Identification of a new function model for the AC-impedance of thermally evaporated undoped selenium films using the Eigen-coordinates method

The experimental AC-impedance data of undoped amorphous and polycrystalline selenium films were taken at T = 300K in the frequency range 100 Hz-10 kHz in the dark and under band-gap illumination. The data were analyzed using the Eigen-coordinates method in conjunction with a 'separation' procedure without prior use of equivalent circuits. A unified circuit model with generalized impedances was recognized to parameterize well the observed AC-impedance behavior. The features of this electrical model were linked to the fractality of the heterogeneous structural regions in these selenium specimens via one or two recap elements, each represented by a complex impedance of fractional power-law frequency behavior. These recap elements reflect the electric properties of scale-invariant circuits of self-affine normal (ideal) resistor-capacitor (RC) cells of the Cauer/Forster type. © 2001 Elsevier Science B.V. All rights reserved

DichroMatch: a website for similarity searching of circular dichroism spectra

Circular dichroism (CD) spectroscopy is a widely used method for examining the structure, folding and conformational changes of proteins. A new online CD analysis server (DichroMatch) has been developed for identifying proteins with similar spectral characteristics by detecting possible structurally and functionally related proteins and homologues. DichroMatch includes six different methods for determining the spectral nearest neighbours to a query protein spectrum and provides metrics of how similar these spectra are and, if corresponding crystal structures are available for the closest matched proteins, information on their secondary structures and fold classifications. By default, DichroMatch uses all the entries in the Protein Circular Dichroism Data Bank (PCDDB) for its comparison set, providing the broadest range of publicly available protein spectra to match with the unknown protein. Alternatively, users can download or create their own specialized data sets, thereby enabling comparisons between the structures of related proteins such as wild-type versus mutants or homologues or a series of spectra of the same protein under different conditions. The DichroMatch server is freely available at http://dichromatch.cryst.bbk.ac.uk

Recognition of a new permittivity function for glycerol by the use of the eigen-coordinates method

Measurements of real and imaginary parts of the relative complex permittivity of glycerol were carried out in the frequency range 1 mHz-1 MHz at different temperatures between 188 and 263 K. The permittivity data have been analyzed thoroughly by a new data curve-fitting approach that involves the so-called eigen-coordinates method in conjunction with a separation procedure and the inverse permittivity formulas. A new single permittivity function, based on the so-called recap element picture for a self-similar (fractal) structure, has been recognized to describe well such data over the entire frequency range studied. The recognized dielectric function enabled us to infer an electrical equivalent-circuit network for the glycerol sample studied that involves a series combination of two recap elements, reflecting the existence of two different dielectric relaxation processes in glycerol. The temperature dependence of the relaxation times τ1(T) and τ2(T) entering into the identified permittivity function was found to obey nearly an Arrhenius behaviour with activation energies E1 ≈ 114 kJ/mol and E2 ≈ 94 kJ/mol. The recognized permittivity function can be justified by presuming that the processes represented by the recap elements characterized by the parameters (ν1, τ1, E1) and (ν2, τ2, E2) are linked to 'donor-like' and 'acceptor-like' charges formed from the infinite hydroxyl hydrogen bonds. © 2002 Elsevier Science B.V. All rights reserved

Stabilisation of Na,K-ATPase structure by the cardiotonic steroid ouabain

Cardiotonic steroids such as ouabain bind with high affinity to the membrane-bound cation-transporting P-type Na,K-ATPase, leading to complete inhibition of the enzyme. Using synchrotron radiation circular dichroism we show that the enzyme-ouabain complex is less susceptible to thermal denaturation (unfolding) than the ouabain-free enzyme, and this protection is observed with Na,K-ATPase purified from pig kidney as well as from shark rectal glands. It is also shown that detergent-solubilised preparations of Na,K-ATPase are stabilised by ouabain, which could account for the successful crystallisation of Na,K-ATPase in the ouabain-bound form. The secondary structure is not significantly affected by the binding of ouabain. Ouabain appears however, to induce a reorganization of the tertiary structure towards a more compact protein structure which is less prone to unfolding; recent crystal structures of the two enzymes are consistent with this interpretation. These circular dichroism spectroscopic studies in solution therefore provide complementary information to that provided by crystallography

ValiDichro: a website for validating and quality control of protein circular dichroism spectra

Circular dichroism (CD) spectroscopy is widely used in structural biology as a technique for examining the structure, folding and conformational changes of proteins. A new server, ValiDichro, has been developed for checking the quality and validity of CD spectral data and metadata, both as an aid to data collection and processing and as a validation procedure for spectra to be included in publications. ValiDichro currently includes 25 tests for data completeness, consistency and quality. For each test that is done, not only is a validation report produced, but the user is also provided with suggestions for correcting or improving the data. The ValiDichro server is freely available at http://valispec.cryst.bbk.ac.uk/circularDichroism/ValiDichro/upload.html

Circular dichroism spectroscopy of membrane proteins

Circular dichroism (CD) spectroscopy is a well-established technique for studying the secondary structures, dynamics, folding pathways, and interactions of soluble proteins, and is complementary to the high resolution but generally static structures produced by X-ray crystallography, NMR spectroscopy, and cryo electron microscopy. CD spectroscopy has special relevance for the study of membrane proteins, which are difficult to crystallise and largely ignored in structural genomics projects. However, the requirement for membrane proteins to be embedded in amphipathic environments such as membranes, lipid vesicles, detergent micelles, bicelles, oriented bilayers, or nanodiscs, in order for them to be soluble or dispersed in solution whilst maintaining their structure and function, necessitates the use of different experimental and analytical approaches than those employed for soluble proteins. This review discusses specialised methods for collecting and analysing membrane protein CD data, highlighting where protocols for soluble and membrane proteins diverge