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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 30, Number 8
BKCSDE 30(8)
August 20, 2009 

Dimerization of Fibril-forming Segments of α-Synuclein
Jeseong Yoon, Soonmin Jang, Kyunghee Lee, Seokmin Shin*
α-Synuclein, Replica-exchange molecular dynamics (REMD), Fibril formation, Antiparallel β-sheet
We have performed replica-exchange molecular dynamics (REMD) simulations on the dimer formation of fibrilforming segments of α-Synuclein (residues 71 - 82) using implicit solvation models with two kinds of force fields-AMBER parm99SB and parm96. We observed spontaneous formation of dimers from the extensive simulations, demonstrating the self-aggregating and fibril forming properties of the peptides. Secondary structure profile and clustering analysis showed that dimers with antiparallel β-sheet conformations, stabilized by well-defined hydrogen boding, are major species corresponding to global free energy minimum. Parallel dimers with partial β-sheets are found to be off-pathway intermediates. The relative instability of the parallel arrangements is due to the repulsive interactions between bulky and polar side chains as well as weaker backbone hydrogen bonds.
1845 - 1850
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