In this paper, we propose a new biomolecular computing method based on Rho family GTPases, and discuss the schemes of representation and operations of molecular computing by Rho family GTPases applied to solve large-scale 3-SAT problems. We also present the optimal condition for the regulation schemes dependent on the temperature, kinase activity, and types of cells. This work is important for potential implementation of biomolecular computers using Rho family GTPases in which an optimized controlling scheme can make the best use of the interactions of signaling pathways in a computing system made by the large-scale abundance of kinases and phosphatases in cells.