Molecular Dynamics Simulation of Amylose-Linoleic Acid Complex Behavior in Water

Abstract

In this paper, the objective was to employ the probability of amylose inclusion complex formation with linoleic acid and estimate the thermodynamic compatibility of complex of amylose with linoleic acid at water. We used Gromacs to make molecular dynamics simulation of amylose-linoleic acid complex behavior in water. Firstly, the amylose alone in water has been simulated by Gromacs, it was found that amylose alone in 373 K had a more extensive chain than that in 300 K, and the former has a larger radius of gyration than the latter, which means the former hydrated more adequately than the latter. Then, the amylose and linoleic acid had been simulated by Gromacs at 300 K and 373 K respectively, after 1 ns simulation, it can be clearly seen that linoleic acid can be included into amylose helical cavity at 373 K but can’t be included at 300 K, through configuration after 1 ns (1 ns = 10−9 s) with or without solvent, root-mean-square deviation, solvent accessible surface area, molecules separation distance, trajectories of molecules movement, the values of those complex have been compared, it was concluded that the complexation of amylose and linoleic acid was much more thermodynamically favored at 373 K than at 300 K. These results suggested that the founded method could help us to prove its probability of amylose inclusion complex formation with small ligands and also estimate the thermodynamic compatibility of complex of amylose with different small ligands complexes at water.