Effect of Protonation on Structural Characteristics and Aggregation Mechanisms of β-Amyloid(1—16) Peptide

doi:10.7503/cjcu20120813

Abstract

Abstract:

Structural characteristics and aggregation mechanisms of Aβ_1—16 fragment under different conditions of pH=7.0, 6.3 and 5.5 were studied by replica exchange molecular dynamics(REMD). The results show that protonated residues and number of Aβ_1—16 depend on the difference of pH. Structural changes indicate that Aβ_1—16 has a transitional trend from the disordered state to the ordered one along with the increase of acidic concentration. β-Sheet intermittently appears in acidic conditions during the simulations, implying that Aβ_1—16 tends to self-aggregation in such case. The protonated positions and structural changes of Aβ_1—16 monomer depicted in the present work can be employed to predict and assess the potential binding positions and coordination numbers for a transition metal ion to approach the monomer.

Key words: Molecular dynamics simulation, Aβ_1—16, Protonation, Structural characteristic, Aggregation

CLC Number:

O641.12⁺1

TrendMD:

SHI Hu, CHENG Shan-Shan, AI Hong-Qi. Effect of Protonation on Structural Characteristics and Aggregation Mechanisms of β-Amyloid(1—16) Peptide[J]. Chem. J. Chinese Universities, 2013, 34(5): 1214.

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Effect of Protonation on Structural Characteristics and Aggregation Mechanisms of β-Amyloid(1—16) Peptide

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