  In this study, we introduced a new unit, named "protein token", as a dynamic
protein structural unit for protein-protein interactions. Unlike the
conventional structural units, protein token is not based on the sequential or
spatial arrangement of residues, but comprises remote residues involved in
cooperative conformational changes during protein interactions. Application of
protein token on Ras GTPases revealed various tokens present in the
superfamily. Distinct token combinations were found in H-Ras interacting with
its various regulators and effectors, directing to a possible clue for the
multiplexer property of Ras superfamily. Thus, this protein token theory may
provide a new approach to study protein-protein interactions in broad
applications.
