α-helical structures drive early stages of self-assembly of amyloidogenic amyloid polypeptide aggregate formation in membranes

Abstract

The human islet amyloid polypeptide (hIAPP) is the primary component in the toxic islet amyloid deposits in type-2 diabetes. hIAPP self-assembles to aggregates that permeabilize membranes and constitutes amyloid plaques. Uncovering the mechanisms of amyloid self-assembly is the key to understanding amyloid toxicity and treatment. Although structurally similar, hIAPP's rat counterpart, the rat islet amyloid polypeptide (rIAPP), is non-toxic. It has been a puzzle why these peptides behave so differently. We combined multiscale modelling and theory to explain the drastically different dynamics of hIAPP and rIAPP: The differences stem from electrostatic dipolar interactions. hIAPP forms pentameric aggregates with the hydrophobic residues facing the membrane core and stabilizing water-conducting pores. We give predictions for pore sizes, the number of hIAPP peptides, and aggregate morphology. We show the importance of curvature-induced stress at the early stages of hIAPP assembly and the α-helical structures over β-sheets. This agrees with recent fluorescence spectroscopy experiments.

Figure 1. Self-assembly of membrane-embedded hIAPP or rIAAP give rise to differently structured peptide aggregates.

Top view from a simulation of peptide aggregation at 300 K for hIAPP (red) and rIAPP (green). Snapshots were taken at 1.0 μs (a,e), 7.0 μs (b,f), 13.0 μs (c,g), 20.0 μs (d,h) respectively. Lipids: blue. Yellow shows the lysine residues.

Figure 2. hIAPP aggregation gives rise to larger peptide assemblies than rIAPP within a μs timescale.

Peptide aggregation in a POPC membrane as a function of time for 36 molecules of rIAPP and hIAPP in 20 μs CG simulations.

Figure 3. Membrane-embedded hIAPP peptides associate into α-helical pentamers.

(A) Pentameric assembly of membrane-bound hIAPP peptides obtained at the end of a 0.3 μs MD simulation at 300 K. Green: polar, white: non-polar, cyan: polar ionizable. (B) Helical wheel representation of hIAPP side chains 14–27. (C) Pentameric aggregate. The vector in the xy-plane represents the hydrophobic moment. The helix dipole moment (not shown) is along the z-axis. Color code (b and c): yellow: hydrophobic (large), light blue: polar ionizable, magenta: polar; gray: hydrophobic (small); pink: polar.

Figure 4. hIAPP pentamers resemble barrel-shaped channels whereas the corresponding rIAPP assemblies look like loose funnels.

Snapshots from AA-MD simulations of hIAPP (red) and rIAPP (green) pentamers after 300 ns. Color code: white-surf-lipids, white-CPK-water.

Figure 5. Conformational preferences of monomeric hIAPP/rIAPP dictate the structural features of the pentameric assemblies.

Snapshots of hIAPP (red) and rIAPP (green) at monomeric state after 40 ns of MD simulation. POPC lipids are shown in white and water molecules in cyan.

Figure 6. Kinetics obtained from the thermodynamic model shows the transient nature of aggregates.

Variation of the chemical potentials of linear (full line) and cyclic (dashed line) vs the aggregation number n. At the intersection, linear and cyclic aggregate have the same energy. Inset: Relative concentration of cyclic aggregates vs. the total protein concentration C. Curves have been calculated for different values of the temperature scaled dipolar energy . From the top to the bottom: = 1, 2, 3.

Figure 7

(a) snapshot at 10 μs (protein/lipid ratio 1/44); (b) snapshot at 8 μs (protein/lipid ratio 1/19); (c) snapshot at 6 μs (protein/lipid ratio 1/24); (d) snapshot taken after 1 μs from the toroid formation (protein/lipid ratio 1/13).

Figure 8. Annular cone-shaped hIAPP assemblies cause membrane curvature.

Snapshots (cross-section) from the MD simulation of 26 hIAPP molecules in POPC bilayer at 400 K.

Figure 9. AFM in liquid of 1 μm² containing POPC/POPS (95/5 molar ratio) LUVs.

Left panel: imagine of vesicles in PBS buffer. Right panel: imagine of vesicles after incubation with hIAPP 5 μM. rIAPP did not show induce any changes in the vesicles shape (not shown).