Structural similarities and differences between amyloidogenic and non-amyloidogenic islet amyloid polypeptide (IAPP) sequences and implications for the dual physiological and pathological activities of these peptides

Abstract

IAPP, a 37 amino-acid peptide hormone belonging to the calcitonin family, is an intrinsically disordered protein that is coexpressed and cosecreted along with insulin by pancreatic islet β-cells in response to meals. IAPP plays a physiological role in glucose regulation; however, in certain species, IAPP can aggregate and this process is linked to β-cell death and Type II Diabetes. Using replica exchange molecular dynamics with extensive sampling (16 replicas per sequence and 600 ns per replica), we investigate the structure of the monomeric state of two species of aggregating peptides (human and cat IAPP) and two species of non-aggregating peptides (pig and rat IAPP). Our simulations reveal that the pig and rat conformations are very similar, and consist of helix-coil and helix-hairpin conformations. The aggregating sequences, on the other hand, populate the same helix-coil and helix-hairpin conformations as the non-aggregating sequence, but, in addition, populate a hairpin structure. Our exhaustive simulations, coupled with available peptide-activity data, leads us to a structure-activity relationship (SAR) in which we propose that the functional role of IAPP is carried out by the helix-coil conformation, a structure common to both aggregating and non-aggregating species. The pathological role of this peptide may have multiple origins, including the interaction of the helical elements with membranes. Nonetheless, our simulations suggest that the hairpin structure, only observed in the aggregating species, might be linked to the pathological role of this peptide, either as a direct precursor to amyloid fibrils, or as part of a cylindrin type of toxic oligomer. We further propose that the helix-hairpin fold is also a possible aggregation prone conformation that would lead normally non-aggregating variants of IAPP to form fibrils under conditions where an external perturbation is applied. The SAR relationship is used to suggest the rational design of therapeutics for treating diabetes.

Figure 1. The four IAPP variants listed with aggregation propensities (Na⁴vSS values from AGGRESCAN server).

The residues that differ from those of hIAPP are mainly located between residues 4–31 (see residues in red in the sequences). While human and cat IAPP has strong aggregation tendency contributing to T2D, rat and pig IAPP doesn't aggregate under normal conditions and is not toxic to β-cells.

Figure 2. Two opposite roles of hIAPP in T2D.

In T2D, over-nutrition and inactivity lead to a high demand for pancreatic β-cells to produce insulin and hIAPP, two hormones that play a critical role in lowering blood glucose. Whereas correctly folded insulin and hIAPP function to reduce blood glucose (left loop), the misfolded form of hIAPP is amyloidogenic and toxic to the β-cells (right loop). +: increase −: decrease.

Figure 3. Secondary structure propensities of the four IAPP variants at 300 K.

Stardard deviation was calculated from the last 3 blocks of the simulation data (100 ns of each) at 300 K.

Figure 4. Position-dependent secondary structure propensities for the four IAPP variants from the last 300 ns at 300 K.

Figure 5. Representative structures of super structural families for each IAPP variant.

Standard deviation was calculated from the last 3 blocks of the simulation data (100 ns of each) at 300 K (See Figures S2 for all structural families in each super family from the last block). The backbone is shown in cartoon and the secondary structure is coded by color: coil in silver, β-sheet in yellow, isolated β-bridge in tan and turn in cyan. The N-terminus is indicated by a red ball.

Figure 6. Root mean square fluctuation (RMSF) of each residue (Cα atom) of the four IAPP variants in the super structural families at 300 K.

Residues 1–17 were aligned preceding the RMSF calculations.

Figure 7. Schematic representation of misfolding/aggregation mechanism of hIAPP.

Left: Helix-coil structure for normal function; Middle: aggregation-prone β-rich monomers; Right: early putative toxic dimers (Dupuis et al. JACS 2011). The question mark indicates the hairpins may further form cylindrin-like toxic oligomers, modeled from the cylindrical barrel of an amyloid peptide (PDB id: 3SGR) (Laganowsky et al. Science 2012). The isomerization symbol indicates that at some, as yet unknown size, the β-strand aggregates must rearrange to the β-sheet aggregates found in the fibrils. N-terminus is indicated by red ball, residues 23–29 in the “mutation region” are in red. In the β-hairpin, residues 19S-20S-21N-22N form a turn and residues 11–19 and 23–33 form two β-strands.