In biological nanocomposites such as bones, teeth and seashells, proteins play an important role in their mechanical response. Proteins in nacre, the inner layer of seashells have been shown to have exceptional mechanical properties. The secondary structures, β-sheets of protein when present close to each other in multiple numbers could take the shape of a planar β-sheath like structure or a β-barrel to form a domain. In natural proteins both these types of structures are commonly found. Effort has been made through this work to study the mechanical response of these β-planar sheath and β-barrel structures when subjected to external loads. Comparative study of the stress-deformation characteristics of these two types of structures has been made. The influence of shear force on the conformation of planar and barrel structure is investigated. Both these structures with almost similar number of amino acids have been extracted from one single spinach protein, Ferredoxin Reductase (1FNR). Steered molecular dynamics has been used to conduct these studies. The paper deals with the separation of the two domains from the main protein, simulation details and results comparing the responses. © 2005 Materials Research Society.