The charge and size of molecules chemically attached to nanoparticles (NPs) play an important role in their interaction behavior in suspensions. Gold nanoparticles (AuNPs) were modified systematically with peptides and the modification was verified with surface-enhanced Raman scattering (SERS). The behavior of the modified AuNPs in suspension and at the liquid-solid interface was monitored using small angle X-ray scattering (SAXS), UV/Vis spectroscopy and dynamic light scattering (DLS) in suspension, and atomic force microscopy (AFM) at the solid-liquid interface. It was found that while negatively charged peptide modified AuNPs behave very similar to citrate reduced AuNPs due to their negatively charged surface, positively charged peptide modified AuNPs showed significantly different assembly/aggregation properties in suspension. The formation of linear assemblies of positively charged peptide (CKRHSKRHRSKRHSKRHSKRHSKR) modified AuNPs was clearly observed from the AFM analysis of the droplet areas of its colloidal suspension. The combined analyses of data obtained from the employed techniques suggest that the positively charged large peptide modified AuNPs can form linear and 3D-like networks in the suspension. This study reveals important information regarding the surface property dependent behavior of NPs that may help in efforts to build higher structures using NPs as building blocks.