The aroma of apples is one of the major sensory characteristics to evaluate the quality of apples. The mechanism for perceiving the aroma of apples is currently unclear. In this study, the interactions between the aroma compounds and olfactory receptors were explored by the S-curve modeling, molecular docking, and molecular dynamics simulation (MDS) technology. Hexyl acetate and β-damascenone(D = 0.46),hexyl acetate and phenethyl alcohol (D = 0.15), linalool and trans-2-hexenal (D = 0.30) etc., have synergistic effects. The molecular docking results revealed noticeable changes in the stability and affinity between the binary and single compounds combined with olfactory receptors (OR1A1 and OR2W1). In addition, molecular dynamic simulation (MDS) analysis indicated that the hydrogen bonding residues of the OR2W1-hexyl acetate were changed from ASN155 to TRP149 and ASN65 after the addition of β-damascenone. Similarly, the hydrophobic interactions of the system were increased, which played an indispensable role in forming a stable ternary system between β-damascenone-hexyl acetate and OR2W1. Meanwhile, the binding free energy decreased from −36.69 kcal/mol (hexyl acetate- OR2W1) to −37.7 kcal/mol (β-damascenone-hexyl acetate-OR2W1), which showed that the new ternary system has better stability. The results provided a theoretical basis and technical guidance for improving apple flavor and its products.
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