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FEDMA - a simple algorithm for theoretical modeling of linear metabolic pathways: from fuzzy data sets to prediction and experiment.

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Pawlowski P. H., Zielenkiewicz P.

2005

vol. 52

issue 1

71-86

A theoretical model of a chain of irreversible Michaelis-Menten reactions proceeding inside a living cell, taking cell growth, division and subcellular compartmentation into account, was proposed. It became a basis for the construction of a "fuzzy" enzymatic data-modeling algorithm (FEDMA) - a procedure allowing the estimation of missing parameter values for the modeled system, in accordance both with the derived theoretical rules and the available experimental data. The obtained tool was tested to model the heme biosynthesis pathway in Saccharomyces cerevisiae, where about 40% of parameters remain unknown. The missing parameters estimated by means of FEDMA fall in the range of expected values.

Theoretical model explaining the relationship between the molecular mass and the activation energy of the enzyme revealed by a large-scale analysis of bioinformatics data

100%

Pawlowski P. H., Zielenkiewicz P.

2013

vol. 60

issue 2

239-247

A general dependence of the enzyme catalytic rate on its mass was revealed when a statistical analysis of 17065 records from the EMP database was performed. The estimated activation energy of the catalytic process decreases asymptotically with the enzyme molecular mass increase. The proposed theoretical model postulates the existence of an intermediate complex of the enzyme and the departing product. It allows for the explanation of the discovered mass-energy relationship, as an effect of the global enzyme-product interactions during complex dissociation. Fitted parameters of the model seem to be in agreement with those widely accepted for the van der Waals energy of molecular interactions. Their values also agree with the picture of the hydrogen bonding in the catalytic process and suggest that surface walk can be the favorable way of the product departure.

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2 Acta Biochimica Polonica

1 2013

1 2005

2 Pawlowski P. H.

2 Zielenkiewicz P.

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FEDMA - a simple algorithm for theoretical modeling of linear metabolic pathways: from fuzzy data sets to prediction and experiment.

Theoretical model explaining the relationship between the molecular mass and the activation energy of the enzyme revealed by a large-scale analysis of bioinformatics data