Residue‐Specific Dynamics and Local Environmental Changes in Aβ40 Oligomer and Fibril Formation

Abstract

Elucidating local dynamics of protein aggregation is crucial for understanding the mechanistic details of protein amyloidogenesis. Herein, we studied the residue-specific dynamics and local environmental changes of Ab40 along the course of aggregation by using para-cyanophenylalanine (PheCN) as a fluorescent and vibrational probe. Our results show that the PheCN residues introduced at various positions all exhibited an immediate decay of fluorescence intensity, indicating a relatively synergistic process in early oligomer formation. The fast decreases in the fluorescence intensities of residues 19 and 20 in the central hydrophobic core region and residue 10 in the N-terminal region suggest that they play crucial roles in the formation of the oligomeric core. The PheCN4 residue exhibits a remarkably slower decrease in fluorescence intensity, implicating its dynamic conformational characteristics in oligomer and fibril formation. Our results also suggest that the N-terminal residues in fibrils are surrounded by a relatively hydrophobic local environment, as opposed to being solvated.

Interference with Amyloid-β Nucleation by Transient Ligand Interaction

“…In fact, the content of β-sheet structures in Aβ42 and D3 complexes (~5%) is much lower than that observed for the Aβ42 dimer (~15%) in previous simulations in the same force field [50]. The rather unordered structure of Aβ42 monomers in complex with D3 makes them incapable of participating in Aβ nuclei growth and amplification processes encompassing the accumulation of a certain amount of ordered structures [51,52,53]. The experimental data, together with MD simulations, also reveal that when bound to D3, Aβ42 maintains unordered structures similar to those in free solution.…”

Vibrational Approach to the Dynamics and Structure of Protein Amyloids

“…For instance, after amyloid formation, the peak of the CN stretching band of the Phe CN 19 residue shows a significant red shift from 2237 cm −1 to 2229 cm −1 (Aβ 1–23 M2, Figure 4), indicating a more hydrophobic and less solvent accessible environment for the CN probe in fibrillar structure [163]; whereas the CN band of the Phe CN 20 residue only shows a red shift of only 2 cm −1 of the peak upon aggregation (Aβ 1–23 M3, Figure 4), suggesting a much more polar local environment of this residue in fibrils. In a similar study of the Aβ 1–40 , the CN stretching vibration band in the Raman spectra of all the mutants is centered at approximately 2229 cm −1 after aggregation, suggesting a dehydrated and hydrophobic local environment at the mutating positions in the amyloids [173].…”

Deuteron Solid‐State NMR Relaxation Measurements Reveal Two Distinct Conformational Exchange Processes in the Disordered N‐Terminal Domain of Amyloid‐β Fibrils

“…[10][11][12][13][14][15][16] It contains the main binding and regulatory sites for interaction with metals [17][18][19][20][21][22][23] as well as several regulatory sites that have recently been implicated to be controlled via post-translational modifications.. [14][15][24][25][26][27] Multiple works have revealed the flexibility of the N-terminal domain. [5][6][7][28][29][30]31,[32][33][34][35][36] Site-specific studies of the dynamics of the insoluble aggregates of Aβ are rare due to challenges in obtaining the necessary resolution and sensitivity in the solid non-crystalline state. [28,[37][38][39][40][41][42] Of note are the works of Fawzi et al, [43][44] who utilized solution NMR saturation transfer approaches to probe the binding of monomeric Aβ to the surface of protofibrils and detected several states as part of the pathways of the binding of the monomer to protofibrils.…”

“…. Multiple works have revealed the flexibility of the N‐terminal domain . Site‐specific studies of the dynamics of the insoluble aggregates of Aβ are rare due to challenges in obtaining the necessary resolution and sensitivity in the solid non‐crystalline state .…”