Designed peptide conjugate molecules are used to simultaneously direct both the synthesis and assembly of gold nanoparticles into various complex 1-D nanoparticle superstructures. We show how synthetic conditions, including reaction time and temperature, can be varied to carefully control the structure of the gold nanoparticle assembly and also the size and density of the nanoparticles within the assembly. We also demonstrate that particle capping agents such as citrate and adenosine triphosphate can be used to adjust the metrics of double-helical gold nanoparticle assemblies, in particular interhelical distances and particle size.