Understanding amyloid fibril formation using protein fragments: structural investigations via vibrational spectroscopy and solid-state NMR

Abstract

It is well established that amyloid proteins play a primary role in neurodegenerative diseases. Alzheimer's, Parkinson's, type II diabetes, and Creutzfeldt-Jakob's diseases are part of a wider family encompassing more than 50 human pathologies related to aggregation of proteins. Although this field of research is thoroughly investigated, several aspects of fibrillization remain misunderstood, which in turn slows down, or even impedes, advances in treating and curing amyloidoses. To solve this problem, several research groups have chosen to focus on short fragments of amyloid proteins, sequences that have been found to be of great importance for the amyloid formation process. Studying short peptides allows bypassing the complexity of working with full-length proteins and may provide important information relative to critical segments of amyloid proteins. To this end, efficient biophysical tools are required. In this review, we focus on two essential types of spectroscopic techniques, i.e., vibrational spectroscopy and its derivatives (conventional Raman scattering, deep-UV resonance Raman (DUVRR), Raman optical activity (ROA), surface-enhanced Raman spectroscopy (SERS), tip-enhanced Raman spectroscopy (TERS), infrared (IR) absorption spectroscopy, vibrational circular dichroism (VCD)) and solid-state nuclear magnetic resonance (ssNMR). These techniques revealed powerful to provide a better atomic and molecular comprehension of the amyloidogenic process and fibril structure. This review aims at underlining the information that these techniques can provide and at highlighting their strengths and weaknesses when studying amyloid fragments. Meaningful examples from the literature are provided for each technique, and their complementarity is stressed for the kinetic and structural characterization of amyloid fibril formation.

Keywords: Amyloid fragments; IR spectroscopy; Polymorphism; Raman spectroscopy; VCD spectroscopy; ssNMR.

Fig. 1

Typical hierarchical description of the amyloid formation steps, from the single β-strand to the mature fibril (from secondary to quaternary structure). Molecular variations occurring at any level affect all the subsequent formation steps and thus are sources of fibril polymorphism. Figure based on a similar figure reported by Fitzpatrick et al.

Fig. 2

Typical IR spectra of parallel (upper spectrum) and antiparallel (lower spectrum) intermolecular β-sheets. The major component is at low wavenumbers (blue-shaded area) and the less intense one at higher wavenumbers (red asterisks). Figure based on a similar figure reported by Sarroukh et al.

Fig. 3

IR amide I bands (a) and corresponding VCD spectra (b) of HET-s_218–289 amyloid fibrils at pH 2.0 (red) and pH 6.0 (blue). Fibrils initially formed at pH 2.0 exhibited a left-handed twist, and when the pH was increased to 6.0, the chirality of the fibrils reversed, as proved by the inversion of the VCD signal. This example highlights the complementarity of VCD to IR, where spectra at both pHs look very alike. Reprinted with permission from Shanmugasundaram et al. . Copyright © 2015 American Chemical Society

Fig. 4

a Simplified correlation pulse sequence schemes, with indirect chemical shift evolution periods indicated by black arrows. b Intramolecular magnetization flows corresponding to the color-matching correlation pulse sequences presented in (a). 2D cross-sections of ¹⁵N- (blue and red) and ¹³C′-linked (orange and cyan) H^α-detected spectra of c HET-s_218–289, d GB1, e AP205CP and the respective intra-residue C^β-C^α-H^α correlations for AP205 (f). Reprinted with permission from Stanek et al. . Copyright © 2016 by John Wiley & Sons, Inc.

Fig. 5

Lateral view (a) and cross-section (b) of TTR_105–115 protofilament. β-Sheets are parallel and in-register along the fibril axis (a) and stacked in an antiparallel manner at the protofilament interface (b). Distances indicated in (b) were obtained via TEDOR measurements (black) and R²TRW (red). Reprinted with permission from Debelouchina et al. . Copyright © 2013 American Chemical Society