Journal Title
Title of Journal: J Mol Model
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Abbravation: Journal of Molecular Modeling
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Publisher
Springer-Verlag
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Authors: Zanxia Cao Lei Liu Liling Zhao Haiyan Li Jihua Wang
Publish Date: 2012/11/18
Volume: 19, Issue: 3, Pages: 1237-1250
Abstract
The effects of Cu2+ binding and the utilization of different force fields when modeling the structural characteristics of αsyn12 peptide were investigated To this end we performed extensive temperature replica exchange molecular dynamics TREMD simulations on Cu2+bound and unbound αsyn12 peptide using the GROMOS 43A1 OPLSAA and AMBER03 force fields Each replica was run for 300 ns The structural characteristics of αsyn12 peptide were studied based on backbone dihedral angle distributions freeenergy surfaces obtained with different reaction coordinates favored conformations the formation of different Turn structures and the solvent exposure of the hydrophobic residues The findings show that AMBER03 prefers to sample helical structures for the unbound αsyn12 peptide and does not sample any βhairpin structure for the Cu2+bound αsyn12 peptide In contrast the central structure of the major conformational clusters for the Cu2+bound and unbound αsyn12 peptide according to simulations performed using the GROMOS 43A1 and OPLSAA force fields is a βhairpin with Turn96 Cu2+ can also promote the formation of the βhairpin and increase the solvent exposure of hydrophobic residues which promotes the aggregation of αsyn12 peptide This study can help us to understand the mechanisms through which Cu2+ participates in the fibrillation of αsyn12 peptide at the atomic level which in turn represents a step towards elucidating the nosogenesis of Parkinson’s disease
Keywords:
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