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Int. J. Mol. Sci. 2015, 16(7), 14291-14304; doi:10.3390/ijms160714291

Effect of pH on the Aggregation of α-syn12 Dimer in Explicit Water by Replica-Exchange Molecular Dynamics Simulation

1
Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou 253023, China
2
College of Physics and Electronic information, Dezhou University, Dezhou 253023, China
3
College of Computer Science and Technology, Dezhou University, Dezhou 253023, China
*
Author to whom correspondence should be addressed.
Academic Editor: Lukasz Kurgan
Received: 31 March 2015 / Revised: 9 June 2015 / Accepted: 10 June 2015 / Published: 24 June 2015
View Full-Text   |   Download PDF [4412 KB, uploaded 24 June 2015]   |  

Abstract

The dimeric structure of the N-terminal 12 residues drives the interaction of α-synuclein protein with membranes. Moreover, experimental studies indicated that the aggregation of α-synuclein is faster at low pH than neutral pH. Nevertheless, the effects of different pH on the structural characteristics of the α-syn12 dimer remain poorly understood. We performed 500 ns temperature replica exchange molecular dynamics (T-REMD) simulations of two α-syn12 peptides in explicit solvent. The free energy surfaces contain ten highly populated regions at physiological pH, while there are only three highly populated regions contained at acidic pH. The anti-parallel β-sheet conformations were found as the lowest free energy state. Additionally, these states are nearly flat with a very small barrier which indicates that these states can easily transit between themselves. The dimer undergoes a disorder to order transition from physiological pH to acidic pH and the α-syn12 dimer at acidic pH involves a faster dimerization process. Further, the Lys6–Asp2 contact may prevent the dimerization. View Full-Text
Keywords: α-synuclein; different pH; dimerization; structural character; molecular dynamics simulation α-synuclein; different pH; dimerization; structural character; molecular dynamics simulation
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Cao, Z.; Zhang, X.; Liu, L.; Zhao, L.; Li, H.; Wang, J. Effect of pH on the Aggregation of α-syn12 Dimer in Explicit Water by Replica-Exchange Molecular Dynamics Simulation. Int. J. Mol. Sci. 2015, 16, 14291-14304.

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