Showing papers on "Circular dichroism published in 2006"
TL;DR: This protocol details the basic steps of obtaining and interpreting CD data, and methods for analyzing spectra to estimate the secondary structural composition of proteins.
Abstract: Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using recombinant techniques or purified from tissues. The most widely used applications of protein CD are to determine whether an expressed, purified protein is folded, or if a mutation affects its conformation or stability. In addition, it can be used to study protein interactions. This protocol details the basic steps of obtaining and interpreting CD data, and methods for analyzing spectra to estimate the secondary structural composition of proteins. CD has the advantage that measurements may be made on multiple samples containing < or =20 microg of proteins in physiological buffers in a few hours. However, it does not give the residue-specific information that can be obtained by x-ray crystallography or NMR.
3,093 citations
TL;DR: Circular dichroism is an excellent spectroscopic technique for following the unfolding and folding of proteins as a function of temperature and may be used to determine the van't Hoff enthalpy and entropy of unfolding, the midpoint of the unfolding transition and the free energy of unfolding.
Abstract: Circular dichroism (CD) is an excellent spectroscopic technique for following the unfolding and folding of proteins as a function of temperature. One of its principal applications is to determine the effects of mutations and ligands on protein and polypeptide stability. If the change in CD as a function of temperature is reversible, analysis of the data may be used to determined the van't Hoff enthalpy and entropy of unfolding, the midpoint of the unfolding transition and the free energy of unfolding. Binding constants of protein-protein and protein-ligand interactions may also be estimated from the unfolding curves. Analysis of CD spectra obtained as a function of temperature is also useful to determine whether a protein has unfolding intermediates. Measurement of the spectra of five folded proteins and their unfolding curves at a single wavelength requires approximately 8 h.
743 citations
TL;DR: A new reference dataset is created which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets.
Abstract: Motivation: Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined.
This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology.
Contact: b.wallace@mail.cryst.bbk.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
399 citations
TL;DR: Using soft x-ray absorption spectroscopy and magnetic circular dichroism at the Co-L(2,3) edge, the spin state transition in LaCoO3 can be well described by a low-spin ground state and a triply degenerate high-spin first excited state as mentioned in this paper.
Abstract: Using soft x-ray absorption spectroscopy and magnetic circular dichroism at the Co-L(2,3) edge, we reveal that the spin state transition in LaCoO3 can be well described by a low-spin ground state and a triply degenerate high-spin first excited state From the temperature dependence of the spectral line shapes, we find that LaCoO3 at finite temperatures is an inhomogeneous mixed-spin state system It is crucial that the magnetic circular dichroism signal in the paramagnetic state carries a large orbital momentum This directly shows that the currently accepted low- or intermediate-spin picture is at variance Parameters derived from these spectroscopies fully explain existing magnetic susceptibility, electron spin resonance, and inelastic neutron data
396 citations
TL;DR: The complete conformational path was investigated in detail with the aid of molecular‐dynamics simulations in explicit solvent, which led to the localization of residues that might seed β conformations, which could aid the design of molecules able to inhibit fibril deposition or revert oligomerization processes.
Abstract: Current views of the role of beta-amyloid (Abeta) peptide fibrils range from regarding them as the cause of Alzheimer's pathology to having a protective function. In the last few years, it has also been suggested that soluble oligomers might be the most important toxic species. In all cases, the study of the conformational properties of Abeta peptides in soluble form constitutes a basic approach to the design of molecules with "antiamyloid" activity. We have experimentally investigated the conformational path that can lead the Abeta-(1-42) peptide from the native state, which is represented by an alpha helix embedded in the membrane, to the final state in the amyloid fibrils, which is characterized by beta-sheet structures. The conformational steps were monitored by using CD and NMR spectroscopy in media of varying polarities. This was achieved by changing the composition of water and hexafluoroisopropanol (HFIP). In the presence of HFIP, beta conformations can be observed in solutions that have very high water content (up to 99 % water; v/v). These can be turned back to alpha helices simply by adding the appropriate amount of HFIP. The transition of Abeta-(1-42) from alpha to beta conformations occurs when the amount of water is higher than 80 % (v/v). The NMR structure solved in HFIP/H2O with high water content showed that, on going from very apolar to polar environments, the long N-terminal helix is essentially retained, whereas the shorter C-terminal helix is lost. The complete conformational path was investigated in detail with the aid of molecular-dynamics simulations in explicit solvent, which led to the localization of residues that might seed beta conformations. The structures obtained might help to find regions that are more affected by environmental conditions in vivo. This could in turn aid the design of molecules able to inhibit fibril deposition or revert oligomerization processes.
