Protein assembly has received significant attention due to its unique function and applicability in nanobiotechnology. Despite recent efforts to design protein materials, the design principles of two-dimensional protein assembly on a nanomaterial has remained elusive. In this work, we report the computational design of two-dimensional protein assembly on a pristine graphene based on statistical analysis of protein structures existing in nature and atomistic simulation-based structure predictions. We designed the protein sequence by optimizing protein-protein and protein-graphene interactions. The designed protein assemblies on a graphene were validated by AFM imaging and their surface properties were measured using Raman spectroscopy and wetting experiment (and simulation). Our work sheds light on the design principles of protein assemblies for further development of nano-bio-composite materials.