Circular Dichroism Spectral Similarity Plots to Extend Validation and Correction to All Measured Wavelengths

2022 ◽  
pp. 000370282110571
Author(s):  
Curtis W. Meuse
Keyword(s):  
Circular Dichroism ◽  
Wavelength Range ◽  
Tertiary Structure ◽  
Spectral Intensity ◽  
Cd Spectra ◽  
Spectral Similarity ◽  
Interlaboratory Validation ◽  
Calibration Techniques ◽  
Spectral Intensities ◽  
Circular Dichroïsm

Interlaboratory comparisons of circular dichroism (CD) spectra are useful for developing confidence in the measurements associated with optically active molecules. These measurements also help define the higher-order (secondary and tertiary) structure of biopolymers. Unfortunately, the extent of the validity of these measurements has been unclear. In this work, a method is described to extend CD validation over the entire observed wavelength range using what will be called spectral similarity plots. The method involves plotting, wavelength by wavelength, all measured spectral intensities of a sample at one concentration against the intensity values of the same material at a different concentration or pathlength. These spectral similarity plots validate the instrument in terms of spectral shape and whether the shape is shifted in intensity and/or in wavelength. This comparison tests the linearity of instrument’s signal, the balance of its left and right polarizations, its wavelengths, and its spectral intensity scales. When the process is applied to materials with accepted and archived intensity values, the method can be linked to older single-wavelength and double-wavelength calibration techniques. Further, spectral similarity testing of CD spectra from samples with different concentrations run in different labs suggests that improved interlaboratory validation of CD data is possible. Since a database of archival CD measurements is available online, spectral similarity comparisons could possibly provide the ability to compare linearity, polarization balance, wavelength, and spectral intensity between all current CD instruments. If the preliminary results published here prove robust and transferable, then comparisons of full-wavelength range spectra to archived data using spectral similarity plots should become part of the standard process to validate and calibrate the performance of CD instruments.

scholarly journals Measurement of Circular Dichroism Spectra without Control of a Phase Modulator using Retardation Domain Analysis

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1418
Author(s):  
Hiroshi Satozono
Keyword(s):  
Circular Dichroism ◽  
Wavelength Range ◽  
Linear Dichroism ◽  
Domain Analysis ◽  
Phase Modulator ◽  
Cd Spectra ◽  
Circular Dichroism Spectra ◽  
Circular Dichroïsm ◽  
Modulation Degree

This study investigated the measurement of circular dichroism (CD) spectra without controlling a phase modulator. In a conventional CD system, the peak retardation of the phase modulator must remain constant over the observed wavelength range. Thus, the phase modulator must be controlled to maintain an appropriate modulation degree at an observed wavelength. In contrast, CD obtained using retardation domain analysis is not affected by peak retardation. Consequently, CD spectra can be measured without control of the phase modulator, which was experimentally demonstrated in this study. Additionally, linear dichroism spectra were obtained using retardation domain analysis.

scholarly journals Messung und Berechnung der CD-Spektren der Biaryl-Alkaloide Ancistrocladein und Dioncophyllein A [1] / Detection and Calculation of the CD Spectra from the Biaryl Alkaloids Ancistrocladeine and Dioncophylleine A [1]

1993 ◽  
Vol 48 (2) ◽  
pp. 140-148 ◽  
Author(s):  
J. Fleischhauer ◽  
A. Koslowski ◽  
B. Kramer ◽  
E. Zobel ◽  
G. Bringmann ◽  
...  
Keyword(s):  
Circular Dichroism ◽  
Absolute Configuration ◽  
Cd Spectra ◽  
Circular Dichroïsm

AbstractThe circular dichroism (CD) of the biaryls ancistrocladeine and dioncophylleine A has been studied. The CNDO/S method in combination with a Boltzmann weighting o f different structures using AM 1 energies has been applied to reproduce the experimental CD spectra o f the two alkaloids with known absolute configuration at with those o f the exciton chirality method.

scholarly journals The effects of Ca2+ and Cd2+ on the secondary and tertiary structure of bovine testis calmodulin. A circular-dichroism study

1986 ◽  
Vol 238 (2) ◽  
pp. 485-490 ◽  
Author(s):  
S R Martin ◽  
P M Bayley
Keyword(s):  
Circular Dichroism ◽  
Conformational Changes ◽  
Metal Ion ◽  
Tertiary Structure ◽  
Thermal Unfolding ◽  
Apparent Effect ◽  
Thermally Induced ◽  
Circular Dichroïsm ◽  
Secondary And Tertiary Structure

Near-u.v. and far-u.v. c.d. spectra of bovine testis calmodulin and its tryptic fragments (TR1C, N-terminal half, residues 1-77, and TR2C, C-terminal half, residues 78-148) were recorded in metal-ion-free buffer and in the presence of saturating concentrations of Ca2+ or Cd2+ under a range of different solvent conditions. The results show the following: if there is any interaction between the N-terminal and C-terminal halves of calmodulin, it has not apparent effect on the secondary or tertiary structure of either half; the conformational changes induced by Ca2+ or Cd2+ are substantially greater in TR2C than they are in TR1C; the presence of Ca2+ or Cd2+ confers considerable stability with respect to urea-induced denaturation, both for the whole molecule and for either of the tryptic fragments; a thermally induced transition occurs in whole calmodulin at temperatures substantially below the temperature of major thermal unfolding, both in the presence and in the absence of added metal ion; the effects of Cd2+ are identical with those of Ca2+ under all conditions studied.

