Lyotropic liquid crystals (LLCs) are at the frontline of current research for the release of target therapeutic molecules due to their unique structural complexity and possibility of engineering the stimuli-triggered release of various molecules. The most suitable lipidic mesophases for encapsulation and delivery of drugs are the reversed hexagonal phase and respectively the double diamond bicontinuous cubic phase. In the case of the unperturbed cubic phase, two distinct and parallel networks of ~4 nm-large water channels percolate independently through the lipid bilayers, following a Pn3m space group symmetry and acting as autonomous and non-communicating three-dimensional transport pathways. Here, we introduce a novel type of bicontinuous cubic phase, where the presence of OmpF membrane proteins provides unique topological interconnectivities among the two distinct sets of water channels, enabling molecular active gating among them. By a combination of small angle x-ray scattering, release and ion conductivity experiments, we demonstrate that -without altering the Pn3m space group symmetry or the water channels diameter-, the newly designed “perforated” bicontinuous cubic phase attains transport properties well beyond those of the standard mesophase, allowing faster, sustained release of bioactive target molecules. By further exploiting the pH-mediated pore-closing response mechanism of the double amino acid half-ring architecture in the membrane protein, we also provide the “perforated” mesophase with a pH-triggered ON-OFF opening of the pores, enabling a fine modulation of the transport properties via moderate changes in pH. Moreover, we reveal that reconstitution of these pore-forming membrane proteins can also occur within the highly curved lipidic bilayers of reverse hexagonal phases, for which the mean-curvature is significantly different from zero. The functional reconstitution of the membrane proteins provides once more unique topological interconnectivities between the LLCs aqueous nanochannels, significantly enhancing their transport properties and opening previously unexplored opportunities in the targeted delivery of bioactive compounds.