Computer simulation: probing the dynamic binding mechanism of the azo pigment allure red to meat-derived proteins

Elucidating the interactions between the azo dye Allura Red (AR) and meat-derived proteins is crucial for understanding its safe application in complex food systems. This study investigated the interactions between AR and actin (AC), glutamate dehydrogenase (GDH), and myosin (MS) using molecular docking and molecular dynamics simulations. Molecular docking results revealed that AR primarily binds to the central hydrophobic cavities of AC/GDH and the hydrophobic side-chain regions of MS. MM-PBSA calculations demonstrated binding strengths in the order GDH (-14.50 kJ/mol) > MS (-12.67 kJ/mol) > AC (-12.57 kJ/mol), this computational result aligns with the molecular docking findings, both demonstrating that AR exhibits the strongest binding affinity with GDH, and the interactions between AR and all proteins are driven by electrostatic forces and van der Waals interactions. Molecular dynamics trajectory analysis showed that RMSD, Rg, hydrogen bond counts, and principal component data of protein systems exhibited enhanced conformational stability after AR binding. Specifically, the AR-AC system displayed structural expansion leading to increased surface hydrophobicity, while AR-GDH/MS systems achieved reduced hydrophobic region exposure through structural contraction. A comparison of protein conformations between 0 ns and 100 ns revealed that AC exhibited the least displacement, followed by GDH and MS, indicating its highest conformational stability. Although GDH underwent alterations in secondary structure, its core region remained stable. These results establish a theoretical foundation for implementing AR technology in the meat processing industry.