389 citations
TL;DR: The results suggest that the 22 nt in K(+) solution exists as a mixture of mixed-parallel/antiparallel and chair-type G-quadruplex, and the possible implications of the structure in understanding higher-order telomeric DNA structure and T-loop formation are discussed.
344 citations
TL;DR: Measurements of electron energy-loss magnetic chiral dichroism with XMCD spectra obtained from the same specimen are compared to show that chiral atomic transitions in a specimen are accessible with inelastic electron scattering under particular scattering conditions, which could have important consequences for the study of magnetism on the nanometre and subnanometre scales.
Abstract: The electron microscope, already a powerful research instrument, could become even more powerful following the discovery that magnetic circular dichroism can be detected with a conventional transmission electron microscope. Materials display magnetic circular dichroism if the absorption of left and right circularly polarized light differs in the presence of an applied magnetic field. Application of this effect using synchrotron X-ray photons is a powerful tool for the investigation of magnetic phenomena. The new technique — EMCD or energy loss magnetic chiral dichroism — exploits the similarities between X-ray absorption and inelastic electron scattering to give a TEM capabilities normally associated with expensive synchrotrons. EMCD could be useful in many fields including spintronics and nanomagnetism. Comparison of measurements of electron energy-loss magnetic chiral dichroism with X-ray magnetic circular dichroism spectra obtained from the same specimen, together with theoretical calculations, show that chiral atomic transitions in a specimen are accessible with inelastic electron scattering under particular scattering conditions. A material is said to exhibit dichroism if its photon absorption spectrum depends on the polarization of the incident radiation. In the case of X-ray magnetic circular dichroism (XMCD), the absorption cross-section of a ferromagnet or a paramagnet in a magnetic field changes when the helicity of a circularly polarized photon is reversed relative to the magnetization direction. Although similarities between X-ray absorption and electron energy-loss spectroscopy in a transmission electron microscope (TEM) have long been recognized, it has been assumed that extending such equivalence to circular dichroism would require the electron beam in the TEM to be spin-polarized. Recently, it was argued on theoretical grounds that this assumption is probably wrong1. Here we report the direct experimental detection of magnetic circular dichroism in a TEM. We compare our measurements of electron energy-loss magnetic chiral dichroism (EMCD) with XMCD spectra obtained from the same specimen that, together with theoretical calculations, show that chiral atomic transitions in a specimen are accessible with inelastic electron scattering under particular scattering conditions. This finding could have important consequences for the study of magnetism on the nanometre and subnanometre scales, as EMCD offers the potential for such spatial resolution down to the nanometre scale while providing depth information—in contrast to X-ray methods, which are mainly surface-sensitive.
308 citations
TL;DR: It is concluded that the DNA templated Ag nanocrystals had a preferred structural handedness.
Abstract: Silver nanocrystals grown on a poly(dG)-poly(dC) double stranded DNA scaffold displayed circular dichroism at their surface plasmon excitation band. This chiral plasmon signature was not observed in a control experiment where silver nanocrystals of similar size were produced without the DNA template and adsorbed to the DNA. It is concluded that the DNA templated Ag nanocrystals had a preferred structural handedness.
