By applying a novel self-assembly peptide design template, we synthesized a nanofibrous bio-functional scaffold with a laminin-derived signal sequence isoleucine-lysine-valine-alanine-valine (IKVAV) inserting between repeating blocks of arginine-alanine-aspartate-alanine (RADA). The new material supported the growth of neural progenitor cells (PC12). Furthermore, cellular proliferation and differentiation could be controlled by the interplay of signal presentation format and matrix dimensionality. Enhanced and prolonged proliferation of PC12 cells as aggregates was observed in 3-D culture while pronounced neurite outgrowth was found in 2-D culture. Interestingly, cells previously exposed to 3-D culture were more prone to neural differentiation and synapse formation. In addition to characterizing the degree of differentiation by morphology and immunostaining, the stages of cell differentiation were detected by RT-PCR to better understand the cell-material interactions.