Paper Citing NAMD - Abstract
Ma, Buyong; Nussinov, Ruth
Polymorphic C-terminal beta-Sheet Interactions Determine the Formation of Fibril or Amyloid beta-derived Diffusible Ligand-like Globulomer for the Alzheimer A beta 42 Dodecamer
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:37102-37110, NOV 19 2010
The relationship between amyloid deposition and cellular toxicity is still controversial. In addition to fibril-forming oligomers, other soluble A beta forms (amyloid beta-derived diffusible ligands (ADDLs)) were also suggested to form and to present different morphologies and mechanisms of toxicity. One ADDL type, the "globulomer," apparently forms independently of the fibril aggregation pathway. Even though many studies argue that such soluble A beta oligomers are off fibril formation pathways, they may nonetheless share some structural similarity with protofibrils. NMR data of globulomer intermediates, "preglobulomers," suggested parallel in-register C-terminal beta-sheets, with different N-terminal conformations. Based on experimental data, we computationally investigate four classes of A beta dodecamers: fibril, fibril oligomer, prefibril/preglobulomer cluster, and globulomer models. Our simulations of the solvent protection of double-layered fibril and globulomer models reproduce experimental observations. Using a single layer A beta fibril oligomer beta-sheet model, we found that the C-terminal beta-sheet in the fibril oligomer is mostly curved, preventing it from quickly forming a fibril and leading to its breaking into shorter pieces. The simulations also indicate that beta-sheets packed orthogonally could be the most stable species for A beta dodecamers. The major difference between fibril-forming oligomers and ADDL-like oligomers (globulomers) could be the exposure of Met-35 patches. Although the Met-35 patches are necessarily exposed in fibril-forming oligomers to allow their maturation into fibrils, the Met-35 patches in the globulomer are covered by other residues in the orthogonally packed A beta peptides. Our results call attention to the possible existence of certain "critical intermediates" that can lead to both seeds and other soluble ADDL-like oligomers.