305 citations
TL;DR: Employing displacement cum fluorimetry using site-specific binding ligands, such as dansylproline and dansylamide, indicated that SQ binds with protein selectively at site II involving hydrophobic, hydrogen bonding, and electrostatic interactions.
Abstract: With the objective of developing small molecule based probes for proteins, interactions of polyhydroxyl-substituted squaraine dye (SQ) with bovine serum albumin (BSA) have been investigated by absorption, steady-state and time-resolved fluorescence, circular dichroism (CD), cyclic voltammetry (CV), 1H NMR, scanning electron, and tapping mode atomic force microscopic techniques. Increase in addition of BSA resulted in increase in absorbance and fluorescence quantum yields (80-fold) of SQ, along with significant bathochromic shifts in the absorption and fluorescence maxima. Half-reciprocal analysis of the absorption data gave a 1:1 stoichiometry for the complex between BSA and SQ with high association (Kass) constant of (1.4 +/- 0.1) x 106 M-1 and change in free energy of -35 kJ/mol. The complex formation was further confirmed by observation of induced CD signal corresponding to the SQ chromophore at 610 nm, upfield shift (about Deltadelta 0.1 ppm) of aromatic protons of SQ in 1H NMR spectra, and decrease in current intensity (CV) of SQ when bound to BSA. The picosecond time-resolved fluorescence studies indicated that the BSA-SQ complex exhibits biexponential decay with significantly enhanced lifetimes of 0.5 and 1.5 ns when compared to the lifetime of SQ (tau = 121 ps) in the absence of BSA. Employing displacement cum fluorimetry using site-specific binding ligands, such as dansylproline and dansylamide, indicated that SQ binds with protein selectively at site II involving hydrophobic, hydrogen bonding, and electrostatic interactions. The uniqueness of this molecular system is that it interacts with BSA selectively at site II and signals the binding event through dual mode recognition of "visual color" change and "turn on" fluorescence mechanism.
275 citations
TL;DR: The observations are consistent with a mechanism based on a chiral footprint on the metal core imparted by the adsorbed thiol, which was manifested in a color change with particle size.
Abstract: We have prepared gold nanoparticles covered with N-isobutyryl-l-cysteine and N-isobutyryl-d-cysteine, respectively. These particles with a mean particle size smaller than 2 nm are highly soluble in water and are amenable to chiroptical techniques such as vibrational circular dichroism (VCD) and circular dichroism (CD) spectroscopy. Density functional theory shows that the VCD spectra are sensitive toward the conformation of the adsorbed thiol. Based on the comparison between the experimental VCD spectrum and the calculated VCD spectra for different conformers, a preferential conformation of the thiol adsorbed on the gold particles can be proposed. In this conformation the carboxylate group interacts with the gold particle in addition to the sulfur. The particles could furthermore be separated according to their charge and size into well-defined compounds. The optical absorption spectra revealed a well-quantized electronic structure and a systematic red-shift of the absorption onset with increasing gold core size, which was manifested in a color change with particle size. Some compounds showed basically identical absorption spectra as analogous gold particles protected with l-glutathione. This shows that these particles have identical core sizes (10-12, 15 and 18 gold atoms, respectively) and indicates that the number and arrangement of the adsorbed thiol are the same, independent of the two thiols, which have largely different sizes. Some separated compounds show strong optical activity with opposite sign when covered with the d- and l-enantiomer, respectively, of N-isobutyryl-cysteine. The origin of the optical activity in the metal-based transitions is discussed. The observations are consistent with a mechanism based on a chiral footprint on the metal core imparted by the adsorbed thiol.
262 citations
TL;DR: This work examines the inherent stability of NV-VLPs over a range of pH and temperature values and provides detailed insight into structural perturbations that accompany disassembly and suggests that the two domains of VP1 unfold independently in a pH-dependent manner.
TL;DR: The technique of Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy and its advantages over conventional circular dichroism spectroscopic are described in this tutorial review, as well as recent applications of the technique in structural and functional genomics.
