Reaction routes in biochemical reaction Systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism
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Reaction routes in biochemical reaction Systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism. / Schuster, S; Hilgetag, C; Woods, J H; Fell, D A.
In: J MATH BIOL, Vol. 45, No. 2, 08.2002, p. 153-81.Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review
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TY - JOUR
T1 - Reaction routes in biochemical reaction Systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism
AU - Schuster, S
AU - Hilgetag, C
AU - Woods, J H
AU - Fell, D A
PY - 2002/8
Y1 - 2002/8
N2 - Elementary flux modes (direct reaction routes) are minimal sets of enzymes that can operate at steady state, with all irreversible reactions used in the appropriate direction. They can be interpreted as component pathways of a (bio)chemical reaction network. Here, two different definitions of elementary modes are given and their equivalence is proved. Several algebraic properties of elementary modes are then presented and proved. This concerns, amongst other features, the minimal number of enzymes of the network not used in an elementary mode and the situations where irreversible reactions are replaced by reversible ones. Based on these properties, a refined algorithm is presented, and it is formally proved that this algorithm will exclusively generate all the elementary flux modes of an arbitrary network containing reversible or irreversible reactions or both. The algorithm is illustrated by a biochemical example relevant in nucleotide metabolism. The computer implementation in two different programming languages is discussed.
AB - Elementary flux modes (direct reaction routes) are minimal sets of enzymes that can operate at steady state, with all irreversible reactions used in the appropriate direction. They can be interpreted as component pathways of a (bio)chemical reaction network. Here, two different definitions of elementary modes are given and their equivalence is proved. Several algebraic properties of elementary modes are then presented and proved. This concerns, amongst other features, the minimal number of enzymes of the network not used in an elementary mode and the situations where irreversible reactions are replaced by reversible ones. Based on these properties, a refined algorithm is presented, and it is formally proved that this algorithm will exclusively generate all the elementary flux modes of an arbitrary network containing reversible or irreversible reactions or both. The algorithm is illustrated by a biochemical example relevant in nucleotide metabolism. The computer implementation in two different programming languages is discussed.
KW - Adenine Nucleotides
KW - Algorithms
KW - Animals
KW - Catalysis
KW - Humans
KW - Kinetics
KW - Models, Biological
KW - Multienzyme Complexes
KW - Reproducibility of Results
KW - Journal Article
U2 - 10.1007/s002850200143
DO - 10.1007/s002850200143
M3 - SCORING: Journal article
C2 - 12181603
VL - 45
SP - 153
EP - 181
JO - J MATH BIOL
JF - J MATH BIOL
SN - 0303-6812
IS - 2
ER -