Microwave-Induced Improvement in the Structural Compactness of Starch–Lauric Acid–Whey Protein Ternary Complexes: Enhanced Encapsulation of Butyl Butyrate and Prebiotic Potential of the Quaternary Complex

Starch-based multicomponent complexes are promising carriers for functional molecules, but their limited stability and encapsulation efficiency constrain practical applications. Microwave (MW)-pretreated starch and whey protein (WP) were assembled with lauric acid to form a ternary complex (MTC), followed by butyl butyrate (BB) loading to produce MTC-B. Characterization and molecular dynamics simulations showed that MW altered amylopectin branching and partially unfolded WP, strengthening hydrogen bonding, van der Waals forces, electrostatic interactions, and hydrophobic interactions. Compared with the hydrothermally assembled control (TC-B), MTC-B exhibited a compact V-type structure, improved short-range order, thermal stability, and BB encapsulation. Its resistance and rapidly digestible starch contents were 59% and 19%, respectively. During in vitro fecal fermentation, MTC-B increased butyric acid and total short-chain fatty acid production and selectively reshaped the microbiota with significant Bifidobacterium enrichment and upward trends in Roseburia and Collinsella. These findings support MW pretreatment for the development of potential colon-targeted BB delivery systems in foods.