Abstract: The technique of Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy and its advantages over conventional circular dichroism spectroscopy are described in this tutorial review, as well as recent applications of the technique in structural and functional genomics.
Circular dichroism (CD) spectroscopy is a well-established method in biological chemistry and structural biology, but its utility can be limited by the low flux of the light source in the far ultraviolet and vacuum ultraviolet wavelength regions in conventional CD instruments. The development of synchrotron radiation circular dichroism (SRCD), using the intense light of a synchrotron beam, has greatly expanded the utility of the method, especially as a tool for both structural and functional genomics. These applications take advantage of the enhanced features of SRCD relative to conventional CD: the ability to measure lower wavelength data containing more electronic transitions and hence more structural information, the higher signal-to-noise hence requiring smaller samples, the higher intensity enabling measurements in absorbing buffers and in the presence of lipids and detergents, and the ability to do faster measurements enabling high throughput and time-resolved spectroscopy.
This article discusses recent developments in SRCD instrumentation, software, sample preparation and methods of analyses, with particular emphasis on their applications to the study of proteins. These advances have led to new applications in structural genomics (SG), including the potential for fold recognition as a means of target selection and the examination of membrane proteins, a class of proteins usually excluded from SG programmes. Other SG uses include detection of macromolecular interactions as a screen for complex formation, and examination of glycoproteins and sugar components. In functional genomics (FG) new applications include screening for ligand binding as a means of identifying function, and examination of structural differences in mutant proteins as a means of gaining insight into function.
TL;DR: A convenient method to monitor in real time protein aggregation during thermal folding/ unfolding transition by recording turbidity or 90° light scattering data in circular dichroism (CD) spectroscopic experiments is proposed.
Abstract: Thermal unfolding monitored by spectroscopy or calorimetry is widely used to determine protein stability. Equilibrium thermodynamic analysis of such unfolding is often hampered by its irreversibility, which usually results from aggregation of thermally denatured protein. In addition, heat-induced protein misfolding and aggregation often lead to formation of amyloid-like structures. We propose a convenient method to monitor in real time protein aggregation during thermal folding/ unfolding transition by recording turbidity or 90° light scattering data in circular dichroism (CD) spectroscopic experiments. Since the measurements of turbidity and 90° light scattering can be done simultaneously with far- or near-UV CD data collection, they require no additional time or sample and can be directly correlated with the protein conformational changes monitored by CD. The results can provide useful insights into the origins of irreversible conformational changes and test the linkage between protein unfolding or misfolding and aggregation in various macromolecular systems, including globular proteins and protein–lipid complexes described in this study, as well as a wide range of amyloid-forming proteins and peptides.
TL;DR: Fluorescence experiments suggest that formation of the G-quadruplex and i-motif can compete with duplex formation and a polymerase arrest assay indicated that formationThe G- quadruplex structure in the Rb gene acts as a barrier in DNA synthesis.
Abstract: The formation of G-quadruplex and i-motif structures in the 5' end of the retinoblastoma (Rb) gene was examined using chemical modifications, circular dichroism (CD) and fluorescence spectroscopy. It was found that substitutions of 8-methylguanine at positions that show syn conformations in antiparallel G-quadruplexes stabilize the structure in the G-rich strand. The complementary C-rich 18mer forms an i-motif structure, as suggested by CD spectroscopy. Based on the C to T mutation experiments, C bases participated in the C-C+ base pair of the i-motif structure were determined. Experiments of 2-aminopurine (2-AP) substitution reveal that an increase of fluorescence in the G-quadruplex relative to duplex is attributed to unstacked 2-AP within the loop of G-quadruplex. The fluorescence experiments suggest that formation of the G-quadruplex and i-motif can compete with duplex formation. Furthermore, a polymerase arrest assay indicated that formation the G-quadruplex structure in the Rb gene acts as a barrier in DNA synthesis.
