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

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

1,2
,
1,3
,
1,2
and
1,2,*
1
Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou University, 566 University Rd. West, Dezhou 253023, China
2
Department of Physics, Dezhou University, 566 University Rd. West, Dezhou 253023, China
3
Department of Computer Science and Technology, Dezhou University, 566 University Rd. West, Dezhou 253023, China
*
Author to whom correspondence should be addressed.
Received: 22 July 2011 / Revised: 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. View Full-Text
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 (CC BY 3.0).

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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.

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