Paper Citing NAMD - Abstract
Zhao, Jun; Yu, Xiang; Liang, Guizhao; Zheng, Jie
Heterogeneous Triangular Structures of Human Islet Amyloid Polypeptide (Amylin) with Internal Hydrophobic Cavity and External Wrapping Morphology Reveal the Polymorphic Nature of Amyloid Fibrils
BIOMACROMOLECULES, 12:1781-1794, MAY 2011
The misfolding and self-assembly of human islet amyloid polypeptide (hIAPP or amylin) into amyloid fibrils is pathologically linked to type II diabetes. The polymorphic nature of both hIAPP oligomers and fibrils has been implicated for the molecular origin of hIAPP toxicity to islet beta-cells, but little is known about the polymorphic structure and dynamics of these hIAPP oligomers/fibrils at the atomic level. Here, we model the polymorphism of full length hIAPP(1-37) oligomers based on experimental data from solid-state NMR, mass per length, and electron microscopy using all-atom molecular dynamics simulation with explicit solvent. As an alternative to steric zipper structures mostly presented in the 2-fold symmetrical fibrils, the most striking structural feature of our proposed hIAPP oligomers is the presence of 3-fold symmetry along the fibril growth axis, in which three beta-sheet-layers wind around a hydrophobic core with different periodicities. These 3-fold triangular hIAPP structures dramatically differ in the details of the beta-layer assembly and core-forming sequence at the cross section, but all display a high structural stability with favorable layer-to-layer interactions. The 3-fold hIAPP structures can also serve as templates to present triple-stranded helical fibrils via peptide elongation, with different widths from 8.7 to 9.9 nm, twists from 2.8 degrees to 11.8 degrees, and pitches from 14.5 to 61.1 nm, in reasonable agreement with available biophysical data. Because similar 3-fold A beta oligomers are also observed by both NMR experiments and our previous simulations, the 3-fold structure could be a general conformation to a broad range of amyloid oligomers and fibrils. Most importantly, unlike the conventional stacking sandwich model, the proposed wrapping-cord structures can readily accommodate more than three beta-layers via a two dimension conformation search by rotating and translating the beta-layers to adopt different favorable packings, which can greatly enrich the polymorphism of amyloid oligomers and fibrils.