TL;DR: The observation of fluorescence-detected circular dichroism (FDCD) from single (bridgedtriarylamine) helicene molecules by using an excitation wavelength in the vicinity of an electronic transition that shows circular dichROism in bulk samples is reported.
Abstract: Chirally sensitive measurement techniques have generally been restricted to bulk samples. Here, we report the observation of fluorescence-detected circular dichroism (FDCD) from single (bridgedtriarylamine) helicene molecules by using an excitation wavelength (457 nanometers) in the vicinity of an electronic transition that shows circular dichroism in bulk samples. The distributions of dissymmetry (g) parameters by analysis of signals from pure M- and P-type diastereomers are almost perfect mirror images of one another, each spanning a range of both positive and negative values. In addition, we observe a well-defined structure in the histogram of dissymmetry parameters suggestive of specific molecular orientations at the polymer interface. These single-molecule results highlight strong intrinsic circular dichroism responses that can be obscured by cancellation effects in ensemble measurements of a randomly oriented bulk sample.
TL;DR: The results are consistent with the view that the antibodies undergo limited conformational change, and that incubation at 4°C at low pH results in no time‐dependent conformational changes.
Abstract: Exposure of antibodies to low pH is often unavoidable for purification and viral clearance. The conformation and stability of two humanized monoclonal antibodies (hIgG4-A and -B) directed against different antigens and a mouse monoclonal antibody (mIgG1) in 0.1M citrate at acidic pH were studied using circular dichroism (CD), differential scanning calorimetry (DSC), and sedimentation velocity. Near- and far-UV CD spectra showed that exposure of these antibodies to pH 2.7-3.9 induced only limited conformational changes, although the changes were greater at the lower pH. However, the acid conformation is far from unfolded or so-called molten globule structure. Incubation of hIgG4-A at pH 2.7 and 3.5 at 4 degrees C over the course of 24 h caused little change in the near-UV CD spectra, indicating that the acid conformation is stable. Sedimentation velocity showed that the hIgG4-A is largely monomeric at pH 2.7 and 3.5 as well as at pH 6.0. No time-dependent changes in sedimentation profile occurred upon incubation at these low pHs, consistent with the conformational stability observed by CD. The sedimentation coefficient of the monomer at pH 2.7 or 3.5 again suggested that no gross conformational changes occur at these pHs. DSC analysis of the antibodies showed thermal unfolding at pH 2.7-3.9 as well as at pH 6.0, but with decreased melting temperatures at the lower pH. These results are consistent with the view that the antibodies undergo limited conformational change, and that incubation at 4 degrees C at low pH results in no time-dependent conformational changes. Titration of hIgG4-A from pH 3.5 to 6.0 resulted in recovery of native monomeric proteins whose CD and DSC profiles resembled those of the original sample. However, titration from pH 2.7 resulted in lower recovery of monomeric antibody, indicating that the greater conformational changes observed at this pH cannot be fully reversed to the native structure by a simple pH titration.
TL;DR: In this paper, the valence, spin, and orbital state of the Co ions in the one-dimensional cobaltate Ca3Co2O6 were investigated using x-ray absorption and magnetic circular dichroism at the Co-L2,3 edges.
Abstract: We have investigated the valence, spin, and orbital state of the Co ions in the one-dimensional cobaltate Ca3Co2O6 using x-ray absorption and x-ray magnetic circular dichroism at the Co-L2,3 edges. The Co ions at both the octahedral Cooct and trigonal Cotrig sites are found to be in a 3+ state. From the analysis of the dichroism we established a low-spin state for the Cooct and a high-spin state with an anomalously large orbital moment of 1.7B at the Co trig ions. This large orbital moment along the c-axis chain and the unusually large magnetocrystalline anisotropy can be traced back to the double occupancy of the d2 orbital in trigonal crystal field.
TL;DR: Different processing conditions can greatly affect the functional properties of conjugated polymer films employed in various optoelectronic applications.
