| Summary: | Thesis (PhD (Biochemistry))--University of Stellenbosch, 2009. === ENGLISH ABSTRACT:
With the recent advances in the field of molecular biology, there is an increased need to
integrate data on the various constituents of the cell in kinetic models that can predict and
describe cellular behavior. When working towards a description of the entire cell using
such kinetic models, the question arises: How do we compare different models for a given
biological network? This is the central question addressed in my thesis and I developed
and applied mathematical and computational methods for comparing dozens of existing
models of erythrocyte and yeast glycolysis.
To compare the steady-state behavior in models of erythrocyte glycolysis, I focussed
on the function of the pathway, which is to supply the cell with Gibbs-free energy (γ-
phosphate of ATP). I used supply-demand analysis in the framework of metabolic control
analysis to make this comparison, which revealed that the ATP concentrations were
homeostatically buffered at varying supply rates. I also applied this approach to compare
steady-state behavior in models of yeast glycolysis, finding that they were not necessarily
optimized for homeostatic maintenance of the ATP concentration and that in models for
this organism the rate of ATP production is often determined by the supply reactions of
glycolysis.
In addition, I tested whether a kinetic model can describe novel behavior if it is adjusted
to conditions different from those for which the model was originally constructed.
More specifically, using a model of steady-state yeast glycolysis, I showed that small
adjustments to the original enzyme concentrations are enough to obtain an oscillating
model, which shows a remarkable resemblance to the experimentally observed oscillations.
Importantly, some of these enzyme concentrations changes are known to occur
during the pre-treatment of the cells which is necessary to obtain oscillatory behavior.
To the best of my knowledge, the resulting model is the first detailed kinetic model that describes the experimentally observed strong synchronization of glycolytic oscillations
in yeast populations.
To analyze the dynamic behavior of yeast glycolytic models and to compare different
models in terms of dynamics, I introduced a framework used in physics and engineering
to create a vector based, two dimensional graphical representation of the oscillating
metabolites and reactions of glycolysis. Not only was it possible to make a concise comparison
of the set of models, but with the method I could also quantify the contribution
of the interactions in the network to the transduction of the oscillations. Furthermore I
could distinguish between different mechanisms of oscillation for each of the models, and
demonstrated how the framework can be used to create such representations for experimental
data sets. === AFRIKAANSE OPSOMMING:
Met die onlangse vooruitgang in die veld van molekulere biologie, is daar ?n toenemende
behoefte om data rakende die verskeie komponente van die sel in kinetiese modelle te
integreer, om sodanig selgedrag te voorspel en te beskryf. As daar gepoog word om ’n
beskrywing van die sel as geheel te verkry d.m.v. sulke kinetiese modelle, onstaan die
vraag: Hoe vergelyk ons verskillende modelle van ’n gegewe biologiese netwerk? Dit
is die sentrale vraag wat my tesis aanspreek en ek het wiskundige en numeriese metodes
ontwikkel en toegepas om talle bestaande modelle van gis- en eritrosietglikolise te vergelyk.
Om die bestendige-toestand gedrag in modelle van eritrosietglikolise te vergelyk, het
ek gefokus op die funksie van die padweg, naamlik om die sel met Gibbs-vrye energie
(γ-fosfaat van ATP) te voorsien. Ek het vraag-aanbod analiese in die raamwerk van
metaboliese kontrole analiese gebruik om hierdie vergelyking te maak, wat getoon het
dat die ATP konsentrasies homeostaties gebuffer was by verskillende aanbod tempos. Ek
het ook hierdie aanpak gebruik om die bestendige-toestand gedrag in modelle van gisglikolise
te vergelyk, en het bevind dat hulle nie noodwendig geoptimiseer is om ?n homeostatiese
balans in die ATP konsentrasie te handhaaf nie, en dat in modelle vir hierdie
organisme, die tempo van ATP produksie dikwels bepaal word deur die aanbod reaksies
van glikoliese.
Ek het verder ook bepaal of so ?n kinetiese model nuwe soorte gedrag kan beskryf,
as dit aangepas word aan omstandighede wat verskil van dié waarvoor die model oorspronklik
gekonstrueer was. Meer spesifiek, deur ?n model van bestendige-toestand gisglikolise
te gebruik, kon ek wys dat klein veranderinge aan die oorspronkline ensiem
konsentrasies genoeg was om ?n ossilerende model te verkry, wat opmerklik ooreenstem
met die eksperimenteel waargenome ossilasies. Let ook daarop dat sommige van hierdie ensiem konsentrasie veranderinge plaasvind tydens die voorafbehandeling van die selle,
wat essensieel is om die ossilasies waar te neem. Tot die beste van my kennis is die model
wat ek met hierdie prosedures verkry het, die eerste gedetaileerde kinetiese model wat die
eksperimenteel waargenome sterk sinkronisasie in ossilerende gis populasies voorspel.
Om gis glikolitiese modelle te vergelyk in terme van hul dinamiese gedrag, het ek ?n
raamwerk wat in fisika en ingeneurswese gebruik word, ingespan om ?n vektor-gebasseerde,
twee dimensionele grafiese voorstelling van die ossilerende metaboliete en reaksies te
maak. Hierdie raamwerk het dit nie net moontlik gemaak om ?n kompakte vergelyking
van ?n stel modelle te maak nie, maar ek kon ook die bydrae van interaksies in die netwerk
tot transduksie van die ossilasies kwantifiseer. Ek kon verder onderskeid tref tussen die
verskillende ossilasiemeganismes vir elk van die modelle, en het ook gedemonstreer hoe
die raamwerk gebruik kan word om sulke voorstellings vir eksperimentele datastelle te
skep.
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