Here we show that Au NPs with an isotropic, amphiphilic surface functionalization can spontaneously form anisotropic NP aggregates, whose topology can be finely tuned by the ratio between hydrophobic and charged ligands on the NP surface. Using coarse-grained molecular dynamics, we observe these NPs self-assembling into highly anisotropic supra-molecular structures such as dumbbells, chains, and ribbons, depending on the charged-to-hydrophobic ligand ratio. We further show that NP-NP connections can either be stable, hydrophobic interactions or weak, ion-mediated electrostatic interactions. The former interactions determine the topology of the primary structure of the aggregates, while the latter drive the folding of the primary structure into a secondary structure, which has a more dynamic and reversible nature.