Abstract: The dynamic transfer of a conjugated polymer's organization-dependent properties from the solution state to the solid film state was probed by circularly polarized luminescence (CPL) and circular dichroism (CD) spectroscopy. Different supramolecular organizations within films and aggregate solutions of a chiral poly(p-phenylenevinylene) derivative led to opposite CPL and CD spectra. These dramatic property differences were controlled by regulating the polymer's self-assembly through solvent selection and film annealing. Therefore, different processing conditions can greatly affect the functional properties of conjugated polymer films employed in various optoelectronic applications.
TL;DR: Circular dichroism spectroscopy, transmission electron microscopy, and microrheology techniques revealed that the self-assembly of TZ1H coincides with a distinct coil-helix conformational transition that occurs within a narrow pH range near the pKa of the imidazole side chains of the core histidine residues.
Abstract: Peptide TZ1H, based on the heptad sequence of a coiled-coil trimer, undergoes fully reversible, pH-dependent self-assembly into long-aspect-ratio helical fibers. Substitution of isoleucine residues with histidine at the core d-positions of alternate heptads introduces a mechanism by which self-assembly is coupled to the protonation state of the imidazole side chain. Circular dichroism spectroscopy, transmission electron microscopy, and microrheology techniques revealed that the self-assembly of TZ1H coincides with a distinct coil-helix conformational transition that occurs within a narrow pH range near the pKa of the imidazole side chains of the core histidine residues.
TL;DR: A number of published physical measurements, computational algorithms, and structural modeling methods have been used to create a molecular model of 19 kDa alpha-zein (Z19) as discussed by the authors.
Abstract: A variety of published physical measurements, computational algorithms, and structural modeling methods have been used to create a molecular model of 19 kDa alpha-zein (Z19). Zetaeins are water-insoluble storage proteins found in corn protein bodies. Analyses of the protein sequence using probability algorithms, structural studies by circular dichroism, infrared spectroscopy, small-angle X-ray scattering (SAXS), light scattering, proton exchange, NMR, and optical rotatory dispersion experiments suggest that Z19 has approximately 35-60% helical character, made up of nine helical segments of about 20 amino acids with glutamine-rich "turns" or "loops". SAXS and light-scattering experiments suggest that in alcohol/water mixtures alpha-zein exists as an oblong structure with an axial ratio of approximately 6:1. Furthermore, ultracentifugation, birefringence, dielectric, and viscosity studies indicate that alpha-zein behaves as an asymmetric particle with an axial ratio of from 7:1 to 28:1. Published models of alpha-zein to date have not been consistent with the experimental data, and for this reason the structure was re-examined using molecular mechanics and dynamics simulations creating a new three-dimensional (3D) structure for Z19. From the amino acid sequence and probability algorithms this analysis suggested that alpha-zein has coiled-coil tendencies resulting in alpha-helices with about four residues per turn in the central helical sections with the nonpolar residue side chains forming a hydrophobic face inside a triple superhelix. The nine helical segments of the 19 kDa protein were modeled into three sets of three interacting coiled-coil helices with segments positioned end to end. The resulting structure lengthens with the addition of the N- and C-terminal sections, to give an axial ratio of approximately 6 or 7:1 in agreement with recent experiments. The natural carotenoid, lutein, is found to fit into the core of the triple-helical segments and help stabilize the configuration. Molecular dynamics simulations with explicit methanol/water molecules as solvent have been carried out to refine the 3D structure.
TL;DR: Single-stranded nucleic acids, which carry multiple negative charges in an aqueous medium at near neutral pH, are found to induce the aggregation and self-assembly of the positively charged alkynylplatinum(II) terpyridyl complexes via electrostatic binding of the platinum complexes to the single- Stranded nuclei acids.
