Heparin-induced circular dichroism of chloroquine

Circular dichroism (CD) and UV/Visible absorption (UV/Vis) spectroscopy techniques were used to investigate the interaction between heparin and chloroquine, an antimalarial drug that has shown potential as an anti-prion agent. CD spectra of rac-chloroquine upon addition of heparin provide evidence of glycosaminoglycan (GAG) binding, support recent findings suggesting that interactions between heparin and antimalarial drugs are largely due to electrostatic interactions, and represent the first reported GAG-induced CD signal of a bicyclic, aromatic compound. The association constant (∼10³ M⁻¹) between chloroquine and heparin was calculated from a UV titration curve and provided additional insight into the nature of the association between these two compounds.     

Absorption, circular dichroism, magnetic circular dichroism and emission study of rat kidney Cd,Cu-metallothionein

Absorption, circular dichroism (CD), magnetic circular dichroism (MCD) and emission spectra of rat liver and rat kidney cadmium-, zinc- and copper-containing metallothioneins (MT) are reported. The absorption, CD and MCD data of native rat kidney Cd,Cu-MT protein closely resemble data recorded for the rat liver Cd,Zn-MT. This suggests that the major features in all three spectra of the native Cd,Cu-MT are dominated by cadmium-related bands. The CD spectrum of the Cd,Cu-MT recorded at pH 2.7 has the same band envelope that is observed for a Cd,Cu-MT formed in vitro by titration of Cd,Zn-MT with Cu(I), suggesting that the copper occupies the zinc sites in Cd,Cu-MT formed both in vivo and, at low molar ratios, in vitro. Remetallalion of the metallothionein from low pH in the presence of both copper and cadmium results in considerably less cadmium bound to the protein than was present in the native sample. It is suggested that this is due to the effect of the distribution of the copper amongst all available binding sites, thus inhibiting cluster formation by the cadmium. Emission spectra are reported for the first time for a cadmium- and copper-containing metallothionein. An emission band at 610 nm is shown to be a sensitive indicator of Cu(I) binding to metallothionein. Both the native Cd,Cu-MT and a Cd,Cu-MT formed in vitro exhibit an excitation spectrum with a band in the copper-thiolate charge-transfer region.     

Capillary circular dichroism

Circular dichroism (CD) has become an increasingly important tool in the study of biological molecules as it enables structural information to be obtained nondestructively on solution-phase samples. However, sample requirements for CD are often seen as being too high with protein backbone measurements in standard cuvettes typically requiring ～100-300 μL of 0.1 mg/ml protein. To address this issue, we have designed a new form of CD sample holder, which reduces the sample requirements of the technique by two orders of magnitude, with a sample requirement of less than 3 μl. This sample saving has been achieved through the use of extruded quartz capillaries, the sample being held within the internal diameter of the quartz capillary through capillary action. The extruded quartz capillaries exhibit remarkably little birefringence, although still transmitting high energy UV circularly polarized light. The optics associated with capillaries were investigated. A configuration has been adopted with the light beam of the spectrophotometer being focused in front of the front face of the capillary using a biconvex lens and advantage being taken of the additional focusing effect of the capillary itself. The focusing is vital to the low wavelength performance of the cell, where we have acquired reliable data down to 180 nm using a Jasco J-815 spectrophotometer. The system performance was validated with Na[Co(EDDS)].H(2)O (EDDS = N,N-ethylenediaminedisuccinic acid), concanavalin A, lysozyme, and progesterone.     

Circular dichroism and magnetic circular dichroism of bismuth-induced,metallothionein-like proteins

Optical studies have been carried out on bismuth-containing proteins which were isolated from the livers and kidneys of rats following injections of BiCl₃. Absorption, circular dichroism and magnetic circular dichroism spectra of hepatic Bi,Zn-metallothionein 1 and 2 indicate that the spectra are dominated by transitions from the zinc thiolate chromophore. The data from the renal Bi,Cu-metallothionein 2 are quite different and it is suggested that these spectra involve a mixture of transitions from the bismuth and copper thiolate binding sites.     

