Analysis of the conformational dynamics of amylose oligomers using molecular dynamics simulations

Amylose contributes to starch crystallinity, but the stability of packed amylose double helices in water at elevated temperature remains insufficiently characterized. Here, we used molecular dynamics simulations to test whether chain length affects the stability of A-type amylose oligomers in water. Six systems differing in chain length (6, 12, or 24 glucose units per chain) and oligomer size (isolated double strand or dodecamer of six double strands) were simulated, and five independent 1-µs production runs were analyzed for each simulated condition. Oligomers with six glucose units showed early structural disordering, with increased water penetration becoming more pronounced as the disordered state developed. By contrast, dodecamers with 12 or 24 glucose units largely retained packed double-helical organization over the simulated timescale, although fraying was observed at their ends. These results indicate that chain length and lateral packing strongly affect the early structural response of amylose-like crystalline segments under high-temperature aqueous conditions. The present simulations identify a relative stability difference that is relevant to molecular interpretations of hydration-driven disordering in starch.