Inter-species cross-seeding: stability and assembly of rat-human amylin aggregates

Abstract

Diseases such as type 2 diabetes, Alzheimer's and Parkinson's share as common feature the accumulation of mis-folded disease-specific protein aggregates into fibrillar structures, or plaques. These fibrils may either be toxic by themselves, or act as reservoirs for smaller cytotoxic oligomers. This suggests to investigate molecules as potential therapeutics that either reduce fibril formation or increase fibril stability. One example is rat amylin, which can inhibit aggregation of human amylin, a hallmark of type 2 diabetes. In the present paper, we use molecular dynamics to compare the stability of various preformed aggregates, built out of either human amylin, rat amylin, or mixtures of both. We considered two types of fibril-like oligomers: a single-layer in-register conformation, and a double-layer conformation in which the first U-shaped layer consists of rat amylin and the second layer of human amylin. Our results explain the weak amyloid-inhibiting properties of rat amylin and suggest that membrane leakage due to pore formation is responsible for the toxicity of rat amylin observed in a recent experiment. Together, our results put in question the use of rat amylin or the similar FDA approved drug pramlintide as an inhibitor of human amylin aggregation. They also point to mixed human-rat amylin fibril-like oligomers as possible model-systems for studies of amyloid formation that involve cross-species transmission.

Figure 1. Structural details of the single and double layer decamers of rat amylin, human amylin and rat-human amylin mixtures.

(A) Single layer conformation of human amylin, (B) single layer conformation of rat amylin, (C) single layer conformation of human-rat complex, (D) Double layer conformation of human amylin with CC interface (E) Double layer conformation of rat amylin with CC interface, (F) Double layer conformation of rat and human amylin mixtures with CC interface, (G) Double layer conformation of rat amylin with NN interface and (H) Double layer conformation of rat–human amylin complex with NN interface. Different colors are applied for the rat (red) and human amylin (green).

Figure 2. The structural changes in each model, from the trajectory with the largest average root-mean-square-deviations, at the end of 300 ns of molecular dynamics in explicit solvent (water molecules omitted for clarity).

A) Single layer conformation of human amylin, (B) single layer conformation of rat amylin, (C) single layer conformation of human-rat complex, (D) Double layer conformation of human amylin with CC interface (E) Double layer conformation of rat amylin with CC interface, (F) Double layer conformation of rat and human amylin mixtures with CC interface, (G) Double layer conformation of rat amylin with NN interface and (H) Double layer conformation of rat–human amylin complex with NN interface. The segments that are colored yellow are the N terminal segments (residue 8–17) and the C terminal segment (residue 28–37). Different colors are applied for the rat (red) and human amylin (green). The initial structures are depicted in blue. Root-mean-square-deviation values calculated for each peptide with respect to the start configurations are included in parentheses.

Figure 3. Average number of main chain and side chain hydrogen bonds.

(A) Total number of main chain hydrogen bonds; (B) total number of side chain hydrogen bonds. Legend: (I) Single layer conformation of rat amylin, (II) single layer conformation of human amylin, (III) single layer conformation of human-rat complex, (IV) Double layer conformation of rat amylin with CC interface (V) Double layer conformation of human amylin with CC interface, (VI) Double layer conformation of rat and human amylin mixtures with CC interface, (VII) Double layer conformation of human amylin with NN interface and (VIII) Double layer conformation of rat–human amylin complex with NN interface.

Figure 4. Root-mean-square fluctuation (RMSF) of the Cα atoms calculated from the three molecular dynamics simulations.

A) Single layer conformation of human amylin, (B) single layer conformation of rat amylin, (C) single layer conformation of human-rat complex, (D) Double layer conformation of human amylin with CC interface (E) Double layer conformation of rat amylin with CC interface, (F) Double layer conformation of rat and human amylin mixtures with CC interface, (G) Double layer conformation of rat amylin with NN interface and (H) Double layer conformation of rat–human amylin complex with NN interface.

Figure 5. Representative snapshot of water molecules in the amylin single layer, double layer, and the complexes between human and rat amylin model.

(A) Single layer conformation of human amylin, (B) single layer conformation of rat amylin, (C) single layer conformation of human-rat complex, (D) Double layer conformation of human amylin with CC interface (E) Double layer conformation of rat amylin with CC interface, (F) Double layer conformation of rat and human amylin mixtures with CC interface, (G) Double layer conformation of rat amylin with NN interface and (H) Double layer conformation of rat–human amylin complex with NN interface. Different colors mark rat (red) and human amylin (green).