Abstract: Single-stranded nucleic acids, which carry multiple negative charges in an aqueous medium at near neutral pH, are found to induce the aggregation and self-assembly of the positively charged alkynylplatinum(II) terpyridyl complexes via electrostatic binding of the platinum complexes to the single-stranded nucleic acids, as revealed by the appearance of new UV-vis absorption and emission bands upon addition of single-stranded nucleic acids to a buffer solution of the complex. Changes in the intensity and pattern of circular dichroism (CD) spectroscopy are also observed, many of which are consistent with the assembly of the platinum complexes into helical structures, via metal⋯metal and π⋯π stacking interactions. The induced spectroscopic property changes are found to depend on the structural properties of the nucleic acids.
TL;DR: Observations seem to suggest that Zn2+ coordination is dominated by inter-molecular coordination and the formation of polymeric species.
TL;DR: A series of novel phenylacetylenes bearing optically active cyclodextrin (CyD) residues such as alpha-, beta-, and gamma-CyD and permethylated beta- CyD residues as the pendant groups was synthesized and polymerized with a rhodium catalyst to give highly cis-transoidal poly(phenylacetylene)s.
Abstract: A series of novel phenylacetylenes bearing optically active cyclodextrin (CyD) residues such as α-, β-, and γ-CyD and permethylated β-CyD residues as the pendant groups was synthesized and polymerized with a rhodium catalyst to give highly cis−transoidal poly(phenylacetylene)s, poly-1α, poly-2β, poly-3γ, and poly-2β-Me, respectively. The polymers exhibited an induced circular dichroism (CD) in the UV−visible region of the polymer backbones, resulting from the prevailing one-handed helical conformations. The Cotton effect signs were inverted in response to external chiral and achiral stimuli, such as temperature, solvent, and interactions with chiral or achiral guest molecules. The inversion of the Cotton effect signs was accompanied by a color change due to a conformational change, such as inversion of the helicity of the polymer backbones with a different twist angle of the conjugated double bonds, that was readily visible with the naked eye and could be quantified by absorption and CD spectroscopies. Th...
TL;DR: Methods to obtain and analyze circular dichroism spectra to measure changes in the folding of proteins as a function of denaturants, osmolytes or ligands to determination of the free energy of folding of a protein.
Abstract: Circular dichroism (CD) is an excellent tool for examining the interactions and stability of proteins. This protocol covers methods to obtain and analyze circular dichroism spectra to measure changes in the folding of proteins as a function of denaturants, osmolytes or ligands. Applications include determination of the free energy of folding of a protein, the effects of mutations on protein stability and the estimation of binding constants for the interactions of proteins with other proteins, DNA or ligands, such as substrates or inhibitors. The experiments require 2-5 h.
TL;DR: Data obtained by fluorescence spectroscopy, CD, and FTIR experiments along with the docking studies suggest that EGCG binds to residues located in subdomains IIa and IIIa of HSA, suggesting that apart from an initial hydrophobic association, the complex is held together by van der Waals interactions and hydrogen bonding.
Abstract: (-)-Epigallocatechin-3-gallate (EGCG), the major constituent of green tea has been reported to prevent many diseases by virtue of its antioxidant properties. The binding of EGCG with human serum albumin (HSA) has been investigated for the first time by using fluorescence, circular dichroism (CD), Fourier transform infrared (FTIR) spectroscopy, and protein-ligand docking. We observed a quenching of fluorescence of HSA in the presence of EGCG. The binding parameters were determined by a Scatchard plot and the results were found to be consistent with those obtained from a modified Stern-Volmer equation. From the thermodynamic parameters calculated according to the van't Hoff equation, the enthalpy change deltaH degrees and entropy change deltaS degrees were found to be -22.59 and 16.23 J/mol K, respectively. These values suggest that apart from an initial hydrophobic association, the complex is held together by van der Waals interactions and hydrogen bonding. Data obtained by fluorescence spectroscopy, CD, and FTIR experiments along with the docking studies suggest that EGCG binds to residues located in subdomains IIa and IIIa of HSA. Specific interactions are observed with residues Trp 214, Arg 218, Gln 221, Asn 295 and Asp 451. We have also looked at changes in the accessible surface area of the interacting residues on binding EGCG for a better understanding of the interaction.
