Computational functions in biochemical reaction networks

A. Arkin, J. Ross
1994 Biophysical Journal  
In pnor work we demonstrated Fte implementation of logic gates, sequential computers (universal Turing machines), and parallel computers by means of the kinetics of chemical reaction mechanisms. In the present arficle we develop this subject further by first investigating the computational properties of several enzymatic (single and multiple) reaction mechanisms: we show their steady states are analogous to either Boolean or fuzzy logic gates. Nearly perfect digital function is obtained only in
more » ... the regime in which the enzymes are saturated with their substrates. With these enzymatic gates, we constru combinational chemical networks that execute a given trut-table. The dynamic range of a network's output is strongly affected by "input/output matching conditions among the intemal gate elements. We find a simple mechanism, similar to the interconversion of fructose-ctposphate between its two bisphWphate forns (fructose-1,bisphophate and fructose-2,6bposphate), that functons analogously to an AND gate. When the simple model is supplanted with one in which the enzyme rate laws are derived from experimental data, the steady state of the mechanism furnions as an asymmetric fuzzy aggregation operator with properties akin to a fuzzy AND gate. The qualitative behavior of the mechanism does not change when sitated within a large model of glycolysis/gluconeogenesis and the TCA cycle. The mehanism, in this case, switches the pathway's mode from glycolysis to gluconeogenesis in response to chemical signals of low blood glucose (cAMP) and abundant fuel for the TCA cycle (acetyl coenzyme A).
doi:10.1016/s0006-3495(94)80516-8 pmid:7948674 pmcid:PMC1225399 fatcat:ich7esd7fjbydjsi6g7as7r6oi