Circulardichroismusuntersuchungen von Polyalkohol- und Zucker-Vanadat(V)-Komplexen / Circular Dichroism Studies of Polyalcohol and Sugar Vanadate(V) Complexes

1989 ◽  
Vol 44 (11) ◽  
pp. 1464-1472 ◽  
Author(s):  
Hermann Bauer ◽  
Jeanine Brun ◽  
Alexius R. Hernanto ◽  
Wolfgang Voelter ◽  
Spyridon Paraskewas
Keyword(s):  
Circular Dichroism ◽  
Wavelength Range ◽  
Optically Active ◽  
Hydroxyl Groups ◽  
Pyranose Ring ◽  
Cotton Effects ◽  
Circular Dichroïsm

The complexes of tetravanadate ions with optically active polyols and carbohydrates with suitable steric properties show up to four separate cotton effects in the wavelength range of λ = 200-350 nm. Thus it is possible to classify pyranoses into four groups according to their circular dichroitic behaviour and determine the configuration and the conformation of the hydroxyl groups attached to the pyranose ring.

scholarly journals Water-Mediated Electronic Structure of Oligopeptides Probed by Their UV Circular Dichroism, Absorption Spectra, and Time-Dependent DFT Calculations

2020 ◽  
Author(s):  
Anshuman Kumar ◽  
Siobhan E. Toal ◽  
David DiGuiseppi ◽  
Reinhard Schweitzer-Stenner ◽  
Bryan Wong
Keyword(s):  
Circular Dichroism ◽  
Absorption Spectra ◽  
Density Functional ◽  
Time Dependent ◽  
Water Model ◽  
Cd Spectra ◽  
Influence Of Water ◽  
Explicit Consideration ◽  
A Charge ◽  
Circular Dichroïsm

<p>We investigate the UV absorption spectra of a series of cationic GxG (where x denotes a guest residue) peptides in aqueous solution and find that the spectra of a subset of peptides with x = A, L, I, K, N, and R (and, to a lesser extent, peptides with x = D and V) vary as a function of temperature. To explore whether or not this observation reflects conformational dependencies, we carry out time-dependent density functional calculations for the polyproline II (pPII) and β-strand conformations of a limited set of tripeptides (x = A, V, I, L, and R) in implicit and explicit water. We find that the calculated CD spectra for pPII can qualitatively account for the experimental spectra irrespective of the water model. The reproduction of the <i>β</i>-strand UV-CD spectra, however, requires the explicit consideration of water. Based on the calculated absorption spectra, we explain the observed temperature dependence of the experimental spectra as being caused by a reduced dispersion (larger spectral density) of the overlapping NV<sub>2</sub> band and the influence of water on electronic transitions in the β-strand conformation. Contrary to conventional wisdom, we find that both the NV<sub>1</sub> and NV<sub>2</sub> band are the envelopes of contributions from multiple transitions that involve more than just the HOMOs and LUMOs of the peptide groups. A natural transition orbital analysis reveals that some of the transitions with significant oscillator strength have a charge-transfer character. The overall manifold of transitions, in conjunction with their strengths and characters, depends on the peptide’s backbone conformation, peptide hydration, and also on the side chain of the guest residue. It is particularly noteworthy that molecular orbitals of water contribute significantly to transitions in <i>β</i>-strand conformations. Our results reveal that peptide groups, side chains, and hydration shells must be considered as an entity for a physically valid characterization of UV absorbance and circular dichroism. </p>

scholarly journals BeStSel: From Secondary Structure Analysis to Protein Fold Prediction by Circular Dichroism Spectroscopy

2020 ◽  
pp. 175-189
Author(s):  
András Micsonai ◽  
Éva Bulyáki ◽  
József Kardos
Keyword(s):  
Circular Dichroism ◽  
Secondary Structure ◽  
Classical Method ◽  
Cd Spectroscopy ◽  
Protein Fold ◽  
Cd Spectra ◽  
Secondary Structure Analysis ◽  
Β Sheets ◽  
Α Helix ◽  
Circular Dichroïsm

Abstract Far-UV circular dichroism (CD) spectroscopy is a classical method for the study of the secondary structure of polypeptides in solution. It has been the general view that the α-helix content can be estimated accurately from the CD spectra. However, the technique was less reliable to estimate the β-sheet contents as a consequence of the structural variety of the β-sheets, which is reflected in a large spectral diversity of the CD spectra of proteins containing this secondary structure component. By taking into account the parallel or antiparallel orientation and the twist of the β-sheets, the Beta Structure Selection (BeStSel) method provides an improved β-structure determination and its performance is more accurate for any of the secondary structure types compared to previous CD spectrum analysis algorithms. Moreover, BeStSel provides extra information on the orientation and twist of the β-sheets which is sufficient for the prediction of the protein fold. The advantage of CD spectroscopy is that it is a fast and inexpensive technique with easy data processing which can be used in a wide protein concentration range and under various buffer conditions. It is especially useful when the atomic resolution structure is not available, such as the case of protein aggregates, membrane proteins or natively disordered chains, for studying conformational transitions, testing the effect of the environmental conditions on the protein structure, for verifying the correct fold of recombinant proteins in every scientific fields working on proteins from basic protein science to biotechnology and pharmaceutical industry. Here, we provide a brief step-by-step guide to record the CD spectra of proteins and their analysis with the BeStSel method.

Chiral 2D Organic Inorganic Hybrid Perovskite with Circular Dichroism Tunable Over Wide Wavelength Range

2020 ◽  
Vol 142 (9) ◽  
pp. 4206-4212 ◽  
Author(s):  
Jihoon Ahn ◽  
Sunihl Ma ◽  
Ji-Young Kim ◽  
Jihoon Kyhm ◽  
Wooseok Yang ◽  
...  
Keyword(s):  
Circular Dichroism ◽  
Wavelength Range ◽  
Inorganic Hybrid ◽  
Hybrid Perovskite ◽  
Wide Wavelength Range ◽  
Circular Dichroïsm
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