Going deep into protein secondary structure with synchrotron radiation circular dichroism spectroscopy

Abstract

Circular dichroism (CD) spectroscopy is a fast, powerful, well-established, and widely used analytical technique in the biophysical and structural biology community to study protein secondary structure and to track changes in protein conformation in different environments. The use of the intense light of a synchrotron beam as the light source for collecting CD measurements has emerged as an enhanced method, known as synchrotron radiation circular dichroism (SRCD) spectroscopy, that has several advantages over the conventional CD method, including a significant spectral range extension for data collection, deeper access to the lower limit (cut-off) of conventional CD spectroscopy, an improved signal-to-noise ratio to increase accuracy in the measurements, and the possibility to collect measurements in highly absorbing solutions. In this review, we discuss different applications of the SRCD technique by researchers from Latin America. In this context, we specifically look at the use of this method for examining the secondary structure and conformational behavior of proteins belonging to the four main classes of the hierarchical protein domain classification CATH (Class, Architecture, Topology, Homology) database, focusing on the advantages and improvements associated with SRCD spectroscopy in terms of characterizing proteins composed of different structural elements.

Structural diversity in the Mycobacteria DUF3349 superfamily

“…Note that while the 208 nm band minimum for both proteins superpose, the frequency of the longer wavelength minimum band differ for the two proteins, at 220 nm for MSMEG_1063 versus 228 nm for MSMEG_1066. A potential explanation for the red‐shift may be excitation interactions of adjacent conserved tryptophan residues (W96) at two out of the four interfaces in the MSMEG_1066 tetramer (Figure c) that do not exist in the MSMEG_1063 monomer . There is also a difference in the relative intensity of the double minimum bands which are almost equal for MSMEG_1063 but skewed in favor of the shorter wavelength band for MSMEG_1066.…”

“…A potential explanation for the red-shift may be excitation interactions of adjacent conserved tryptophan residues (W96) at two out of the four interfaces in the MSMEG_1066 tetramer ( Figure 4c) that do not exist in the MSMEG_1063 monomer. 26 There is also a difference in the relative intensity of the double minimum bands which are almost equal for MSMEG_1063 but skewed in favor of the shorter wavelength band for MSMEG_1066. An increase in the ratio of the intensity of the minimum between 200 and 210 nm and the minimum near 222 nm has been used as a gauge of helical content increase (R2), 27,28 however, Table 1 shows that there is no correlation with the R2 value and percent helical secondary structure observed in the DUF3349 structures.…”

The Secondary Structure of a Major Wine Protein is Modified upon Interaction with Polyphenols

“…The high photon flux and brilliance of the synchrotron radiation used in SRCD spectroscopy allows for obtaining a high signal to noise ratio when compared to bench-top instruments. Additionally, a photo-denaturation of the ordered proteins is observed when consecutive repeated scans are collected, providing useful information on the protein photo-stability as well as on the influence of ligands and medium composition [39]. These techniques have been adopted here for the investigation of the interactions of a major wine protein (VVTL1) with a total wine tannin extract (WTE) and five individual phenolic compounds that were chosen based on their structural diversity.…”

Sample Volume Reduction Using the Schwarzschild Objective for a Circular Dichroism Spectrophotometer and an Application to the Structural Analysis of Lysine-36 Trimethylated Histone H3 Protein

“…The use of synchrotron radiation (SR) as a light source for CD spectroscopy allows more precise structural information to be obtained, because an SR beam can expand the measurement region to the vacuum-ultraviolet (VUV) region where additional CD peaks are often observed. Indeed, synchrotron radiation circular dichroism (SRCD) spectroscopy has produced successful outcomes over the past two decades [ 2 ]. It has also become desirable to reduce the sample volume with the increasing interest in scarce proteins that are difficult to synthesize.…”