Accurate control of charge transfer pathways is critical to unlocking the full potential of charge transfer proteins (CTPs) and exploring their diverse applications. We show that the intentional manipulation of junctions in Al nanocrosses on graphene induces asymmetry, unlocking unexpected charge transfer pathways and facilitating the generation of coupled resonators. The junction asymmetry, which is induced by nanotrench formation facilitated by focused electron beam irradiation, provides a versatile means to achieve precise and controlled interconnect manipulation. We find that tuning the nanotrench dimensions in nanocrosses allows for the tailored modulation of the charge transfer speed and the energies of CTPs. Furthermore, CTPs excited in our experimental nanocrosses, featuring nanotrenches, exhibit weak coupling. This crucial insight underscores the importance of controlled trench formation in unlocking various functionalities of CTPs for use in sensing, catalysis, and energy conversion applications. The controlled manipulation of interconnects in Al nanocrosses thus emerges as a promising avenue for advancing the device performance in these fields.