Molecular Dynamics Analysis of Linoleic Acid Retention in a Preformed Amylose Inclusion Structure

Previous molecular dynamics studies have examined the conformational stability and concentration-dependent complexation of amylose–LA systems, but persistence after explicit removal of a host–guest distance restraint has not been directly addressed. Here, atomistic molecular dynamics simulations were used to examine linoleic acid (LA) retention in a preformed 27-residue amylose inclusion structure at 363 K. A 400 ns pull-restrained trajectory was followed by four 100 ns post-pull runs in which the amylose–LA distance restraint was removed while the amylose glycosidic dihedral restraints remained active; all four runs were initiated from the same structural endpoint with independently assigned initial velocities. LA remained closely associated with amylose in all four runs. Across the run means, the amylose radius of gyration was 0.923 ± 0.011 nm, the minimum amylose–LA heavy-atom distance was 0.316 ± 0.004 nm, the contact count within 0.45 nm was 92.7 ± 1.8, and the O3n–C5n+3 cavity descriptor was 1.268 ± 0.003 nm. Direct amylose–LA hydrogen bonds were rare, whereas preserved cavity geometry and distributed close contacts characterized the retained state. Although the extent of host conformational relaxation varied among runs, it did not lead to sustained guest loss over the sampled 100 ns period. These results indicate that short-timescale LA retention in this preorganized complex is characterized by preserved cavity geometry and close host–guest contacts, while direct amylose–LA hydrogen bonding remains rare.