Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 19, Issue 2, Pages -Publisher
MDPI
DOI: 10.3390/ijms19020571
Keywords
Alzheimer's disease; amyloid beta; replica exchange; molecular dynamics; U-shaped; S-shaped; assembly; fibril; gromacs; aggregation
Funding
- Swiss National Supercomputing Centre (CSCS)
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Alzheimer's disease is the most fatal neurodegenerative disorder characterized by the aggregation and deposition of Amyloid (A) oligomers in the brain of patients. Two principal variants of A exist in humans: A(1-40) and A(1-42). The former is the most abundant in the plaques, while the latter is the most toxic species and forms fibrils more rapidly. Interestingly, fibrils of A(1-40) peptides can only assume U-shaped conformations while A(1-42) can also arrange as S-shaped three-stranded chains, as recently discovered. As alterations in protein conformational arrangement correlate with cell toxicity and speed of disease progression, it is important to characterize, at molecular level, the conformational dynamics of amyloid fibrils. In this work, Replica Exchange Molecular Dynamics simulations were carried out to compare the conformational dynamics of U-shaped and S-shaped A(17-42) small fibrils. Our computational results provide support for the stability of the recently proposed S-shaped model due to the maximized interactions involving the C-terminal residues. On the other hand, the U-shaped motif is characterized by significant distortions resulting in a more disordered assembly. Outcomes of our work suggest that the molecular architecture of the protein aggregates might play a pivotal role in formation and conformational stability of the resulting fibrils.
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