Nanomaterial defects occur widely due to various situations such as synthesis imperfections, exposure to harsh environment, or even intentional designs. However, the consequence of nanomaterial defects on their interfacing biological systems remains largely unknown. Here, we study the interaction of a defective graphene nanosheet with a widely used model protein, YAP65WW-domain, using molecular dynamics simulations. We find that local defects on graphene consistently act to unfold the YAP65WW-domain. Protein residues bound to the graphene defect are tightly anchored due to favorable electrostatic interactions. While the residues at the interface are highly restrained, thermal movements of other parts of the protein act to denature and unfold the entire protein. In contrast, control simulations of protein binding on ideal graphene reveal a well preserved native structure with no unfolding events detected. Our present findings elucidate the role of graphene defects on protein adsorption and emphasize the need for improved understanding of nanomaterial defects in potential biomedical applications.