A novel programmable molecular computing method based on signaling pathways regulated by rho-GTPases in living MDCK epithelial mammalian cells

Abstract

In this paper, we propose a new biomolecular computing method based on the crosstalked pathways of living cells and the corresponding kinasephosphatase networks under the regulation of Rho family GTPases. Owing to their merits of efficient regulation in controlled pathway complexity and low cost in implementation, we propose a feasible protocol (the algorithm) for kinase-and-phosphatase-based computers (called kinase computers for short) and the materials and methods for their implementation. In order to obtain high programmability in molecular computation, we have successfully designed pathway regulation schemes for computation. Here we report our latest simulation results on a designed controllable crosstalk mechanism and efficient schemes for engineered GTPase-based signaling communications for stable kinase computing under the dynamical environment of a cell culture assay. This is significant for the application of molecular computing to medical nanobioinformatics and also provides a testbed for new and unconventional computing paradigms inspired by nature. © Springer-Verlag 2004.