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Int. J. Mol. Sci. 2011, 12(11), 8259-8274; doi:10.3390/ijms12118259
Article

Effects of Different Force Fields and Temperatures on the Structural Character of Abeta (12–28) Peptide in Aqueous Solution

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Received: 22 July 2011; in revised form: 12 October 2011 / Accepted: 7 November 2011 / Published: 21 November 2011
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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Abstract: The aim of this work is to investigate the effects of different force fields and temperatures on the structural character of Aβ (12–28) peptide in aqueous solution. Moreover, the structural character of Aβ (12–28) peptide is compared with other amyloid peptides (such as H1 and α-syn12 peptide). The two independent temperature replica exchange molecular dynamics (T-REMD) simulations were completed by using two different models (OPLS-AA/TIP4P and GROMOS 43A1/SPC). We compared the models by analyzing the distributions of backbone dihedral angles, the secondary structure propensity, the free energy surface and the formation of β-hairpin. The results show that the mostly populated conformation state is random coil for both models. The population of β-hairpin is below 8 percent for both models. However, the peptide modeled by GROMOS 43A1 form β-hairpin with turn located at residues F19-E22, while the peptide modeled by OPLS-AA form β-hairpin with turn located at residues L17-F20.
Keywords: Aβ (12–28) peptide; different force field; different temperature; molecular dynamics simulation; structural character; free energy surface Aβ (12–28) peptide; different force field; different temperature; molecular dynamics simulation; structural character; free energy surface
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.

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MDPI and ACS Style

Cao, Z.; Liu, L.; Zhao, L.; Wang, J. Effects of Different Force Fields and Temperatures on the Structural Character of Abeta (12–28) Peptide in Aqueous Solution. Int. J. Mol. Sci. 2011, 12, 8259-8274.

AMA Style

Cao Z, Liu L, Zhao L, Wang J. Effects of Different Force Fields and Temperatures on the Structural Character of Abeta (12–28) Peptide in Aqueous Solution. International Journal of Molecular Sciences. 2011; 12(11):8259-8274.

Chicago/Turabian Style

Cao, Zanxia; Liu, Lei; Zhao, Liling; Wang, Jihua. 2011. "Effects of Different Force Fields and Temperatures on the Structural Character of Abeta (12–28) Peptide in Aqueous Solution." Int. J. Mol. Sci. 12, no. 11: 8259-8274.


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