Directly Probing Intermolecular Structural Change of a Core Fragment of β2-Microglobulin Amyloid Fibrils with Low-Frequency Raman Spectroscopy

Raman Microspectroscopy of Hair: Low-Frequency Markers of Protein Secondary Structure

Low-frequency intervals that can be used to study the secondary structure of proteins are determined. Compared are Raman spectra of keratins from unpigmented human hair, measured in two experimental configurations: with excitation radiation coaxial with the hair and perpendicular to it. Based on the polarization sensitivity, the bands peaked at 150 and 221 cm-1 are assigned to vibrations of α-helical structures. The comparison of Raman spectra of hair fragments with different contents of secondary structure elements shows that the vibrations of β-structure are manifested in a spectral interval of 270-340 cm-1. The results obtained for a particular object (hair keratin) can be used in the study of the secondary structure of proteins.

pH-controlled stacking direction of the β-strands in peptide fibrils

Peptides provide a framework for generating functional biopolymers. In this study, the pH-dependent structural changes in the 21-29 fragment peptide of β2-microglobulin (β2m21-29) during self-aggregation, i.e., the formation of an amyloid fibril, were discussed. The β-sheet structures formed during parallel stacking under basic conditions (pH ≥ 7.7) adopted an anti-parallel stacking configuration under acidic conditions (pH ≤ 7.6). The parallel and anti-parallel β-sheets existed separately at the intermediate pH (pH = 7.6-7.7). These results were attributed to the rigidity of the β-sheets in the fibrils, which prevented the stable hydrogen bonding interactions between the parallel and anti-parallel β-sheet moieties. This observed pH dependence was ascribed to two phenomena: (i) the pH-dependent collapse of the β2m21-29 fibrils, which consisted of 16 ± 3 anti-parallel β-sheets containing a total of 2000 β-strands during the deprotonation of the NH3+ group (pKa = 8.0) of the β-strands that occurred within 0.7 ± 0.2 strands of each other and (ii) the subsequent formation of the parallel β-sheets. We propose a framework for a functional biopolymer that could alternate between the two β-sheet structures in response to pH changes.

The noncoincidence phenomenon of acetonylacetone CO stretching in a binary mixture and the aggregation-induced split theory

This article aims to correlate the noncoincidence effect phenomenon with the aggregation state of acetylacetone CO stretching in a binary mixture. CO stretching noncoincidence effect (NCE) was observed not only between IR and Raman spectra but also between the isotropic and anisotropic Raman spectra of acetonylacetone. The difference in CO stretching wavenumbers of the isotropic and anisotropic Raman spectra (NCE value) in a binary mixture at different concentrations has been calculated. We found that both isotropic and anisotropic Raman wavenumbers of CO stretching increase with the dilution of acetonylacetone by CCl₄ while the NCE value decreases. These noncoincidence and concentration effect phenomena seem to go against the quantum theory. Herein, we proposed an aggregation-induced split (AIS) model to explain the NCE phenomenon and concentration effect. The experimental data were consistent with the DFT calculations performed at the B3LYP-D3/6-311++G (d,p) levels based on the proposed model. The dynamics of transformation from monomers to an aggregated structure can be easily controlled by tuning the concentration. Solvent dependent experiments show that the value of NCE decreased with the increase of the solvent dielectric constant at the same concentration, which is in accordance with Logan's theory.

Both the isotropic and anisotropic Raman wavenumbers of the CO stretch increase with the dilution of acetonylacetone by CCl₄, while the separation between isotropic and anisotropic Raman wavenumbers (Δυ) decrease.

Investigation of the cis–trans structures and isomerization of oligoprolines by using Raman spectroscopy and density functional theory calculations: solute–solvent interactions and effects of terminal positively charged amino acid residues

Using low-wavenumber Raman spectroscopy in combination with theoretical calculations via solid-state density functional theory (DFT)-D3, we studied the vibrational structures and interaction with solvent of poly-l-proline and the oligoproline P12 series. The P12 series includes P12, the positively charged amino acid residue (arginine and lysine) N-terminus proline oligomers RP11 and KP11, and the C-terminus P11R and P11K. We assigned the spring-type phonon mode to 74–76 cm⁻¹ bands for the PPI and PPII conformers and the carbonyl group ring-opening mode 122 cm⁻¹ in the PPI conformer of poly-l-proline. Amide I and II were assigned based on the results of mode analysis for O, N, and C atom displacements. The broad band feature of the H-bond transverse mode in the Raman spectra indicates that the positively charged proline oligomers PPII form H-bonds with water in the solid phase, whereas P12 is relatively more hydrophobic. In propanol, the PPI conformer of the P12 series forms less H-bond network with the solvent. The PPII conformer exhibits a distinct Raman band at 310 cm⁻¹, whereas the PPI has bands at 365, 660, and 960 cm⁻¹ with reasonable intensity that can be used to quantitatively determine these two conformational forms. The 365 cm⁻¹ mode comprising the motion of a C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> O group turning to the helix axis was used to monitor the isomerization reaction PPI ↔ PPII. In pure propanol, RP11 and KP11 were found to have mostly PPI present, but P11R and P11K preferred PPII. After adding 20% water, the PPI in P11R and P11K was completely converted to PPII, whereas a small fraction of PPI remained in RP11 and KP11. The substituted positively charged amino acid affected the balance of the PPI/PPII population ratio.

The low-wavenumber Raman spectra in combination with theoretical calculations via solid-state density functional theory (DFT)-D3 are displayed. The vibrational structures and interaction with solvent of poly-l-proline and the oligoproline P12 series are identified.