Magnetic circular dichroism of netropsin and natural circular dichroism of the netropsin-DNA complex

We report the first measurement of the magnetic circular dichroism (MCD) of the basic polypeptide antibiotic netropsin (Nt). The MCD shows that the longest wavelength absorption band of Nt is the sum of more than one component and permits a radically new interpretation of the circular dichroism of the complex which Nt forms with DNA. We conclude that Nt has no major effect on the CD and thus the helical structure of the bases of the DNA to which it is bound. Thus the ability of Nt to inhibit the function of DNA polymerase, RNA polymerase, and the photoreactivating enzyme must be mediated by factors other than a distortion of the helical structure of the bases.     

A circular dichroism microspectrophotometer

A microscope capable of measuring the CD of intact single eukaryotic cells, DNA microcrystals, and other microscopic structures has been constructed and tested. It can measure the CD spectra in the 200- and 800-nm wavelength range and consists of a modification to a standard Cary 60 CD machine in combination with a Zeiss uv microspectrometer. Preliminary CD spectra of red blood cells and lymphocytes are presented.     

The protein circular dichroism data bank, a Web-based site for access to circular dichroism spectroscopic data

The Protein Circular Dichroism Data Bank (PCDDB) is a newly released resource for structural biology. It is a web-accessible (http://pcddb.cryst.bbk.ac.uk) data bank for circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectra and their associated experimental and secondary metadata, with links to protein sequence and structure data banks. It is designed to provide a public repository for CD spectroscopic data on macromolecules, to parallel the Protein Data Bank (PDB) for crystallographic, electron microscopic, and nuclear magnetic resonance spectroscopic data. Similarly to the PDB, it includes validation checking procedures to ensure good practice and the integrity of the deposited data. This paper reports on the first public release of the PCDDB, which provides access to spectral data that comprise standard reference datasets.     

Linear dichroism and circular dichroism in photosynthesis research

The efficiency of photosynthetic light energy conversion depends largely on the molecular architecture of the photosynthetic membranes. Linear- and circular-dichroism (LD and CD) studies have contributed significantly to our knowledge of the molecular organization of pigment systems at different levels of complexity, in pigment–protein complexes, supercomplexes, and their macroassemblies, as well as in entire membranes and membrane systems. Many examples show that LD and CD data are in good agreement with structural data; hence, these spectroscopic tools serve as the basis for linking the structure of photosynthetic pigment–protein complexes to steady-state and time-resolved spectroscopy. They are also indispensable for identifying conformations and interactions in native environments, and for monitoring reorganizations during photosynthetic functions, and are important in characterizing reconstituted and artificially constructed systems. This educational review explains, in simple terms, the basic physical principles, and theory and practice of LD and CD spectroscopies and of some related quantities in the areas of differential polarization spectroscopy and microscopy.     

Conformations of alanine-based peptides in water probed by FTIR, Raman, vibrational circular dichroism, electronic circular dichroism, and NMR spectroscopy

We have used a combination of FTIR, VCD, ECD, Raman, and NMR spectroscopies to probe the solution conformations sampled by H-(AAKA)-OH by utilizing an excitonic coupling model and constraints imposed by the 3JCalphaHNH coupling constants of the central residues to simulate the amide I' profile of the IR, isotropic Raman, anisotropic Raman, and VCD spectra in terms of a mixture of three conformations, i.e., polyproline II, beta-strand and right-handed helical. The representative coordinates of the three conformations were obtained from published coil libraries. Alanine was found to exhibit PPII fractions of 0.60 or greater, mixed with smaller fractions of helices and beta-strand conformations. Lysine showed no clear conformational propensity in that it samples polyproline II, beta-strand, and helical conformations with comparable probability. This is at variance with results obtained earlier for ionized polylysine, which suggest a high polyproline II propensity. We reanalyzed previously investigated tetra- and trialanine by combining published vibrational spectroscopy data with 3JCalphaHNH coupling constants and obtained again blends dominated by PPII with smaller admixtures of beta-strand and right-handed helical conformations. The polyproline II propensity of alanine was found to be higher in tetraalanine than in trialanine. For all peptides investigated, our results rule out a substantial population of turn-like conformations. Our results are in excellent agreement with MD simulations on short alanine peptides by Gnanakaran and Garcia [(2003) J. Phys. Chem. B 107, 12555-12557] but at variance with multiple MD simulations particularly for the alanine dipeptide.     

