛋白质折叠

以溶菌酶为模拟体系对体积排阻色谱法进行蛋白质折叠过程实验研究 .圆二色性光谱法分析结果证实了复性溶菌酶与天然溶菌酶的二级结构一致性 ;复性溶菌酶与天然溶菌酶色谱保留体积的差异揭示出折叠过程中无活性蛋白质聚集体的存在及其向复性蛋白质转化的机制 ;不同初始浓度的复性实验证实了蛋白质聚集体的存在及其与变性蛋白质初始浓度的关系 ;采用短色谱柱的折叠分离实验结果表明蛋白质折叠是一个快速过程 ;不同尿素浓度下的折叠分离实验结果表明尿素在SEC法中具有非常重要的作用 .与稀释复性法的对比实验表明 :体积排阻色谱法具有稀释倍数小、复性产品活性收率高、复性蛋白质浓度高等优点 .