Designing metabolism

Alternative connectivities for the pentose phosphate pathway

Jay E. Mittenthal, Ao Yuan, Bertrand S Clarke, Alexander Scheeline

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

We present a method for generating alternative biochemical pathways between specified compounds. We systematically generated diverse alternatives to the nonoxidative stage of the pentose phosphate pathway, by first finding pathways between 5-carbon and 6-carbon skeletons. Each solution of the equations for the stoichiometric coefficients of skeleton-changing reactions defines a set of networks. Within each set we selected networks with modules; a module is a coupled set of reactions that occurs more than one in a network. The networks can be classified into at least 53 families in at least seven superfamilies, according to the number, the input-output relations, and the internal structure of their modules. We then assigned classes of enzymes to mediate transformations of carbon skeletons and modifications of functional groups. The ensemble of candidate networks was too large to allow complete determination of the optimal network. However, among the networks we studied the real pathway is especially favorable in several respects. It has few steps, uses no reducing or oxidizing compounds, requires only one ATP in one direction of flux, and does not depend on recurrent inputs.

Original languageEnglish (US)
Pages (from-to)815-856
Number of pages42
JournalBulletin of Mathematical Biology
Volume60
Issue number5
DOIs
StatePublished - Jan 1 1998

Fingerprint

Pentoses
Pentose Phosphate Pathway
pentoses
Phosphate
Metabolism
Skeleton
skeleton
connectivity
Pathway
Connectivity
Phosphates
Carbon
metabolism
phosphate
phosphates
carbon
Alternatives
Adenosinetriphosphate
Functional groups
functional group

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology
  • Mathematics(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Environmental Science(all)
  • Pharmacology
  • Agricultural and Biological Sciences(all)
  • Computational Theory and Mathematics

Cite this

Designing metabolism : Alternative connectivities for the pentose phosphate pathway. / Mittenthal, Jay E.; Yuan, Ao; Clarke, Bertrand S; Scheeline, Alexander.

In: Bulletin of Mathematical Biology, Vol. 60, No. 5, 01.01.1998, p. 815-856.

Research output: Contribution to journalArticle

Mittenthal, Jay E. ; Yuan, Ao ; Clarke, Bertrand S ; Scheeline, Alexander. / Designing metabolism : Alternative connectivities for the pentose phosphate pathway. In: Bulletin of Mathematical Biology. 1998 ; Vol. 60, No. 5. pp. 815-856.
@article{95e88713864a47599d7fb37e25ca683b,
title = "Designing metabolism: Alternative connectivities for the pentose phosphate pathway",
abstract = "We present a method for generating alternative biochemical pathways between specified compounds. We systematically generated diverse alternatives to the nonoxidative stage of the pentose phosphate pathway, by first finding pathways between 5-carbon and 6-carbon skeletons. Each solution of the equations for the stoichiometric coefficients of skeleton-changing reactions defines a set of networks. Within each set we selected networks with modules; a module is a coupled set of reactions that occurs more than one in a network. The networks can be classified into at least 53 families in at least seven superfamilies, according to the number, the input-output relations, and the internal structure of their modules. We then assigned classes of enzymes to mediate transformations of carbon skeletons and modifications of functional groups. The ensemble of candidate networks was too large to allow complete determination of the optimal network. However, among the networks we studied the real pathway is especially favorable in several respects. It has few steps, uses no reducing or oxidizing compounds, requires only one ATP in one direction of flux, and does not depend on recurrent inputs.",
author = "Mittenthal, {Jay E.} and Ao Yuan and Clarke, {Bertrand S} and Alexander Scheeline",
year = "1998",
month = "1",
day = "1",
doi = "10.1006/bulm.1997.0043",
language = "English (US)",
volume = "60",
pages = "815--856",
journal = "Bulletin of Mathematical Biology",
issn = "0092-8240",
publisher = "Springer New York",
number = "5",

}

TY - JOUR

T1 - Designing metabolism

T2 - Alternative connectivities for the pentose phosphate pathway

AU - Mittenthal, Jay E.

AU - Yuan, Ao

AU - Clarke, Bertrand S

AU - Scheeline, Alexander

PY - 1998/1/1

Y1 - 1998/1/1

N2 - We present a method for generating alternative biochemical pathways between specified compounds. We systematically generated diverse alternatives to the nonoxidative stage of the pentose phosphate pathway, by first finding pathways between 5-carbon and 6-carbon skeletons. Each solution of the equations for the stoichiometric coefficients of skeleton-changing reactions defines a set of networks. Within each set we selected networks with modules; a module is a coupled set of reactions that occurs more than one in a network. The networks can be classified into at least 53 families in at least seven superfamilies, according to the number, the input-output relations, and the internal structure of their modules. We then assigned classes of enzymes to mediate transformations of carbon skeletons and modifications of functional groups. The ensemble of candidate networks was too large to allow complete determination of the optimal network. However, among the networks we studied the real pathway is especially favorable in several respects. It has few steps, uses no reducing or oxidizing compounds, requires only one ATP in one direction of flux, and does not depend on recurrent inputs.

AB - We present a method for generating alternative biochemical pathways between specified compounds. We systematically generated diverse alternatives to the nonoxidative stage of the pentose phosphate pathway, by first finding pathways between 5-carbon and 6-carbon skeletons. Each solution of the equations for the stoichiometric coefficients of skeleton-changing reactions defines a set of networks. Within each set we selected networks with modules; a module is a coupled set of reactions that occurs more than one in a network. The networks can be classified into at least 53 families in at least seven superfamilies, according to the number, the input-output relations, and the internal structure of their modules. We then assigned classes of enzymes to mediate transformations of carbon skeletons and modifications of functional groups. The ensemble of candidate networks was too large to allow complete determination of the optimal network. However, among the networks we studied the real pathway is especially favorable in several respects. It has few steps, uses no reducing or oxidizing compounds, requires only one ATP in one direction of flux, and does not depend on recurrent inputs.

UR - http://www.scopus.com/inward/record.url?scp=0032170434&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0032170434&partnerID=8YFLogxK

U2 - 10.1006/bulm.1997.0043

DO - 10.1006/bulm.1997.0043

M3 - Article

VL - 60

SP - 815

EP - 856

JO - Bulletin of Mathematical Biology

JF - Bulletin of Mathematical Biology

SN - 0092-8240

IS - 5

ER -