Biomolecular studies by circular dichroism

Abstract

In this review, we shall outline the basic principles of circular dichroism (CD) indicating the types of structural information relevant to the study of biomolecules, such as proteins or DNA. We are mainly interested to show the utility of this technique to study protein-ligand, DNA-ligand and protein-DNA interactions.

SilE is an intrinsically disordered periplasmic “molecular sponge” involved in bacterial silver resistance

“…With strong negative signals around 200 nm, the spectrum obtained for apo ‐SilE in 10 mM HEPES, 20mM NaF, pH7.5, is typical of an unstructured, random coil polypeptide. Slight negative shoulders on the CD spectrum, at 207 and 221 nm, are consistent with a minor fraction (<20%) of α‐helical secondary structure for apo‐ SilE (Sreerama et al ., ; Greenfield, ; Dodero et al ., ). However, these bands become considerably more prominent (∼54%) when bound to Ag + in the holo‐ SilE, with a strong negative band at 207 nm, a weaker negative ellipticity at 221 nm and a strong positive band at 190 nm (Fig.…”

“…A scan of buffer alone was subtracted from the protein curve. Data were converted to molar CD per residue and spectra analysis was carried out by comparing the profile of the obtained curve to those illustrated and quantified in literature (Sreerama et al ., ; Greenfield et al ., ; Dodero et al ., ). Secondary structure percentages were calculated using the DichroWeb (Lobley et al ., ) interfaces analysis programme CONTINLL, which implements the locally linearised algorithm in selecting protein sets from the reference database (Provencher and Glockner, ; Van Stokkum et al ., ; Sreerama and Woody, ).…”

Peptide Amphiphile Supramolecular Nanostructures as a Targeted Therapy for Atherosclerosis

“…Dynamic light scattering was used as an indicator of nanofiber formation, as higher β‐sheet content is correlated with increased light scattering . PA nanofiber formation was indicated by significantly higher molar light scattering values than peptide controls at both 25 °C ( p < 0.034) and at 37 °C ( p < 0.004), as shown in Figure C.…”

“…The ApoA1 PA co‐assembly retained the alpha‐helical secondary structure of the targeting sequence alone (4F peptide), evidenced by the negative ellipticity peaks near 208 and 222 nm ( Figure 1 A). The ApoA1 PA also showed β‐sheet character with a shifted positive ellipticity peak, an effect likely caused by co‐assembly with the diluent PA, which showed strong β‐sheet character, demonstrated by the presence of a broad negative peak near 218 nm . In contrast, the secondary structure of PA nanofibers co‐assembled with a scrambled targeting sequence (Scr PA) closely resembled the β‐sheet structure of the diluent PA.…”

“…The ApoA1 PA also showed β-sheet character with a shifted positive ellipticity peak, an effect likely caused by coassembly with the diluent PA, which showed strong β-sheet character, demonstrated by the presence of a broad negative peak near 218 nm. [16] In contrast, the secondary structure of PA nanofibers co-assembled with a scrambled targeting sequence (Scr PA) closely resembled the β-sheet structure of the diluent PA. Incorporating LXR into either the ApoA1 PA co-assembly (ApoA1-LXR PA) or the 4F peptide (4F-LXR) dampened the alpha-helical structure, as shown in Figure 1B and Figure S1, Supporting Information.…”