C3 photosynthesis in silico

Photosynth Res. 2006 Oct;90(1):45-66. doi: 10.1007/s11120-006-9109-1. Epub 2006 Nov 28.


A computer model comprising light reactions, electron-proton transport, enzymatic reactions, and regulatory functions of C3 photosynthesis has been developed as a system of differential budget equations for intermediate compounds. The emphasis is on electron transport through PSII and PSI and on the modeling of Chl fluorescence and 810 nm absorptance signals. Non-photochemical quenching of PSII excitation is controlled by lumenal pH. Alternative electron transport is modeled as the Mehler type O2 reduction plus the malate-oxaloacetate shuttle based on the chloroplast malate dehydrogenase. Carbon reduction enzymes are redox-controlled by the ferredoxin-thioredoxin system, sucrose synthesis is controlled by the fructose 2,6-bisphosphate inhibition of cytosolic FBPase, and starch synthesis is controlled by ADP-glucose pyrophosphorylase. Photorespiratory glycolate pathway is included in an integrated way, sufficient to reproduce steady-state rates of photorespiration. Rate-equations are designed on principles of multisubstrate-multiproduct enzyme kinetics. The parameters of the model were adopted from literature or were estimated from fitting the photosynthetic rate and pool sizes to experimental data. The model provided good simulations for steady-state photosynthesis, Chl fluorescence, and 810 nm transmittance signals under varying light, CO2 and O2 concentrations, as well as for the transients of post-illumination CO2 uptake, Chl fluorescence induction and the 810 nm signal. The modeling shows that the present understanding of photosynthesis incorporated in the model is basically correct, but still insufficient to reproduce the dark-light induction of photosynthesis, the time kinetics of non-photochemical quenching, 'photosynthetic control' of plastoquinone oxidation, cyclic electron flow around PSI, oscillations in photosynthesis. The model may find application for predicting the results of gene transformations, the analysis of kinetic experimental data, the training of students.

MeSH terms

  • Carbon / metabolism
  • Chloroplasts / enzymology
  • Kinetics
  • Malate Dehydrogenase / metabolism
  • Models, Biological*
  • Oxidation-Reduction
  • Photons
  • Photosynthesis*
  • Silicon


  • Carbon
  • Malate Dehydrogenase
  • Silicon