TL;DR: It is concluded that the one side of the thymine moieties in the stacked assemblies of 8 complexes with a single chain of 9 formed and induced helical stack of the oligo(p-phenylenevinylene)s in the binary self-assembly.
Abstract: The nucleotide-appended oligo(p-phenylenevinylene), {bis[2,5-bis(2-methoxyethoxy)-1,4-phenylene]bis(2,1-ethenediyl-1,4-phenylenemethylene)}bis(2'-deoxy-3'-thymidylic acid) (8), has been synthesized, and self-assembly of the single-component 8 and binary self-assembly of 8 with a complementary single-stranded 20-meric oligodeoxyadenylic acid (9) have been examined in aqueous solutions. Atomic force microscopy (AFM), UV-visible (UV-vis), and circular dichroism (CD) measurements revealed that right-handed helical stacks with 6.4- and 5.1-nm diameters self-assemble from the binary components of 8 and 9 as a template depending on the residual stoichiometry of the two components (thymine (T):adenine (A) = 1:1 and T:A = 2:1, respectively). The concentration of 9 was found to strongly influence the CD spectra of 8 in aqueous solutions. Consequently, we concluded that the one side of the thymine moieties in the stacked assemblies of 8 complexes with a single chain of 9. Complementary T-A base pairs thus formed and induced helical stack of the oligo(p-phenylenevinylene)s in the binary self-assembly. In contrast, self-assembly of the single-component 8 and binary self-assembly of 8 with the noncomplementary 20-meric oligothymidylic acid (10) produced no remarkable formation of fibrous structures like helical stacks.
TL;DR: Eight-residue oligoureas designed to mimic globally amphiphilic alpha-helical host-defense peptides are effective against both gram-negative and gram-positive bacteria and exhibit selectivity for bacterial versus mammalian cells.
TL;DR: It is found that racemic mixtures of chiral single-walled nanotubes (SWNTs) wrapped with d(GT)20 DNA oligomer exhibit circular dichroism (CD), and induced CD arising from the coupling of transition moments of the SWNTs and the DNA is attributed.
Abstract: We have found that racemic mixtures of chiral single-walled nanotubes (SWNTs) wrapped with d(GT)20 DNA oligomer exhibit circular dichroism (CD). We attribute the CD signal to induced CD arising from the coupling of transition moments of the SWNTs and the DNA. Although the nanotube mixture appears to contain both enantiomers in equal amounts, DNA-SWNT transition moment interaction is more constructive for one SWNT enantiomer over the other, resulting in an overall CD signal.
TL;DR: A twisted two-dimensional core-shell tape is proposed as a structure model, in which the peptide segments form an antiparallel beta-sheet with a polymer shell to form soft, continuous organo-gels.
Abstract: Synthesis and peptide-guided self-assembly of an organo-soluble peptide−polymer conjugate, comprising a sequence-defined polypeptide and a poly(n-butyl acrylate), are described. The amino acid sequence of the peptide encodes a high tendency to adopt an antiparallel β-sheet motif, and thus programs the formation of tapelike microstructures. Easy synthesis and controllable self-assembly is ensured by the incorporation of structure breaking switch defects into the peptide segment. This suppresses temporarily the aggregation tendency of the conjugate as shown by circular dichroism, infrared spectroscopy (FT-IR), and atomic force microscopy (AFM). A pH-controlled rearrangement in the switch segments restores the native peptide backbone, triggering the self-assembly process and leading to the formation of densely twisted tapelike microstructures as could be observed by AFM and transmission electron microscopy. The resulting helical superstructures, when deposited on a substrate, are 2.9 nm high, 10 nm wide, and...
TL;DR: It was proved that the fluorescence quenching of BSA by Intal is a result of the formation of Intal-BSA complex and the distance R between the donor and acceptor has been obtained.