Biomolecular computing by encoding of regulated phosphorylation- dephosphorylation and logic of kinase-phosphatase in cells

Abstract

As the first step in studying cell-based computing, a new method of biomolecular computing by cells is proposed based on signaling pathways of kinases and phosphatases for phosphorylation-dephosphorylation (we call this method "kinase computing" for short in the latter parts of this paper). As opposed to the Adleman-Lipton paradigm of DNA computing and other types of cell-based computing, the core mechanism of kinase computing that carries out recursive computation at the biological level is based on (1) encoding the information by phosphorylation and dephosphorylation, (2) running the selection operators by coupled pathways of kinases and phosphatases under certain conditions, and (3) readout by immunofluorescence analysis. The control schemes for the related synchronization processes in 3-SAT computation is studied to clarify the biological feasibility of kinase computing, in which the control-space complexity and time complexity are linear. © Springer-Verlag 2004.