Computer simulation of the dynamics of biochemical pathways

A thesis submitted in candidature for the degree of Doctor of Philosophy of the University of Wales, Aberystwyth
by

Pedro Mendes

Institute of Biological Sciences, University of Wales, Aberystwyth
March 1994

Summary

This thesis is concerned with the use of computer simulation for the study of the dynamics of biochemical systems, with an emphasis on the steady-state properties of pathways containing enzymes that interact by transferring their intermediate metabolite directly (metabolic channelling).

I developed Gepasi, a user-friendly MS-Windows computer program to simulate the dynamics and steady state of biochemical systems. The use of Gepasi and the methods implemented in it are described. The rest of the work in this thesis was executed using Gepasi, providing examples of its application to biochemical modelling.

Metabolic channelling can be dynamic or static, depending on whether the enzyme-enzyme complex can be formed in the absence of the intermediate metabolite which is channelled. It has been shown recently that a pathway containing a dynamic channel does not always result in a lower concentration of the channelled intermediate, compared to the case where channelling is absent, but this was overgeneralized to the extent that it was stated that channelling cannot decrease pool sizes. Later this was loosened, to include only the case of constant net flux. Both statements are here proven to be wrong by an algebraic analysis and by showing instances in which channelling decreases the pool size (even at constant net flux). A model of static channelling is also discussed. Channelling can reduce the concentration of the intermediate metabolite by very large factors, even at constant pathway flux.

Finally, a study is carried out on the effectiveness of methods based on metabolic control analysis for distinguishing dynamic metabolic channelling from other types of enzyme-enzyme interaction, including some cases of bifunctional enzymes. The methods analysed are up- and down-modulation of enzyme concentrations, failure of connectivity and summation theorems, double-inhibitor titrations and double-enzyme titrations. It is shown that no single method can unambiguously distinguish channelling from other enzyme-enzyme interactions.

Full thesis in postscript format (zip file)