Modelling the Bioenergetics of Halobacterium Salinarum with Petri Nets

We present a Petri net model for the membrane potential regulated phosphorylation in Halobacterium salinarum which allows for the analysis of the relationships between the membrane potential and the bioenergetic processes. The membrane potential generating processes are proton extrusion by bacteriorhodopsin and the complexes in the respiratory chain. The light driven pump halorhodopsin also enhances the membrane potential by moving negatively charged chloride ions inside the cell. We consider two cases for the sodium-proton antiporter: electro-neutral and electrogenic, and analysis is made for each. The model is validated by determining the dynamic properties of the Petri net and performing structural and invariant analysis. T-invariant analysis shows that bacteriorhodopsin and respiration can independently drive phosphorylation. On the other hand, T-invariant analysis also shows that the chloride pump halorhodopsin is not able to independently drive photo-phosphorylation. Furthermore, results on T-invariant analysis agree with experimental evidence that movement of sodium and potassium ions are charged balanced. Computation of the Abstract Dependent Transition Sets (ADT-sets) of the network yield exactly the basic components (or modules) consisting of the respiratory chain, bacteriorhodopsin, halorhodopsin, potassium uniport, the antiport and ATP synthesis/hydrolysis.