Growth kinetics of amyloid-like fibrils: An integrated atomistic simulation and continuum theory approach

Exploring Abeta42 monomer diffusion dynamics on fibril surfaces through molecular simulations

This study provides critical insights into the role of surface-mediated processes in Alzheimer's disease, with implications for the aggregation of Abeta42 peptides. Employing coarse-grained molecular dynamics simulations, we focus on elucidating the molecular intricacies of these processes beyond primary nucleation. Central to our investigation is the analysis of a freely diffusing Abeta42 monomer on preformed fibril structures. We conduct detailed calculations of the monomer's diffusion coefficient on fibril surfaces (as a one-dimensional case), along with various monomer orientations. Our findings reveal a strong and consistent correlation between the monomer's diffusion coefficient and its orientation on the surface. Further analysis differentiates the effects of parallel and perpendicular alignments with respect to the fibril axis. Additionally, we explore how different fibril surfaces influence monomer dynamics by comparing the C-terminal and N-terminal surfaces. We find that the monomer exhibits faster diffusion coefficients on the C-terminal surface. Differences in surface roughness (SR), quantified using root-mean-square distances, significantly affect monomer dynamics, thereby influencing its diffusion on the surface. Importantly, this study underscores that fibril twisting acts as a regulatory niche, selectively influencing these orientations and their diffusion properties necessary for facilitating fibril growth within biologically relevant time scales. This discovery opens new avenues for targeted therapeutic strategies aimed at manipulating fibril dynamics to mitigate the progression of Alzheimer's disease.

Pore Formation by Amyloid-like Peptides: Effects of the Nonpolar-Polar Sequence Pattern

One of the mechanisms accounting for the toxicity of amyloid peptides in diseases like Alzheimer's and Parkinson's is the formation of pores on the plasma membrane of neurons. Here, we perform unbiased all-atom simulations of the full membrane damaging pathway, which includes adsorption, aggregation, and perforation of the lipid bilayer accounting for pore-like structures. Simulations are performed using four peptides made with the same amino acids. Differences in the nonpolar-polar sequence pattern of these peptides prompt them to adsorb into the membrane with the extended conformations oriented either parallel [peptide labeled F1, Ac-(FKFE)2-NH2], perpendicular (F4, Ac-FFFFKKEE-NH2), or with an intermediate orientation (F2, Ac-FFKKFFEE-NH2, and F3, Ac-FFFKFEKE-NH2) in regard to the membrane surface. At the water-lipid interface, only F1 fully self-assembles into β-sheets, and F2 peptides partially fold into an α-helical structure. The β-sheets of F1 emerge as electrostatic interactions attract neighboring peptides to intermediate distances where nonpolar side chains can interact within the dry core of the bilayer. This complex interplay between electrostatic and nonpolar interactions is not observed for the other peptides. Although β-sheets of F1 peptides are mostly parallel to the membrane, some of their edges penetrate deep inside the bilayer, dragging water molecules with them. This precedes pore formation, which starts with the flow of two water layers through the membrane that expand into a stable cylindrical pore delimited by polar faces of β-sheets spanning both leaflets of the bilayer.

Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations

Protein self-assembly plays an important role in biological systems, accounting for the formation of mesoscopic structures that can be highly symmetric as in the capsid of viruses or disordered as in molecular condensates or exhibit a one-dimensional fibrillar morphology as in amyloid fibrils. Deposits of the latter in tissues of individuals with degenerative diseases like Alzheimer's and Parkinson's has motivated extensive efforts to understand the sequence of molecular events accounting for their formation. These studies aim to identify on-pathway intermediates that may be the targets for therapeutic intervention. This detailed knowledge of fibril formation remains obscure, in part due to challenges with experimental analyses of these processes. However, important progress is being achieved for short amyloid peptides due to advances in our ability to perform completely unbiased all-atom simulations of the self-assembly process. This perspective discusses recent developments, their implications, and the hurdles that still need to be overcome to further advance the field.