The circular dichroism spectrum of poly-L-acetoxyproline

We report the circular dichroism (CD) spectrum of poly-L acetoxyproline in trifluoroethanol, a solvent in which the form I to form II conformational isomerization occurs slowly enough to permit observation of the spectral changes. A comparison is made to poly-L proline. As judged by the similarity of the CD spectra, the conformations of the corresponding forms of the two polymers must be nearly the same. Transition assignments are proposed; these are shown to agree with the theoretical calculations of Pysh. There is a serious unexplained discrepancy between our solution data and those of Fasman for poly-L acetoxyproline.     

Vacuum ultraviolet circular dichroism of galactomannans

The chiroptical behaviour of plant galactomannans has been investigated by a combined vacuum ultraviolet circular dichroism (v.u.c.d) and optical rotatory dispersion (o.r.d.) approach. The samples studied were from Cyamopsis tetragonolobus (guar), Caesalpin'ia spinosa (tara), and Ceratonia siliqua (carob), with galactose levels of 39, 25 and 19%, respectively. V.u.c.d. solid film spectra have been recorded down to 140 nm, and in all cases show a positive band at 169 nm, and a negative band at 149 nm whose relative intensity increases systematically with decreasing galactose content. In solution only the lower energy band is accessible, and has the same position and width as in the solid state but substantially greater amplitude. Residual o.r.d. behaviour, after subtraction of the contribution from the 169 nm band (calculated by Kronig-Kramers transform of fitted c.d. parameters) shows a single band of the same position and width as the high energy solid state transition. The amplitude of both transitions in solution varies linearly with galactose content, consistent with simple additivity of contributions from the two different residues. Extrapolation to 0 and 100% galactose yields molarr ellipticities (10³ x deg cm² dmol^?1) at 169 and 149 nm, respectively, of +14 and ?33 for mannan, and ?8 and ?80 for galactan. Reduction in the net intensity of both transitions in the solid state, and to a lesser degree in carob gels, is attributed to conformational restriction of galactose by chain packing, with consequent increase in c.d. intensity from these residues and hence greater cancellation of mannose backbone contributions.     

Method of oriented circular dichroism.

We present a new method for determining the orientation of alpha-helical sections of proteins or peptides in membrane. To apply this method, membranes containing proteins must be prepared in a multilayer array. Circular dichroism (CD) spectra of the multilayer sample are then measured at the normal as well as oblique incident angles with respect to the bilayer planes; we call such spectra oriented circular dichroism (OCD). The procedure of OCD measurement, particularly the ways to avoid the spectral artifacts due to the effects of dielectric interfaces, linear dichroism and birefringence, and the method of data analysis are described in detail. To illustrate the method, we analyze the OCD of alamethicin in diphytanoylphosphatidylcholine multilayers. We conclude unambiguously that the helical section of alamethicin is parallel to the membrane normal when the sample is in the full-hydration state, but the helical section rotates to the plane of membrane when the sample is in a low-hydration state. We also obtained the parallel and perpendicular CD spectra of alpha-helix, and found them to be in agreement with previous theoretical calculations based on the exciton theory. These spectra are useful for analyzing protein orientations in future experiments.