Modeling Amyloid Aggregation Kinetics: A Case Study with Sup35NM

Prion-like Aggregation of the Heptapeptide GNNQQNY into Amyloid Nanofiber Is Governed by Configuration Entropy

A major cause of prion infectivity is the early formation of small, fibril-like aggregates consisting of the heptapeptide GNNQQNY. The prion aggregates exhibit a unique stacking mode in which the hydrophobic tyrosine (Y) is exposed outward, forming a bilayer β-sheet-stacking zipper structure. This stacking mode of the prion peptides, termed "Y-outward" structure for convenience, goes against the common understanding that, for other amyloid-forming peptides, the hydrophobic residues should be hidden within the peptide fibril, referred to as "Y-inward" structure. To explore the extraordinary stacking behaviors of the prion GNNQQNY peptides, two fibril models are constructed in a fashion of "Y-outward" and "Y-inward" stackings and then studied in silico to examine their thermodynamic stabilities and disaggregation pathways. The "Y-inward" structure indeed exhibits stronger thermodynamic stability than the "Y-outward" structure, according to potential energy and stacking energy calculations. To show how the peptide fibrils dissociate, we illustrated two disaggregation pathways. A dihedral-based free energy landscape was then calculated to examine the conformational degrees of freedom of the GNNQQNY chains in the "Y-outward" and "Y-inward" structures. Peptide chains lose more configurational entropy in the "Y-inward" structure than in the "Y-outward" structure, indicating that the prion peptides are prone to aggregate in a fashion of "Y-outward" stacking pattern due to its low conformational constraints. The prion-like aggregation of the GNNQQNY peptides into amyloid fibrils is primarily governed by the configuration entropy.

The interacting rotifer-biopolymers are anti- and disaggregating agents for human-type beta-amyloid in vitro

Neurodegeneration-related human-type beta-amyloid 1-42 aggregates (H-Aβ) are one of the biochemical markers and executive molecules in Alzheimer's disease. The exogenic rotifer-specific biopolymer, namely Rotimer, has a protective effect against H-Aβ toxicity on Euchlanis dilatata and Lecane bulla monogonant rotifers. Due to the external particle-dependent secreting activity of these animals, this natural exudate exists in a bound form on the surface of epoxy-metal beads, named as Rotimer Inductor Conglomerate (RIC). In this current work the experiential in vitro molecular interactions between Rotimer and Aβs are presented. The RIC form was uniformly used against H-Aβ aggregation processes in stagogram- and fluorescent-based experiments. These well-known cell-toxic aggregates stably and quickly (only taking a few minutes) bind to RIC. The epoxy beads (as carriers) alone or the scrambled version of H-Aβ (with random amino acid sequence) were the ineffective and inactive negative controls of this experimental system. The RIC has significant interacting, anti-aggregating and disaggregating effects on H-Aβ. To detect these experiments, Bis-ANS and Thioflavin T were applied during amyloid binding, two aggregation-specific functional fluorescent dyes with different molecular characteristics. This newly described empirical interaction of Rotimer with H-Aβ is a potential starting point and source of innovation concerning targeted human- and pharmaceutical applications.