47

4

Modeling Metabolism and Finding New

Antibiotics

Abstract

Metabolic modelling allows metabolism to be analysed in detail. Biochemical knowl­

edge and databases such as KEGG determine the set of all enzymes involved. It is then

possible to calculate which metabolic pathways and enzyme chains keep the metabo­

lites in a network in equilibrium (flux balance analysis), which of these are also no

longer decomposable (elementary mode analysis) and which of these are sufficient to

represent all real metabolic situations by combining a few pure flux modes (extreme

pathway analysis). To calculate the flux strength, one needs further data, e.g. gene

expression data and software (e.g. YANA programs). Further analyses look at meta­

bolic control (metabolic control theory) and describe the rates (kinetics) of the enzymes

involved more precisely. This allows a better description and understanding of metabo­

lism, prediction of essential genes and resulting antibiotics as well as metabolic

responses, for example in tumour growth.

The genome sequence allows bioinformatics to gain a much better overview of the organ­

ism. In particular, this allows us to determine much better than before which enzymes and

metabolic pathways occur in an organism.

Is it possible for the bioinformatician to calculate, for a given set of enzymes, what

metabolism might come out of it?

The surprising answer is “yes”; so-called metabolic modeling (Mavrovouniotis et al.

1990; Schuster and Schuster 1993) can indeed answer this question.

© Springer-Verlag GmbH Germany, part of Springer Nature 2023

T. Dandekar, M. Kunz, Bioinformatics,

https://doi.org/10.1007/978-3-662-65036-3_4