Site-specific lipidation of intrinsically disordered proteins provides orthogonal control over biomolecular condensate properties through two distinct axes: the lipid and its local three-residue attachment site sequence program cohesive interactions that determine material state (liquid, gel, or fibrillar solid), while the lipid and global scaffold properties program adhesive interactions that control miscibility and hierarchical multi-phase architecture. These design principles enable rational engineering of condensate-based biomaterials with programmable microstructures that guide functional tissue morphogenesis, establishing lipidation as a versatile post-translational modification for controlling emergent condensate behavior across multiple length scales.

Cells use post-translational modifications (PTMs) to reconfigure biomolecular condensates across length scales, space, and time. While charged PTMs are well-known electrostatic switches, how ubiquitous neutral PTMs shape condensate plasticity and hierarchy remains unclear. Here, we establish a set of design principles for using site-specific lipidation, a class of neutral hydrophobic PTMs, to rationally control properties and interactions of engineered biomolecular condensates. Through systematic analysis of over 80 lipidated synthetic intrinsically disordered proteins (IDPs), we uncovered two distinct axes of control. First, the interplay between the lipid and the local three-residue sequence of its attachment site acts as a programmable switch for cohesion—the homotypic interactions that define the material state of the condensed phase— directing assemblies toward dynamic liquids, arrested gels, or ordered fibrillar solids. Second, the lipid, together with the global properties of the IDP scaffold, tunes adhesion—the heterotypic interactions that govern condensate miscibility and hierarchical organization. We harnessed these principles to rationally engineer complex, multi-phase architectures and create hybrid hydrogels with programmed microstructure and material properties that guide the morphogenesis of functional intestinal organoids. These findings establish a new framework for lipoengineering advanced biomaterials and provide a blueprint for dissecting structure–property relationships across diverse classes of PTMs.