135
Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session II
82-POS
Board 35
Computer Simulations on Amyloid Formation
Seokmin Shin
1
, SeongByeong Park
1
, Soonmin Jang
2
, Kyunghee Lee
2
.
1
Seoul National University, Seoul, South Korea,
2
Sejong University, Seoul, South Korea.
Computational studies can provide basic understanding concerning the detailed mechanism of
amyloid formation, the formation of amyloid fibrils and prefibrilar aggregates of misfolded
proteins and peptides. Understanding amyloid formation is very important to elucidate possible
causes for various neurodegenerative disorders. Systematic replica exchange molecular dynamics
simulations have been performed on the formation of the oligomers and protofibrils of Aβ
peptide and peptides from α-synuclein. We also performed MD simulations on different
structural models of such fibrils including the effects of mutations. The mechanism of
aggregation and growth of these peptides is examined from detailed analysis of such simulations.
It was shown that the steric zipper contacts provided favorable interactions in the aggregation
process and the structural flexibility might play important role for enhancing aggregation. Our
results suggested that amyloid formation is basically a hierarchical process and different
topologies are favored in the different stages of aggregation. Self-assembly of peptide-based
building blocks has been shown to be useful in constructing artificial bionanostructures. We
performed MD simulations on the proposed nanoring structures formed by the self-assembly of
β-sheet forming peptides. The stability of the nanoring structure with respect to the size is
investigated and several factors contributing to the stability are examined. We have also
demonstrated that the sizes of nanorings can be controlled by introducing selective mutations.
