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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 33, Number 3
BKCSDE 33(3)
March 20, 2012 

 
Title
Computational Study on Oligomer Formation of Fibril-forming peptide of α-Synuclein
Author
SeongByeong Park, Jeseong Yoon, Soonmin Jang, Kyunghee Lee, Seokmin Shin*
Keywords
α-Synuclein, Replica-exchange molecular dynamics (REMD), Fibril formation, Antiparallel β- sheet
Abstract
We have studied the oligomerization of a fibril-forming segment of α-Synulcein using a replica exchange molecular dynamics (REMD) simulation. The simulation was performed with trimers and tetramers of a 12 amino acid residue stretch (residues 71-82) of α-Synulcein. From extensive REMD simulations, we observed the spontaneous formation of both trimer and tetramer, demonstrating the self-aggregating and fibril-forming properties of the peptides. Secondary structure profile and clustering analysis illustrated that antiparallel β- sheet structures are major species corresponding to the global free energy minimum. As the size of the oligomer increases from a dimer to a tetramer, conformational stability is increased. We examined the evolution of simple order parameters and their free energy profiles to identify the process of aggregation. It was found that the degree of aggregation increased as time passed. Tetramer formation was slower than trimer formation and a transition in order parameters was observed, indicating the full development of tetramer conformation which is more stable than that of the trimer. The shape of free energy surface and change of order parameter distributions indicate that the oligomer formation follows a dock-and-lock process.
Page
848 - 854
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