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.
Highlights
Alzheimer’s disease is the result of deposition of Aβ peptides [1,2,3]
Experimental research has shown that the H1 peptide in water adopts a β-sheet structure according to several sources of experimental evidence [51,52], Aβ (12–28) peptide co-exists among PPII, β-hairpin and random coil structure
It is difficult to obtain the structural and thermodynamics characters of these peptides monomer in aqueous solutions by using experimental methods
Summary
Alzheimer’s disease is the result of deposition of Aβ peptides [1,2,3]. In particular, the Aβ (12–28)peptide (the 12–28 fragment) is shown to have behavioral effects in mice [4,5], formation of fibril aggregates [6] and toxic effects in vitro [7]. The quality of molecular dynamic simulations for protein and peptide depends greatly on the accuracy of empirical force fields, water model and the detail of simulation [11,12,13,14,15,16]. Force fields are parameterized with special water model. It is necessary to select the possible combination of force field with water model carefully [17]. Matthes et al [20] have presented a systematic study of sampling behavior and secondary structure formation with eight different molecular dynamics models (different force fields, different water models and different schemes for calculating electrostatic interactions). The results indicated that a number of distinct trends in the folding behavior, for example, AMBER99 force field favors helical structure, GROMOS96 [21]
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