Paper Citing NAMD - Abstract
Miller, Yifat; Ma, Buyong; Nussinov, Ruth
The Unique Alzheimer's beta-Amyloid Triangular Fibril Has a Cavity along the Fibril Axis under Physiological Conditions
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:2742-2748, MAR 2 2011
Elucidating the structure of A beta(1-40) fibrils is of interest in Alzheimer's disease research because it is required for designing therapeutics that target A beta(1-40) fibril formation at an early stage of the disease. M35 is a crucial residue because of its potential oxidation and its strong interactions across beta-strands and across beta-sheets in A beta fibrils. Experimentally, data for the three-fold symmetry structure of the A beta(9-40) fibril suggest formation of tight hydrophobic core through M35 interactions across the fibril axis and strong I31-V39 interactions between different cross-beta units. Herein, on the basis of experimental data, we probe conformers with three-fold symmetry of the full-length A beta(1-40). Our all-atom molecular dynamics simulations in explicit solvent of conformers based on the ssNMR data reproduced experimental observations of M35-M35 and I31-V39 distances. Our interpretation of the experimental data suggests that the observed similar to 5-7 angstrom M35-M35 distance in the fibril three-fold symmetry structure is likely to relate to M35 interactions along the fibril axis, rather than across the fibril axis, since our measured M35-M35 distances across the fibril axis are consistently above 15 angstrom. Consequently, we revealed that the unique A beta(1-40) triangular structure has a large cavity along the fibril axis and that the N-termini can assist in the stabilization of the fibril by interacting with the U-turn domains or with the C-termini domains. Our findings, together with the recent cyroEM characterization of the hollow core in A beta(1-42) fibrils, point to the relevance of a cavity in A beta(1-40/1-42) oligorners which should be considered when targeting oligomer toxicity.
